STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0002 INTRON-ENCODED ENDONUCLEASE I- B DOUBLE HELIX OVERHANGING BASES N N N PPOI/DNA COMPLEX PD0003 CRE RECOMBINASE/DNA COMPLEX B DOUBLE HELIX FLIPPED-OUT BASES, N N N STICKY ENDS PD0005 HIV-1 REVERSE B DOUBLE HELIX OVERHANGING BASE N N N TRANSCRIPTASE/FRAGMENT OF FAB 28/DNA COMPLEX PD0006 RESTRICTION ENDONUCLEASE PVUII B DOUBLE HELIX OVERHANGING BASES N N N (MUTANT D34G)/DNA COMPLEX PD0009 3-METHYLADENINE DNA GLYCOSYLASE B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.2.2.21)/DNA COMPLEX PD0010 ECORV ENDONUCLEASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0011 RESTRICTION ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASES Y N N (E.C.3.1.21.4)/DNA COMPLEX PD0013 ECORV ENDONUCLEASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0014 KLENOW FRAGMENT/DNA COMPLEX U SINGLE STRAND n.a. N N N PD0015 KLENOW FRAGMENT OF DNA POLYMERASE U SINGLE STRAND n.a. N Y N I/DNA COMPLEX PD0017 CYTOSINE-SPECIFIC B DOUBLE HELIX FLIPPED-OUT BASE N N N METHYLTRANSFERASE HHAI/DNA COMPLEX PD0018 CYTOSINE-SPECIFIC B DOUBLE HELIX FLIPPED-OUT BASE N N N METHYLTRANSFERASE HHAI/DNA COMPLEX PD0019 CYTOSINE-SPECIFIC B DOUBLE HELIX ABASIC DNA RESIDUE N N N METHYLTRANSFERASE HHAI/DNA COMPLEX PD0023 REVERSE TRANSCRIPTASE B DOUBLE HELIX FLIPPED-OUT BASES, N N N (E.C.2.7.7.49) MUTANT (P1K, Q258C, OVERHANGING BASES E478Q)/DNA COMPLEX PD0026 ENDONUCLEASE I-CREI/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0029 PROTEIN (ENDONUCLEASE BAMHI) B DOUBLE HELIX FLIPPED-OUT BASES, N N N (3.1.21.4)/DNA COMPLEX OVERHANGING BASES PD0030 LARGE FRAGMENT OF DNA POLYMERASE B DOUBLE HELIX FLIPPED-OUT BASES N N N I/DNA COMPLEX PD0031 PROTEIN (RESTRICTION ENDONUCLEASE n.a. n.a. n.a. N N N BAMHI) (3.1.21.4)/DNA COMPLEX PD0032 LARGE FRAGMENT OF DNA POLYMERASE B DOUBLE HELIX FLIPPED-OUT BASES, N N N I/DNA COMPLEX OVERHANGING BASES PD0033 LARGE FRAGMENT OF DNA POLYMERASE B DOUBLE HELIX FLIPPED-OUT BASES, N N N I/DNA COMPLEX OVERHANGING BASES ------------------------------------------------------------------------------------------------------------------------------ Page 1 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0034 CYTOSINE-SPECIFIC B DOUBLE HELIX FLIPPED-OUT BASES Y N N METHYLTRANSFERASE HHAI/DNA COMPLEX PD0037 RESTRICTION ENDONUCLEASE ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0038 RESTRICTION ENDONUCLEASE ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0039 RESTRICTION ENDONUCLEASE ECORV B DOUBLE HELIX FLIPPED-OUT BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0040 RESTRICTION ENDONUCLEASE ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0041 URACIL-DNA GLYCOSYLASE/DNA COMPLEX B DOUBLE HELIX FLIPPED-OUT BASES, N N N OVERHANGING BASES PD0043 HELICASE PCRA (E.C.3.6.1.-)/DNA U SINGLE STRAND FLIPPED-OUT BASES, N N N COMPLEX OVERHANGING BASES PD0044 HELICASE PCRA (E.C. 3.6.1.-)/DNA RH DOUBLE HELIX FLIPPED-OUT BASES, N N Y COMPLEX OVERHANGING BASES PD0047 CRE RECOMBINASE/DNA COMPLEX B DOUBLE HELIX FLIPPED-OUT BASES, N N N OVERHANGING BASES PD0048 BACTERIOPHAGE P1 CRE GENE/DNA n.a. n.a. n.a. N N N COMPLEX PD0049 ENDONUCLEASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0052 URACIL-DNA GLYCOSYLASE (E.C.3.2.2.- RH DOUBLE HELIX OVERHANGING BASES N N N )/DNA COMPLEX PD0053 URACIL-DNA GLYCOSYLASE/DNA COMPLEX RH DOUBLE HELIX FLIPPED-OUT BASE, N N N OVERHANGING BASE PD0054 ENDONUCLEASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PD0055 ENDONUCLEASE ECORI/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PD0062 RESTRICTION ENDONUCLEASE ECO- B DOUBLE HELIX OVERHANGING BASE N N N RI/DNA COMPLEX PD0063 ECO RI ENDONCULEASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0064 KLENOW FRAGMENT OF DNA POLYMERASE U SINGLE STRAND n.a. N N N I (E.C.2.7.7.7)/DNA COMPLEX PD0065 KLENOW FRAGMENT OF DNA POLYMERASE B DOUBLE HELIX FLIPPED-OUT BASES N N N I (E.C.2.7.7.7)/DNA COMPLEX PD0066 KLENOW FRAGMENT OF DNA POLYMERASE B DOUBLE HELIX FLIPPED-OUT BASES N N N I (E.C.2.7.7.7)/DNA COMPLEX ------------------------------------------------------------------------------------------------------------------------------ Page 2 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0067 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX FLIPPED-OUT BASES N N N COMPLEX PD0068 ENDONUCLEASE IV (E.C.3.1.21.2)/DNA B DOUBLE HELIX FLIPPED-OUT BASES N N N PD0072 DNA POLYMERASE I (E.C.2.7.7.7)/DNA U SINGLE STRAND n.a. N N N COMPLEX PD0079 DNA POLYMERASE (E.C.2.7.7.7)/DNA B DOUBLE HELIX FLIPPED-OUT BASES, N N Y COMPLEX OVERHANGING BASES PD0080 DNA POLYMERASE I (E.C.2.7.7.7)/DNA U SINGLE STRAND n.a. N N N COMPLEX PD0085 BSOBI RESTRICTION ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0086 BACTERIOPHAGE T7 RNA B DOUBLE HELIX FLIPPED-OUT BASES, N N N POLYMERASE/DNA COMPLEX OVERHANGING BASES PD0093 MAJOR APURINIC/APYRIMIDINIC B DOUBLE HELIX FLIPPED-OUT BASES N N N ENDONUCLEASE (E.C.4.2.99.18)/DNA COMPLEX PD0094 MAJOR APURINIC/APYRIMIDINIC B DOUBLE HELIX FLIPPED-OUT BASES, N N Y ENDONUCLEASE (E.C.4.2.99.18)/DNA OVERHANGING BASES COMPLEX PD0095 MAJOR APURINIC/APYRIMIDINIC B DOUBLE HELIX OVERHANGING BASES N N N ENDONUCLEASE (E.C.4.2.99.18)/DNA COMPLEX PD0096 INTRON-ENCODED HOMING ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASES N N N I-PPOI (E.C.3.1.-.-)/DNA COMPLEX PD0097 INTRON-ENCODED HOMING ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASES N N N I-PPOI (E.C.3.1.-.-)/DNA COMPLEX PD0098 HOLLIDAY JUNCTION DNA HELICASE RH QUADRUPLE HELIX HOLLIDAY JUNCTION N N N RUVA/DNA COMPLEX PD0099 3-METHYLADENINE DNA GLYCOSYLASE II B DOUBLE HELIX FLIPPED-OUT BASES, N N N (E.C.3.2.2.21)/DNA COMPLEX OVERHANGING BASES PD0100 DNA MISMATCH ENDONUCLEASE n.a. n.a. n.a. N N Y (E.C.3.1.-.-)/DNA COMPLEX PD0101 ENDONUCLEASE BGLII/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0103 CRE RECOMBINASE/DNA COMPLEX RH DOUBLE HELIX OVERHANGING BASES, N N N HOLLIDAY JUNCTION PD0104 CRE RECOMBINASE MUTANT (R173K)/DNA RH DOUBLE HELIX OVERHANGING BASES, N N N COMPLEX HOLLIDAY JUNCTION PD0105 PDNA POLYMERASE I n.a. n.a. n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX PD0106 DNA POLYMERASE I (E.C.2.7.7.7)/DNA U SINGLE STRAND n.a. N Y N COMPLEX ------------------------------------------------------------------------------------------------------------------------------ Page 3 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0108 BGLI RESTRICTION ENDONUCLEASE B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0113 CRE RECOMBINASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES, N N N THREE-WAY JUNCTION PD0117 8-OXOGUANINE DNA GLYCOSYLASE/DNA B DOUBLE HELIX FLIPPED-OUT BASES Y N N COMPLEX PD0125 DNA TOPOISOMERASE I B DOUBLE HELIX n.a. N N N (E.C.5.99.1.2)/DNA COMPLEX PD0126 REVERSE TRANSCRIPTASE B DOUBLE HELIX n.a. N N N (E.C.2.7.7.49)/DNA COMPLEX PD0127 URACIL-DNA GLYCOSYLASE B DOUBLE HELIX FLIPPED-OUT BASES, N N N (E.C.3.2.2.3)/DNA COMPLEX OVERHANGING BASES PD0128 URACIL-DNA GLYCOSYLASE B DOUBLE HELIX FLIPPED-OUT BASES, N N N (E.C.3.2.2.3)/DNA COMPLEX OVERHANGING BASES PD0129 TYPE II RESTRICTION ENZYME ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0130 TYPE II RESTRICTION ENZYME ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0131 TYPE II RESTRICTION ENZYME ECORV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0132 TYPE II RESTRICTION ENZYME ECORV B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0133 TYPE II RESTRICTION ENZYME ECORV B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0134 REVERSE TRANSCRIPTASE B DOUBLE HELIX n.a. N N N (E.C.2.7.7.49)/DNA COMPLEX PD0135 REVERSE TRANSCRIPTASE B DOUBLE HELIX FLIPPED-OUT BASES, N N Y (E.C.2.7.7.49)/DNA COMPLEX OVERHANGING BASES PD0139 TYPE II RESTRICTION ENZYME BAMH B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0140 I-PPOI HOMING ENDONUCLEASE/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0141 3-METHYL-ADENINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.21)/DNA COMPLEX PD0147 TYPE II RESTRICTION ENZYME PVUII B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0149 TYPE II RESTRICTION ENZYME PVUII B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA COMPLEX PD0150 RIBONUCLEASE A/DNA COMPLEX U SINGLE STRAND n.a. N N N ------------------------------------------------------------------------------------------------------------------------------ Page 4 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0151 RESTRICTION ENDONUCLEASE/DNA B DOUBLE HELIX n.a. N N N COMPLEX PD0152 PROTEIN (MOLONEY MURINE LEUKEMIA B DOUBLE HELIX OVERHANGING BASES N N N VIRUS REVERSE TRANSCRIPTASE)/DNA COMPLEX PD0153 RESTRICTION ENDONUCLEASE BGLI/DNA RH DOUBLE HELIX OVERHANGING BASES N N N COMPLEX PD0166 CRE RECOMBINASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES N N N PD0168 3-METHYL-ADENINE DNA GLYCOSYLASE B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.2.2.20)/DNA COMPLEX PD0172 3-METHYL-ADENINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.20)/DNA COMPLEX PD0177 TYPE II RESTRICTION ENZYME NGOMI B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.4)/DNA COMPLEX PD0178 FLP RECOMBINASE/SYMMETRIZED FRT RH DOUBLE HELIX FLIPPED-OUT BASES, N N N DNA COMPLEX HOLLIDAY JUNCTION PD0179 8-OXOGUANINE DNA GLYCOSYLASE 1 B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA COMPLEX PD0188 MODIFICATION METHYLASE TAQI B DOUBLE HELIX n.a. Y N N (E.C.2.1.1.72)/DNA COMPLEX PD0189 DNA ENDONUCLEASE I-CREI (E.C. 3.1.- B DOUBLE HELIX n.a. N N N .-)/DNA COMPLEX PD0190 DNA ENDONUCLEASE I-CREI (E.C. 3.1.- B DOUBLE HELIX n.a. N N N .-)/DNA COMPLEX PD0194 HHAI METHYLTRANSFERASE MUTANT B DOUBLE HELIX OVERHANGING BASES, N N N (T250G) (E.C. 2.1.1.73), DNA AND FLIPPED OUT BASE ADOHCY PD0195 8-OXOGUANINE DNA GLYCOSYLASE 1 B DOUBLE HELIX n.a. N N N (E.C. 3.2.2.-)/DNA COMPLEX PD0196 DNA POLYMERASE BETA/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PD0197 DNA POLYMERASE BETA/DNA COMPLEX B DOUBLE HELIX n.a. N Y N PD0200 INTRON-ASSOCIATED ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASES N N N 1/DNA Complex PD0202 REVERSE TRANSCRIPTASE (E.C. B DOUBLE HELIX OVERHANGING BASES N N N 2.7.7.49)/DNA Complex PD0203 DNA TOPOISOMERASE III (E.C. U SINGLE STRAND n.a. N N N 5.99.1.2)/DNA Complex PD0207 TYPE II RESTRICTION ENZYME NAEI B DOUBLE HELIX n.a. N N N (E.C. 3.1.21.4)/DNA Complex ------------------------------------------------------------------------------------------------------------------------------ Page 5 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0212 DNA POLYMERASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES N N N PD0213 HIN RECOMBINASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASES Y N N PD0216 P2 PROTEIN/DNA Complex U SINGLE STRAND n.a. N N N PD0217 P2 PROTEIN/DNA Complex U SINGLE STRAND n.a. N N N PD0220 Ku Heterodimer/DNA complex U DOUBLE HELIX n.a. N N N PD0228 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, Y N N FLIPPED-OUT BASES PD0229 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, Y N N FLIPPED-OUT BASES PD0234 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, N N N FLIPPED-OUT BASES PD0235 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, N N N FLIPPED-OUT BASES PD0236 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, N N N FLIPPED-OUT BASES PD0237 HIN RECOMBINASE/DNA Complex B DOUBLE HELIX OVERHANGING BASES, N N N FLIPPED-OUT BASES PD0242 BARNASE (E.C.3.1.27.-)/DNA COMPLEX U SINGLE STRAND n.a. N N N PD0251 DNA POLYMERASE IV(FAMILY Y) (E.C. B DOUBLE HELIX OVERHANGING BASES N N N 2.7.7.7)/DNA Complex PD0252 DNA POLYMERASE IV(FAMILY Y) (E.C. B DOUBLE HELIX OVERHANGING BASES Y N N 2.7.7.7)/DNA Complex PD0253 Endonuclease VIII (E.C.3.2.-.- B DOUBLE HELIX n.a. N N N )/DNA Complex PD0254 ENDONUCLEASE VIII (E.C.3.2.-.- B DOUBLE HELIX n.a. Y N N )/DNA Complex PD0255 DNA TOPOISOMERASE I B DOUBLE HELIX n.a. Y N N (E.C.5.99.1.2)/DNA Complex PD0256 DNA TOPOISOMERASE I B DOUBLE HELIX n.a. N N N (E.C.5.99.1.2)/DNA Complex PD0264 Formamidopyrimidine-DNA B DOUBLE HELIX n.a. N N N glycosylase (E.C.3.2.2.23)/DNA Complex PD0267 RECG/DNA Complex U DOUBLE HELIX n.a. N N N ------------------------------------------------------------------------------------------------------------------------------ Page 6 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0271 CRE RECOMBINASE/DNA Complex B DOUBLE HELIX HOLLIDAY JUNCTION N N N PD0272 TYPE II RESTRICTION ENZYME HINCII B DOUBLE HELIX n.a. N N N (E.C.3.1.21.4)/DNA complex PD0275 Terminal U SINGLE STRAND n.a. Y N N deoxynucleotidyltransferase short isoform (E.C.2.7.7.31)/DNA complex PD0277 Formamido-pyrimidine DNA B DOUBLE HELIX n.a. N N N glycosylase (E.C.3.2.2.23)/DNA Complex PD0292 MUTM/DNA Complex B DOUBLE HELIX n.a. N N N PD0293 MutM/DNA Complex B DOUBLE HELIX n.a. N N N PD0295 MutM/DNA Complex B DOUBLE HELIX n.a. N N N PD0296 MutM/DNA Complex B DOUBLE HELIX n.a. N N N PD0300 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES N N N Complex PD0301 DNA Polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES N N N Complex PD0302 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES N N N Complex PD0303 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES N N N Complex PD0304 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES N N N Complex PD0305 RNA polymerase Holoenzyme/DNA B DOUBLE HELIX n.a. N N N PD0306 CATABOLITE GENE ACTIVATOR B DOUBLE HELIX OVERHANGING BASES N N N PROTEIN/DNA-directed RNA polymerase alpha chain (E.C.2.7.7.6)/DNA Complex, ADENOSINE-3',5'-CYCLIC- MONOPHOSPHATE PD0313 DNA topoisomerase I B DOUBLE HELIX n.a. N N N (E.C.5.99.1.2)/DNA Complex PD0316 CRYSTAL STRUCTURE OF MET184ILE B DOUBLE HELIX n.a. N N N MUTANT OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DOUBLE STRANDED DNA TEMPLATE-PRIMER PD0317 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX n.a. N N N Complex PD0319 ENDONUCLEASE PI-SCEI/DNA Complex B DOUBLE HELIX n.a. N N N PD0320 ENDONUCLEASE PI-SCEI/DNA Complex B DOUBLE HELIX n.a. N N N ------------------------------------------------------------------------------------------------------------------------------ Page 7 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0321 8-OXOGUANINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA Complex PD0322 8-OXOGUANINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA Complex PD0323 8-OXOGUANINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA complex PD0327 Modification methylase HhaI/DNA B DOUBLE HELIX FLIPPED OUT BASE N N N Complex PD0331 8-OXOGUANINE DNA GLYCOSYLASE B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA Complex PD0332 8-oxoguanine DNA glycosylase B DOUBLE HELIX n.a. N N N (E.C.3.2.2.-)/DNA Complex PD0333 DNA beta-glucosyltransferase B DOUBLE HELIX FLIPPED-OUT BASES N N N (E.C.2.4.1.27)/DNA Complex PD0334 DNA beta-glucosyltransferase B DOUBLE HELIX FLIPPED-OUT BASES N N N (E.C.2.4.1.27)//DNA Complex PD0335 DNA endonuclease I-MsoI/DNA Complex B DOUBLE HELIX n.a. N N N PD0336 FLP RECOMBINASE/DNA Complex RH DOUBLE HELIX FLIPPED-OUT BASES, N N N HOLLIDAY JUNCTION PD0337 CRE RECOMBINASE/DNA Complex B DOUBLE HELIX HOLLIDAY JUNCTION N N Y PD0340 Tn5 transposase/DNA Complex B DOUBLE HELIX n.a. N N N PD0342 chimera of homing endonuclease I- B DOUBLE HELIX n.a. N N Y DmoI and DNA endonuclease I-CreI (E.C.3.1.-.-)/DNA PD0343 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA Complex PD0344 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA Complex PD0345 DNA-directed RNA polymerase RH DOUBLE HELIX OVERHANGING BASES N N Y (E.C.2.7.7.6)/DNA/RNA Complex PD0346 G/U mismatch-specific DNA B DOUBLE HELIX n.a. N N N glycosylase (E.C.3.2.2.2-)/DNA Complex PD0347 TN5 TRANSPOSASE/DNA COMPLEX B DOUBLE HELIX FLIPPED-OUT BASES N N N PD0349 TN5 TRANSPOSASE/DNA Complex B DOUBLE HELIX FLIPPED-OUT BASES N N N PD0350 TN transposase/DNA Complex B DOUBLE HELIX FLIPPED-OUT BASES N N N ------------------------------------------------------------------------------------------------------------------------------ Page 8 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0353 G/U mismatch-specific DNA B DOUBLE HELIX n.a. N N Y glycosylase (E.C.3.2.2.-)/DNA COMPLEX PD0354 G/U mismatch-specific DNA B DOUBLE HELIX FLIPPED-OUT BASE N N Y glycosylase (E.C.3.2.2.-)/DNA COMPLEX PD0358 DNA polymerase IV (E.C.2.7.7.7)/DNA B DOUBLE HELIX BULGES, FLIPPED-OUT N N Y BASES, OVERHANGING BASES, BASE TRIPLET PD0359 Reverse Transcriptase B DOUBLE HELIX n.a. N N N (E.C.2.7.7.49)/DNA complex PD0360 DNA endonuclease I-CreI (E.C.3.1.- B DOUBLE HELIX n.a. N N N .-)/DNA PD0361 DNA endonuclease I-CreI (E.C.3.1.- B DOUBLE HELIX n.a. N N N .-)/DNA PD0362 DNA polymerase IV(E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASES, N N N FLIPPED-OUT BASES PD0364 reverse transcriptase B DOUBLE HELIX n.a. N N N (E.C.2.7.7.49)/monoclonal antibody fab28 light and heavy chains/DNA PD0365 reverse transcriptase B DOUBLE HELIX n.a. N N Y (E.C.2.7.7.49)/monoclonal antibody fab28 light and heavy chains/DNA PD0370 DNA topoisomerase I/DNA Complex n.a. n.a. n.a. N N N PD0372 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y Complex PD0373 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y COMPLEX PD0374 DNA Polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y Complex PD0375 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y Complex PD0376 DNA POLYMERASE I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y complex PD0377 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y complex PD0378 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX n.a. N N N Complex PD0379 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N N Complex PD0380 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N N Complex PD0381 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y Complex ------------------------------------------------------------------------------------------------------------------------------ Page 9 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0382 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX n.a. N N Y complex PD0383 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N Y complex PD0384 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX n.a. N N Y complex PD0385 DNA polymerase I (E.C.2.7.7.7)/DNA B DOUBLE HELIX OVERHANGING BASE N N N Complex PD0391 tyrosyl-DNA phosphodiesterase U SINGLE STRAND n.a. N N N 1/DNA Complex PD0392 Cre recombinase/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0394 TrwC protein/DNA Complex U SINGLE STRAND HAIRPIN LOOP, N N Y FLIPPED-OUT BASES PD0396 ENDONUCLEASE III/DNA B DOUBLE HELIX OVERHANGING BASE N N N PD0397 ENDONUCLEASE III/DNA B DOUBLE HELIX OVERHANGING BASE N N N PD0402 TRWC PROTEIN/DNA Complex U SINGLE STRAND HAIRPIN LOOP, N N Y FLIPPED-OUT BASES PD0403 Nuclease (E.C.3.1.-.-) B DOUBLE HELIX NICKED N N N PD0404 Cre recombinase/DNA COMPLEX B DOUBLE HELIX n.a. N N Y PD0427 Endonuclease III/5'- B DOUBLE HELIX OVERHANGING BASE N N Y D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*A P*C)-3'/5'- D(*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5I U)P*CP*T)-3' PD0428 Lambda Integrase/DNA Complex B DOUBLE HELIX INTERNAL LOOP, N N Y FLIPPED-OUT BASES PD0433 Intron-encoded endonuclease I- B DOUBLE HELIX n.a. N N N AniI/DNA PD0454 Colicin E7 (E.C.3.1.-.-)/DNA B DOUBLE HELIX n.a. N N N Complex PD0460 DNA adenine methylase B DOUBLE HELIX n.a. N N N (E.C.2.1.1.72)/DNA Complex PD0461 Uracil-DNA glycosylase(E.C.3.2.2.- B DOUBLE HELIX OVERHANGING BASES N N N )/DNA Complex PD0462 Cre recombinase/DNA COMPLEX B DOUBLE HELIX n.a. N N N PD0463 Cre recombinase/DNA COMPLEX B DOUBLE HELIX n.a. N N N ------------------------------------------------------------------------------------------------------------------------------ Page 10 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PD0467 trwC PROTEIN/DNA Complex U SINGLE STRAND LOOP, HAIRPIN LOOP, N N Y FLIPPED-OUT BASES, OVERHANGING BASES PD0473 MutM/DNA Complex B DOUBLE HELIX FLIPPED-OUT BASES N N N PD0474 MutM/DNA Complex B DOUBLE HELIX FLIPPED-OUT BASES N N N PD0477 DNA topoisomerase I B DOUBLE HELIX n.a. N N N (E.C.5.99.1.2)/DNA Complex PD0485 Tyrosyl-DNA phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/Topoisomerase I- Derived peptide/DNA Complex PD0486 Tyrosyl-DNA Phosphodiesterase U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/Topoisomerase I- Derived Peptide/DNA complex PD0487 Tyrosyl-DNA Phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/DNA complex PD0488 Tyrosyl-DNA Phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/DNA complex PD0489 Tyrosyl-DNA Phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/DNA complex PD0490 Tyrosyl-DNA Phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/DNA complex PD0491 Tyrosyl-DNA Phosphodiesterase 1 U SINGLE STRAND n.a. N N N (E.C.3.1.4.-)/DNA complex PD0493 Polynucleotide kinase/DNA U SINGLE STRAND n.a. N N N PD0499 Polynucleotide kinase U SINGLE STRAND n.a. N N N (E.C.2.7.1.78)/DNA Complex PD0500 Polynucleotide kinase U SINGLE STRAND LOOP N N N (E.C.2.7.1.78)/DNA Complex PD0501 Flap structure-specific B DOUBLE HELIX n.a. N N N endonuclease/5'- d(*T*pA*pG*pC*pA*pT*pC*pG*pG) PD0502 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)- B DOUBLE HELIX OVERHANGING BASE N N N 3'/5'- d(*T*pA*pG*pC*pA*pT*pC*pG*pG)- 3'/Flap structure-specific endonuclease PD0503 NA polymerase lambda B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA Complex PD0504 DNA polymerase IV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.2.7.7.7)/DNA Complex PD0505 DNA polymerase IV B DOUBLE HELIX OVERHANGING BASES N N N (E.C.2.7.7.7)/DNA Complex PDE001 ECO RI ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASE, N N N (E.C.3.1.21.4)/DNA COMPLEX KINKED ------------------------------------------------------------------------------------------------------------------------------ Page 11 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE002 ECO RV (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX KINKED N N N PDE003 ECO RV (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX KINKED N N N PDE004 DNA POLYMERASE I KLENOW FRAGMENT B DOUBLE HELIX OVERHANGING BASE N N N (E.C.2.7.7.7) MUTANT/DNA COMPLEX PDE005 DEOXYRIBONUCLEASE I (DNASE I) RH DOUBLE HELIX n.a. N N N (E.C.3.1.21.1)/DNA COMPLEX + N- ACETYL-D-GLUCOSAMINE PDE006 DEOXYRIBONUCLEASE I (DNASE I) B DOUBLE HELIX OVERHANGING BASES N N N (E.C.3.1.21.1)/DNA COMPLEX + N- ACETYL-D-GLUCOSAMINE PDE009 HIN RECOMBINASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDE010 BARNASE (E.C.3.1.27.-)/DNA COMPLEX U n.a. 3'C-3'C BASE N N Y PAIRING, ADJACENT ADENINES STACKED PDE0100 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR PDE0101 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF PYROPHOSPHATE AND MNCL2 PDE0102 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, NO 5'- PHOSPHATE PDE0103 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2',3'- DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MGCL2 PDE0104 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DTTP AND MGCL2 PDE0105 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF PYROPHOSPHATE AND MGCL2 PDE0106 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND MNCL2 PDE0107 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND MNCL2 PDE0108 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2',3'- DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MNCL2 PDE0109 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYGUANOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DGTP AND MNCL2 PDE011 DNA POLYMERASE BETA B DOUBLE HELIX OVERHANGING BASE N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DIDEOXYCYTIDINE-5'-TRIPHOSPHATE PDE0110 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2 PDE0111 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND ZNCL2 ------------------------------------------------------------------------------------------------------------------------------ Page 12 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE0112 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, NATIVE STRUCTURE PDE0113 DNA POLYMERASE BETA (POL B) B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX (NON GAPPED DNA ONLY) PDE0114 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX PDE0115 GAMMA DELTA RESOLVASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDE0116 RIBONUCLEASE A (E.C.3.1.27.5)/DNA n.a. SINGLE STRAND n.a. N N N COMPLEX PDE0117 RIBONUCLEASE A (E.C.3.1.27.5)/DNA n.a. SINGLE STRAND n.a. N N N COMPLEX PDE012 DNA POLYMERASE BETA B DOUBLE HELIX OVERHANGING BASE N N N (E.C.2.7.7.7)/DNA COMPLEX + 2',3'- DIDEOXYCYTIDINE-5'- TRIPHOSPHATE PDE0121 URACIL-DNA GLYCOSYLASE B DOUBLE HELIX OVERHANGING BASE N N N (E.C.2.1.1.73)/DNA COMPLEX + S- PAIR, FLIPPED-OUT ADENOSYL-L-HOMOCYSTEINE BASE PDE0124 DNA POLYMERASE BETA/DNA COMPLEX B DOUBLE HELIX NICKED N N N PDE0125 DNA POLYMERASE BETA/DNA COMPLEX + B DOUBLE HELIX GAPPED N N N 2',3'-DIDEOXYCYTIDINE-5'- TRIPHOSPHATE PDE0126 DNA POLYMERASE BETA/DNA COMPLEX B DOUBLE HELIX GAPPED AND NICKED N N N (EC 2.7.7.7) DNA PDE0127 FOKI RESTRICTION ENDONUCLEASE/DNA B DOUBLE HELIX n.a. N N N COMPLEX PDE0128 TC3 TRANSPOSASE/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDE0129 REP HELICASE/DNA COMPLEX U SINGLE STRAND n.a. N N N (E.C.3.6.1.-) PDE013 ALPHA-THROMBIN (E.C.3.4.21.5)/DNA, n.a. n.a. n.a. N N Y PPACK PEPTIDE PDE0131 DNA POLYMERASE I/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDE0132 DNA POLYMERASE I/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDE0133 DNA POLYMERASE I/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDE0134 NS3 PROTEIN/DNA COMPLEX U SINGLE STRAND n.a. N N N PDE0135 DNA POLYMERASE, THIOREDOXIN/DNA B DOUBLE HELIX FLIPPED-OUT BASE, N N N COMPLEX, 2'-3'DIDEOXYGUANOSINE-5'- OVERHANGING BASE TRIPHOSPHATE ------------------------------------------------------------------------------------------------------------------------------ Page 13 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE0136 DNA POLYMERASE I KLENOW FRAGMENT n.a. SINGLE STRAND n.a. N N N (E.C.2.7.7.7) MUTANT/DNA COMPLEX PDE0137 DNA POLYMERASE I KLENOW FRAGMENT n.a. SINGLE STRAND n.a. N Y N (E.C.2.7.7.7) MUTANT/DNA COMPLEX PDE0138 DNA POLYMERASE I KLENOW FRAGMENT n.a. SINGLE STRAND n.a. N Y N (E.C.2.7.7.7) MUTANT/DNA COMPLEX PDE0139 ECORV ENDONUCLEASE(T93A)/DNA B DOUBLE HELIX KINKED N N N COMPLEX PDE014 ECO RV (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE, N N N KINKED PDE0140 MISMATCH SPECIFIC URACIL DNA n.a. n.a. n.a. N N N GLYCOSYLASE (MUG)/DNA COMPLEX PDE0141 TOPOISOMERASE I/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDE0142 TOPOISOMERASE I (E.C.5.99.1.2)/DNA B DOUBLE HELIX n.a. Y N N COMPLEX PDE0143 HUMAN TOPOISOMERASE I/DNA COMPLEX B DOUBLE HELIX n.a. Y N N PDE0144 INTRON-ENCODED ENDONUCLEASE I- B DOUBLE HELIX OVERHANGING BASES N N N PPOI/DNA COMPLEX PDE0145 ENDONUCLEASE ECORV B DOUBLE HELIX OVERHANGING BASES Y N Y (E.C.3.1.21.4)/DNA COMPLEX PDE0146 ENDONUCLEASE ECORV B DOUBLE HELIX n.a. N N Y (E.C.3.1.21.4)/DNA COMPLEX PDE015 ECO RV (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE, N N N KINKED PDE016 ECO RV (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE, N N N KINKED PDE017 PVUII (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX OVERHANGING BASE N N N PDE020 BAMHI (E.C.3.1.21.4)/DNA COMPLEX B DOUBLE HELIX n.a. N N N PDE022 T4 ENDONUCLEASE V (E.C.3.1.25.1) B DOUBLE HELIX OVERHANGING BASE, N N N MUTANT/DNA COMPLEX KINKED, BULGE PDE023 RIBONUCLEASE B (E.C.3.1.27.5)/DNA U SINGLE STRAND n.a. N N N COMPLEX PDE024 TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B- RH DOUBLE HELIX n.a. N N N OCTYLGLUCOSIDE COMPLEX PDE026 URACIL-DNA GLYCOSYLASE (E.C.3.2.2.- n.a. SINGLE STRAND n.a. N N N )/DNA COMPLEX ------------------------------------------------------------------------------------------------------------------------------ Page 14 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE027 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF KCL AT PH 7.5 PDE028 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF BACL2 PDE029 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CACL2 PDE030 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CACL2 PDE031 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CRCL3 PDE032 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CSCL PDE033 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 6.5 PDE034 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 7.5 PDE035 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF KCL PDE036 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CACL2 AND MGCL2 PDE037 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF KCL AND MGCL2 PDE038 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 AND MGCL2 PDE039 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 PDE040 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF BACL2 AND NACL PDE041 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CACL2 AND NACL PDE042 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF KCL AND NACL PDE043 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 AND NACL PDE044 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF NICL2 PDE045 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF TLCL PDE046 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DATP AND ZNCL2 ------------------------------------------------------------------------------------------------------------------------------ Page 15 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE047 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX PDE048 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CDCL2 PDE049 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CDCL2 PDE050 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF COCL2 PDE051 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CRCL3 PDE052 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CUCL2 PDE053 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MGCL2 PDE054 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 PDE055 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 PDE056 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF NICL2 PDE057 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 PDE058 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 PDE059 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 PDE060 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 PDE061 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 PDE062 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2 PDE063 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CDCL2 PDE064 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR PDE065 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, NO 5'- PHOSPHATE PDE066 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND CDCL2 ------------------------------------------------------------------------------------------------------------------------------ Page 16 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE067 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND MGCL2 PDE068 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DATP AND MGCL2 PDE069 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DCTP AND MGCL2 PDE070 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DGTP AND MGCL2 PDE071 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MGCL2 PDE072 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP, MGCL2, AND MNCL2 PDE073 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND NICL2 PDE074 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DATP, MNCL2, AND AMMONIUM SULFATE PDE075 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + ADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF ATP AND MNCL2 PDE076 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 3'- AZIDO-3'-DEOXYTHYMIDINE-5'- TRIPHOSPHATE, SOAKED IN THE PRESENCE OF AZT-TP AND MNCL2 PDE077 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND MNCL2 PDE078 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF OF DATP AND MNCL2 PDE079 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND MNCL2 PDE080 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND MNCL2 PDE081 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND MNCL2 PDE082 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2',3'- DIDEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDATP AND MNCL2 PDE083 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYGUANOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DGTP AND MNCL2 PDE084 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2 PDE085 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2 PDE086 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2 ------------------------------------------------------------------------------------------------------------------------------ Page 17 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PDE087 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF OF DATP, MNCL2, AND LITHIUM SULFATE PDE088 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MNCL2 AND IN THE ABSENCE OF NACL PDE089 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND CACL2 PDE090 DNA POLYMERASE (E.C.2.7.7.7)/DNA U SINGLE STRAND n.a. N N N COMPLEX PDE091 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-O-(1- THIOTRIPHOSPHATE), SOAKED IN THE PRESENCE OF DATP(ALPHA)S AND MNCL2 PDE092 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND COCL2 PDE093 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND CRCL3 PDE094 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DATP AND CUCL2 PDE095 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N Y N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND ZNCL2 PDE096 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND ZNCL2 PDE097 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX + 2'- DEOXYGUANOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DGTP AND ZNCL2 PDE098 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DTTP AND ZNCL2 PDE099 DNA POLYMERASE BETA B DOUBLE HELIX n.a. N N N (E.C.2.7.7.7)/DNA COMPLEX PDE139 ECORV ENDONUCLEASE B DOUBLE HELIX OVERHANGING BASE N N N (E.C.3.1.21.4)/DNA COMPLEX PDE140 I-PPOL HOMING ENDONUCLEASE/DNA B DOUBLE HELIX OVERHANGING BASE N N N COMPLEX PDE141 CYTOSINE-SPECIFIC B DOUBLE HELIX FLIPPED-OUT BASES Y N N METHYLTRANSFERASE HHAI (E.C.2.1.1.73)/DNA COMPLEX PDEB08 HHAI METHYLTRANSFERASE B DOUBLE HELIX OVERHANGING BASES Y N N (E.C.2.1.1.73)/DNA COMPLEX + S- ADENOSYL-L-HOMOSYTEINE PDEB122 HHAI METHYLTRANSFERASE B DOUBLE HELIX OVERHANGING BASE Y N N (E.C.2.1.1.73)/DNA COMPLEX + S- PAIR, FLIPPED-OUT ADENOSYL-L-HOMOSYTEINE BASE PDEB123 HHAI METHYLTRANSFERASE B DOUBLE HELIX n.a. Y N N (E.C.2.1.1.7)/DNA COMPLEX + S- ADENOSYL-L-HOMOCYSTEINE PDEB19 AEIII METHYLASE (E.C.2.1.1.37)/DNA B DOUBLE HELIX OVERHANGING BASE, Y N N COMPLEX FLIPPED-OUT BASE, SHIFTED BASE, BULGE ------------------------------------------------------------------------------------------------------------------------------ Page 18 created by the NDB Project on Wed May 26 14:33:22 2004 STRUCTURE SUMMARY FOR PROTEIN/DNA COMPLEXES (ENZYMES) ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special NA Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ PH0001 DOUBLE-STRANDED RNA SPECIFIC Z DOUBLE HELIX n.a. N N N ADENOSINE DEAMINASE (ADAR1)/DNA COMPLEX PH0002 BACTERIOPHAGE T7 RNA POLYMERASE B DOUBLE HELIX n.a. N N N (E.C.2.7.7.6)/DNA COMPLEX PH0003 HIV-1 REVERSE B DOUBLE HELIX OVERHANGING BASE N N Y TRANSCRIPTASE/FRAGMENT OF FAB 28//DNA/RNA Complex PH0004 RNA POLYMERASE II/DNA/RNA Complex n.a. n.a. n.a. N N N PH0008 T7 RNA B DOUBLE HELIX n.a. N N N polymerase(E.C.2.7.7.6)/DNA/RNA Complex PH0011 DNA-directed RNA polymerase II A DOUBLE HELIX OVERHANGING BASES N N Y largest subunit (E.C.2.7.7.6)/DNA- directed RNA polymerase II 140 kDa polypeptide (E.C.2.7.7.6)/DNA- directed RNA polymerase II 45 kDa polypeptide (E.C.2.7.7.6)/DNA- directed RNA polymerases I, II, and III 27 kDa polypeptide (E PR0016 DNA POLYMERASE I (E.C.2.7.7.7 U SINGLE STRAND n.a. N N N )/DNA-RNA COMPLEX ------------------------------------------------------------------------------------------------------------------------------ Page 19 created by the NDB Project on Wed May 26 14:33:22 2004