STRUCTURE SUMMARY FOR RNA DOUBLE HELICES WITH SPECIAL FEATURES ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ 1ROQ 5'- RH DOUBLE HELIX HAIRPIN LOOP, N N N R(*GP*GP*UP*AP*UP*CP*AP*CP*GP*GP*UP FLIPPED-OUT BASES *AP*CP*C)-3' AR0005 5'- A DOUBLE HELIX OVERHANGING BASE N N Y R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP *UP*C)-3' AR0007 5'- A DOUBLE HELIX OVERHANGING BASES N N Y R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP *U)-3' AR0023 5'- A DOUBLE HELIX FLIPPED-OUT BASES, N N N R(*AP*AP*CP*GP*GP*GP*CP*GP*CP*AP*GP OVERHANGING BASES *AP*A)-3', 5'- R(*UP*CP*UP*GP*AP*CP*GP*GP*UP*AP*CP *GP*UP*UP*U)-3' AR0024 29-MER FRAGMENT OF SRP RNA HELIX 6 A DOUBLE HELIX OVERHANGING BASES N N Y AR0026 5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)- A DOUBLE HELIX FLIPPED-OUT BASES N N N 3', 5'- R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3' AR0027 5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)- A DOUBLE HELIX FLIPPED-OUT BASES N N N 3', 5'- R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3' AR0028 REV BINDING ELEMENT A DOUBLE HELIX FLIPPED-OUT BASES N N Y AR0029 (5'- A DOUBLE HELIX BULGES, FLIPPED-OUT Y N Y R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP BASES, BASE TRIPLET *AP*(BRO)CP*C)-3') AR0032 BPS-U2 SNRNA DUPLEX A DOUBLE HELIX BULGES, FLIPPED-OUT N N N BASES AR0033 5'- A DOUBLE HELIX BULGES, FLIPPED-OUT Y N N R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP BASES, BASE TRIPLET *AP*(BRO)CP*C)-3' AR0034 5'- A DOUBLE HELIX BULGES Y N N R(*GP*UP*GP*UP*CP*GP*(BRO)CP*AP*C)- 3' AR0035 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)- A DOUBLE HELIX BULGE, FLIPPED-OUT N N Y 3' BASE AR0039 5'- A DOUBLE HELIX OVERHANGING BASES Y N Y R(*GP*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP *AP*GP*CP*AP*(BRO)UP*CP*CP*C)-3' AR0041 5'- A DOUBLE HELIX INTERNAL LOOP, N N Y R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(C MISPAIR B2)CP*G)-3' AR0042 HIV-1(LAI) RNA A DOUBLE HELIX INTERNAL LOOP N N N AR0043 HIV-1(LAI) RNA A DOUBLE HELIX INTERNAL LOOP N N N AR0044 5'- A DOUBLE HELIX FLIPPED-OUT BASES Y Y Y R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP *GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G )-3' AR0045 5'- A DOUBLE HELIX FLIPPED-OUT BASES N N Y R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP *GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G )-3' AR0046 HIV-1 DIS(MAL) DUPLEX RU HEXAMINE- A DOUBLE HELIX FLIPPED-OUT BASES N N Y SOAKED ------------------------------------------------------------------------------------------------------------------------------ Page 1 created by the NDB Project on Wed May 26 14:33:14 2004 STRUCTURE SUMMARY FOR RNA DOUBLE HELICES WITH SPECIAL FEATURES ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ ARHB90 5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3' A DOUBLE HELIX INTERNAL LOOP Y N Y ARM0107 5'- A DOUBLE HELIX OVERHANGING BASE N N N R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP PAIR *UP*C)-3' DR0009 5'- U DOUBLE HELIX INTERNAL LOOP N N Y R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP *GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)- 3', Streptomycin DR0010 5'- U DOUBLE HELIX INTERNAL LOOP N N Y R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP *GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)- 3', Streptomycin UR0001 5'- U DOUBLE HELIX FLIPPED-OUT BASES, N N Y R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP OVERHANGING BASES *AP*G)-3', 5'- R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C) -3' UR0005 5'- RH DOUBLE HELIX FLIPPED-OUT BASES N N N R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP *GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G )-3' UR0009 4.5S RNA DOMAIN IV U DOUBLE HELIX LOOP, FLIPPED-OUT N N N BASES UR0025 RNA BCh12, Short and Long strands A DOUBLE HELIX FLIPPED-OUT BASES, Y N Y OVERHANGING BASES UR0028 5'- U DOUBLE HELIX BULGE, FLIPPED-OUT N N Y R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP BASES, OVERHANGING *AP*G)-3' BASES UR0029 Hammerhead Ribozyme U DOUBLE HELIX BULGE, FLIPPED-OUT N Y Y BASES, OVERHANGING BASES UR0030 5'- U DOUBLE HELIX BULGE, FLIPPED-OUT N N Y R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP BASES, OVERHANGING *AP*G)-3' BASES UR0032 5'- B DOUBLE HELIX HAMMERHEAD, RNA N N Y R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP HAMMERHEAD *GP*AP*GP*GP*CP*C)-3'/Ribozyme RIBOZYME, LOOP URF042 5'-R(*UP*UP*CP*GP*CP*G)-3' A DOUBLE HELIX NICKED, OVERHANGING N N N BASE URL029 5'- A DOUBLE HELIX INTERNAL LOOP N N Y R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP *C)-3' URL050 5'- U DOUBLE HELIX INTERNAL LOOP N N Y R(*GP*GP*CP*GP*CP*UP*UP*GP*CP*GP*UP *C)-3' URL051 5'- U DOUBLE HELIX INTERNAL LOOP Y N Y R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP *C)-3', MN 2+ URL064 5'- U DOUBLE HELIX INTERNAL LOOP, N Y Y R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP OVERHANGING BASE *G)-3', LOOP E FROM 5S RRNA URL065 FRAGMENT I FROM 5S RRNA U DOUBLE HELIX KINKED, INTERNAL N Y Y LOOP, OVERHANGING BASE URL066 FRAGMENT I FROM 5S RRNA RH DOUBLE HELIX OVERHANGING BASE N Y Y URL069 FRAGMENT I FROM 5S RRNA U DOUBLE HELIX KINKED, INTERNAL N Y Y LOOP, OVERHANGING BASE ------------------------------------------------------------------------------------------------------------------------------ Page 2 created by the NDB Project on Wed May 26 14:33:14 2004 STRUCTURE SUMMARY FOR RNA DOUBLE HELICES WITH SPECIAL FEATURES ------------------------------------------------------------------------------------------------------------------------------ NDB ID Descriptor Type NA Description Special Features Base Mod. Phosph.Mod. Mispair ------------------------------------------------------------------------------------------------------------------------------ URX075 5'- U DOUBLE HELIX BULGE, OVERHANGING N N N R(*GP*GP*CP*CP*AP*GP*AP*UP*CP*UP*GP BASES *AP*GP*CP*G)-3' ------------------------------------------------------------------------------------------------------------------------------ Page 3 created by the NDB Project on Wed May 26 14:33:14 2004