A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry
Supplementary Material
3DNA: Analysis & Rebuilding of 3-Dimensional Nucleic Acid Structures
by
Xiang-Jun Lu (xiangjun@rutchem.rutgers.edu)
@ Wilma K. Olson's Laboratory at Rutgers (olson@rutchem.rutgers.edu)
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1. The list of the parameters given below are along the 5' to 3' direction
of strand I and 3' to 5' direction of strand II
2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom
****************************************************************************
File name: pdt012.pdb
Date and time: Mon Mar 6 08:36:53 2000
Number of base-pairs: 12
Number of atoms: 486
****************************************************************************
RMS deviation of the bases (* denotes a non-Watson-Crick base pair)
Base I Base II
1 (0.037) G --- C (0.018)
2 (0.024) T --- A (0.019)
3 (0.027) A --- T (0.032)
4 (0.030) T --- A (0.041)
5 (0.028) A --- T (0.029)
6 (0.027) T --- A (0.062)
7 (0.041) A --- T (0.041)
8 (0.019) A --- T (0.026)
9 (0.071) A --- T (0.032)
10 (0.020) A --- T (0.035)
11 (0.015) C --- G (0.032)
12 (0.025) G --- C (0.024)
****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure
bp Ox Oy Oz Nx Ny Nz
1 G-C 14.89 39.74 65.86 0.45 0.11 -0.88
2 T-A 17.47 40.07 63.45 0.45 0.16 -0.88
3 A-T 19.89 38.63 60.01 0.29 -0.60 -0.74
4 T-A 21.97 36.70 57.32 0.12 -0.81 -0.57
5 A-T 21.20 34.99 54.39 -0.05 -0.88 -0.47
6 T-A 20.10 32.20 52.31 -0.52 -0.80 -0.29
7 A-T 18.24 30.36 49.41 -0.74 -0.62 -0.27
8 A-T 15.31 29.33 47.89 -0.90 -0.38 -0.22
9 A-T 10.98 29.51 45.58 -0.89 0.26 -0.36
10 A-T 7.33 29.04 44.76 -0.88 0.26 -0.41
11 C-G 4.44 30.61 43.45 -0.86 0.24 -0.45
12 G-C 1.51 30.61 41.49 -0.80 0.28 -0.53
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.15 -0.14 -0.01 -10.15 -16.01 -2.03
2 T-A 0.01 -0.10 0.27 -9.07 -4.07 4.58
3 A-T 0.25 -0.01 -0.03 -31.04 13.82 7.53
4 T-A -0.01 0.04 -0.00 -27.24 -6.21 4.48
5 A-T 0.24 0.06 -0.57 -1.69 -5.25 6.22
6 T-A -0.28 -0.05 -0.60 6.33 -2.96 2.80
7 A-T 0.10 -0.12 0.04 21.95 -9.01 1.45
8 A-T -0.17 0.05 0.31 32.13 -15.56 8.20
9 A-T 0.03 -0.10 0.04 4.50 -1.30 6.12
10 A-T 0.25 -0.04 0.11 4.53 -10.03 -3.09
11 C-G 0.17 -0.25 0.19 -0.47 -11.17 -1.29
12 G-C 0.36 -0.37 -0.15 -0.95 -3.40 -2.56
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.07 -0.09 -0.03 -0.93 -5.93 2.70
s.d. 0.20 0.13 0.29 17.78 7.86 4.11
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GT/AC 0.59 -1.03 3.34 1.44 -2.74 36.07
2 TA/TA 0.34 -0.79 4.36 -0.92 46.84 21.48
3 AT/AT -1.39 -0.56 3.61 2.73 18.14 18.20
4 TA/TA 0.08 1.83 2.96 2.14 12.15 22.48
5 AT/AT -0.14 0.73 3.57 0.39 29.53 4.49
6 TA/TA -0.38 2.02 3.33 -2.73 16.24 21.99
7 AA/TT 0.67 0.70 3.32 3.34 16.01 22.15
8 AA/TT 0.68 0.69 4.81 2.10 38.46 19.59
9 AA/TT -1.50 0.46 3.43 -2.23 1.61 36.30
10 AC/GT 0.05 -0.73 3.46 -1.37 2.05 32.94
11 CG/CG 0.58 0.72 3.41 4.63 4.65 39.61
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.04 0.37 3.60 0.87 16.63 25.03
s.d. 0.78 1.04 0.53 2.41 15.93 10.29
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp Rise Incl. Tip Twist
1 GT/AC -1.26 -0.74 3.43 -4.42 -2.32 36.20
2 TA/TA -4.94 -0.47 1.16 66.71 1.30 51.29
3 AT/AT -6.40 3.90 2.03 45.08 -6.78 25.78
4 TA/TA 0.52 0.44 3.46 28.57 -5.03 25.60
5 AT/AT -6.64 0.37 1.26 81.55 -1.07 29.87
6 TA/TA -0.68 -0.03 3.90 36.68 6.17 27.41
7 AA/TT -2.88 -0.51 3.16 36.01 -7.51 27.47
8 AA/TT -5.40 -0.59 2.87 63.94 -3.49 43.05
9 AA/TT 0.49 2.07 3.53 2.58 3.57 36.40
10 AC/GT -1.65 -0.33 3.40 3.60 2.41 33.03
11 CG/CG 0.49 -0.29 3.51 6.80 -6.78 40.13
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -2.58 0.35 2.88 33.37 -1.77 34.20
s.d. 2.82 1.42 0.96 29.18 4.65 8.19
****************************************************************************
lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line
C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair
bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6
1 G-C 52.7 55.1 10.7 9.0 9.8
2 T-A 59.6 60.2 10.2 8.8 9.9
3 A-T 60.4 62.7 10.0 8.5 9.6
4 T-A 58.2 58.3 10.3 8.7 9.7
5 A-T 60.4 55.9 10.6 9.0 10.1
6 T-A 55.4 59.3 10.5 8.9 9.9
7 A-T 58.0 56.7 10.3 8.7 9.7
8 A-T 59.8 66.2 9.9 8.5 9.6
9 A-T 58.7 58.6 10.4 8.8 9.9
10 A-T 55.6 52.4 10.8 9.0 10.0
11 C-G 54.1 53.9 10.6 8.9 9.8
12 G-C 55.6 51.7 10.6 8.8 9.7
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Classification of each dinucleotide step in a right-handed DNA structure
A-like; B-like; TA-like; N: intermediate or other form
step Xp Yp Zp XpH YpH ZpH Form
1 GT/AC -2.94 8.66 1.03 -4.15 8.72 0.42 N
2 TA/TA -3.35 8.80 1.38 -7.81 2.55 8.53 *TA*
3 AT/AT -2.88 9.14 0.25 -8.87 6.39 6.48 *TA*
4 TA/TA -1.76 9.14 -0.78 -1.17 8.45 3.58 B
5 AT/AT -2.63 9.43 -1.44 -9.04 2.86 9.10 *TA*
6 TA/TA -1.77 9.07 -1.06 -2.30 7.98 4.41 *TA*
7 AA/TT -2.73 8.93 -0.73 -5.79 7.68 4.65 *TA*
8 AA/TT -3.72 8.90 -0.41 -8.80 4.50 7.70 *TA*
9 AA/TT -3.38 8.84 -0.29 -2.86 8.85 0.05 B
10 AC/GT -3.04 9.14 0.01 -4.62 9.12 0.55 B
11 CG/CG -2.88 8.89 -0.36 -2.34 8.87 0.62 B
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Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones
Minor Groove Major Groove
P-P Refined P-P Refined
1 GT/AC --- --- --- ---
2 TA/TA --- --- --- ---
3 AT/AT 21.8 --- 18.8 ---
4 TA/TA 23.8 19.6 20.0 18.4
5 AT/AT 24.7 20.2 20.3 19.5
6 TA/TA 24.0 19.7 18.9 17.8
7 AA/TT 22.3 18.8 19.4 18.5
8 AA/TT 19.2 17.0 16.7 15.8
9 AA/TT 15.0 --- 17.1 ---
10 AC/GT --- --- --- ---
11 CG/CG --- --- --- ---
****************************************************************************
Structure classification:
This is a right-handed DNA
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Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Helix: -0.330 0.059 -0.942
Point1: 17.070 33.763 63.928
Point2: 8.913 35.226 40.643
Deviation from regular linear helix: 1.27(2.30)
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Main chain and chi torsion angles:
Note: alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)
chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4
Strand I
base alpha beta gamma delta epsilon zeta chi
1 G --- --- 74.3 81.2 -139.4 -68.4 -179.4
2 T -81.2 176.2 67.0 85.1 -135.7 -67.2 -156.6
3 A -77.4 -168.0 53.9 120.5 -163.2 -92.2 -125.7
4 T -81.0 -178.8 43.9 85.5 -157.9 -94.0 -124.9
5 A -56.9 162.0 48.7 95.9 -147.7 -70.4 -104.1
6 T -70.5 176.5 40.8 86.6 -169.4 -101.4 -97.5
7 A -60.7 162.4 53.8 106.0 -157.0 -80.4 -104.9
8 A -71.1 166.9 55.1 92.8 -133.1 -76.1 -114.4
9 A -66.1 168.2 64.9 140.2 -119.8 -174.7 -100.4
10 A -73.9 143.4 53.2 131.5 -172.5 -96.5 -115.5
11 C -64.8 168.7 61.2 114.6 -164.0 -83.7 -127.6
12 G -91.1 169.6 72.8 135.0 --- --- -103.8
Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -101.8 127.8 82.0 76.1 --- --- -151.0
2 A -67.5 172.1 60.0 146.8 -120.7 -131.4 -103.2
3 T -68.4 173.4 52.8 89.5 -152.4 -84.0 -121.3
4 A -69.5 151.8 60.0 88.6 -147.2 -62.6 -111.8
5 T -69.9 172.7 54.6 87.3 -159.7 -101.1 -108.1
6 A -68.2 162.7 52.1 88.2 -155.4 -78.3 -110.7
7 T -77.7 170.3 46.8 91.1 -157.0 -92.3 -115.3
8 T -81.7 178.1 63.5 105.5 -161.8 -82.8 -119.7
9 T -66.7 169.3 47.5 107.6 -161.9 -89.6 -113.2
10 T -80.2 -178.9 70.0 130.2 -163.0 -95.7 -117.1
11 G -76.6 136.9 48.5 129.1 177.9 -89.9 -114.3
12 C --- --- 54.3 126.2 -98.8 172.5 -101.4
****************************************************************************
Sugar conformational parameters:
Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'
tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring
Strand I
base v0 v1 v2 v3 v4 tm P Puckering
1 G 1.8 -24.6 38.7 -39.4 22.7 40.4 16.7 C3'-endo
2 T -2.8 -19.3 34.0 -36.9 24.3 37.0 23.1 C3'-endo
3 A -25.5 24.1 -14.9 0.6 15.2 25.6 125.6 C1'-exo
4 T -25.0 3.1 18.7 -34.8 37.1 37.4 60.1 C4'-exo
5 A -2.2 -12.2 21.7 -24.3 16.1 23.8 24.5 C3'-endo
6 T -18.9 -2.4 21.5 -34.2 32.5 34.5 51.5 C4'-exo
7 A 5.0 -14.1 17.8 -15.7 6.5 17.8 3.1 C3'-endo
8 A -5.3 -12.2 24.7 -29.1 21.1 28.4 29.6 C3'-endo
9 A -32.5 40.4 -33.6 16.1 10.0 40.0 147.1 C2'-endo
10 A -23.8 28.4 -22.9 10.3 8.3 28.1 144.5 C2'-endo
11 C -36.1 29.6 -14.3 -5.9 25.8 34.7 114.3 C1'-exo
12 G -34.1 39.7 -30.9 12.3 13.4 39.3 141.8 C1'-exo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C -30.0 4.0 21.7 -41.7 43.8 44.5 60.7 C4'-exo
2 A -32.1 42.3 -37.9 20.7 6.5 42.6 152.8 C2'-endo
3 T -19.2 -2.0 21.0 -33.4 32.5 34.2 52.1 C4'-exo
4 A 3.3 -23.5 34.8 -34.2 18.9 35.8 13.8 C3'-endo
5 T -23.4 1.0 20.6 -35.4 36.3 37.4 56.6 C4'-exo
6 A -13.9 -7.3 25.2 -34.5 29.0 34.0 42.1 C4'-exo
7 T -32.2 11.3 11.4 -31.2 39.3 38.8 72.9 O4'-endo
8 T -35.6 23.2 -4.0 -16.4 31.8 35.0 96.6 O4'-endo
9 T -38.6 27.2 -7.5 -14.7 32.7 37.5 101.5 O4'-endo
10 T -37.6 39.1 -28.4 7.4 18.2 40.2 135.0 C1'-exo
11 G -23.9 27.6 -21.4 8.7 9.2 27.3 141.7 C1'-exo
12 C -46.8 45.5 -27.6 2.3 26.5 46.8 126.1 C1'-exo
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances
Strand I Strand II
base P--P C1'--C1' base P--P C1'--C1'
1 G/T --- 5.7 1 C/A 6.8 5.0
2 T/A 5.6 6.4 2 A/T 5.8 5.7
3 A/T 6.2 5.6 3 T/A 6.1 5.3
4 T/A 5.5 5.3 4 A/T 5.9 5.1
5 A/T 5.9 5.6 5 T/A 5.9 5.4
6 T/A 5.8 5.2 6 A/T 5.8 5.3
7 A/A 6.3 5.0 7 T/T 6.3 5.2
8 A/A 5.6 5.8 8 T/T 6.1 5.7
9 A/A 6.8 5.3 9 T/T 6.8 4.7
10 A/C 6.9 4.8 10 T/G 7.0 5.0
11 C/G 6.6 5.0 11 G/C --- 5.2
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)
Strand I Strand II
step P O4' C1' P O4' C1'
1 GT/AC 8.5 6.7 5.9 10.8 7.8 7.1
2 TA/TA 8.2 8.3 8.0 8.3 8.6 8.0
3 AT/AT 15.4 13.4 12.5 7.9 9.1 9.0
4 TA/TA 9.5 7.0 5.9 7.6 5.7 4.4
5 AT/AT 9.9 10.1 9.6 9.0 9.7 9.3
6 TA/TA 7.3 6.1 4.9 9.3 6.8 5.8
7 AA/TT 8.0 7.5 6.8 11.3 8.5 7.6
8 AA/TT 9.2 9.1 8.6 10.7 9.5 8.8
9 AA/TT 11.0 8.3 7.6 7.7 4.5 3.9
10 AC/GT 9.9 7.0 6.4 10.6 7.6 7.1
11 CG/CG 9.1 6.1 5.3 9.3 6.7 5.9
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 GT/AC 16.12 38.54 64.41 0.53 0.13 -0.84
2 TA/TA 17.54 35.14 62.69 -0.63 -0.01 -0.78
3 AT/AT 19.36 31.35 61.98 -0.43 -0.33 -0.84
4 TA/TA 22.20 35.60 55.84 -0.25 -0.56 -0.79
5 AT/AT 14.63 34.39 55.46 -0.27 0.33 -0.90
6 TA/TA 18.63 31.65 50.97 -0.45 -0.41 -0.79
7 AA/TT 15.95 32.55 48.40 -0.60 -0.25 -0.76
8 AA/TT 13.98 34.25 45.54 -0.16 -0.21 -0.96
9 AA/TT 8.65 30.28 46.86 -0.90 0.19 -0.38
10 AC/GT 6.55 29.83 42.63 -0.89 0.18 -0.41
11 CG/CG 2.68 30.58 42.91 -0.83 0.11 -0.55
©1995-2004 The Nucleic Acid Database Project
Rutgers, The State University of New Jersey
