**************************************************************************** 3DNA v2.1 (2013), created and maintained by Xiang-Jun Lu (PhD) **************************************************************************** 1. The list of the parameters given below correspond to 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 units. **************************************************************************** File name: 7bna.min.pdb Date and time: Thu Feb 6 13:59:51 2014 Number of base-pairs: 12 Number of atoms: 766 **************************************************************************** **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.022) ....>A:...1_:[CYT]C-----G[GUA]:..24_:B<.... (0.020) | 2 (0.023) ....>A:...2_:[GUA]G-----C[CYT]:..23_:B<.... (0.010) | 3 (0.023) ....>A:...3_:[CYT]C-----G[GUA]:..22_:B<.... (0.032) | 4 (0.026) ....>A:...4_:[GUA]G-----C[CYT]:..21_:B<.... (0.022) | 5 (0.022) ....>A:...5_:[ADE]A-----T[THY]:..20_:B<.... (0.016) | 6 (0.009) ....>A:...6_:[ADE]A-----T[THY]:..19_:B<.... (0.019) | 7 (0.015) ....>A:...7_:[THY]T-----A[ADE]:..18_:B<.... (0.009) | 8 (0.020) ....>A:...8_:[THY]T-----A[ADE]:..17_:B<.... (0.010) | 9 (0.016) ....>A:...9_:[CYT]C-----G[GUA]:..16_:B<.... (0.016) | 10 (0.018) ....>A:..10_:[GUA]G-----C[CYT]:..15_:B<.... (0.027) | 11 (0.016) ....>A:..11_:[CYT]C-----G[GUA]:..14_:B<.... (0.015) | 12 (0.019) ....>A:..12_:[GUA]G-----C[CYT]:..13_:B<.... (0.005) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 C-----G [3] O2 - N2 2.77 N3 - N1 2.91 N4 - O6 3.13 2 G-----C [3] N2 - O2 2.89 N1 - N3 2.94 O6 - N4 2.85 3 C-----G [3] O2 - N2 2.88 N3 - N1 2.88 N4 - O6 2.78 4 G-----C [3] N2 - O2 2.76 N1 - N3 2.88 O6 - N4 2.91 5 A-----T [2] N1 - N3 2.84 N6 - O4 2.98 6 A-----T [2] N1 - N3 2.94 N6 - O4 3.23 7 T-----A [2] N3 - N1 2.86 O4 - N6 3.11 8 T-----A [2] N3 - N1 2.88 O4 - N6 2.99 9 C-----G [3] O2 - N2 2.77 N3 - N1 2.87 N4 - O6 2.93 10 G-----C [3] N2 - O2 2.77 N1 - N3 2.89 O6 - N4 2.94 11 C-----G [3] O2 - N2 2.87 N3 - N1 2.89 N4 - O6 2.94 12 G-----C [3] N2 - O2 2.86 N1 - N3 2.93 O6 - N4 2.87 **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' 5' j2 /|\ | | | Strand I | | II | | | | | \|/ i1 5' 3' j1 step i1-i2 i1-j2 j1-i2 j1-j2 sum 1 CG/CG 0.00( 0.00) 0.00( 0.00) 0.59( 0.00) 1.71( 0.00) 2.30( 0.00) 2 GC/GC 5.14( 2.62) 0.00( 0.00) 0.00( 0.00) 1.49( 0.21) 6.63( 2.84) 3 CG/CG 2.02( 0.00) 0.00( 0.00) 0.17( 0.00) 3.83( 0.44) 6.02( 0.44) 4 GA/TC 5.17( 2.11) 0.00( 0.00) 0.00( 0.00) 3.16( 0.04) 8.33( 2.16) 5 AA/TT 3.54( 2.03) 0.00( 0.00) 0.00( 0.00) 5.50( 0.19) 9.04( 2.22) 6 AT/AT 6.49( 2.94) 0.00( 0.00) 0.00( 0.00) 5.25( 1.71) 11.74( 4.65) 7 TT/AA 5.41( 0.11) 0.00( 0.00) 0.00( 0.00) 4.15( 2.64) 9.57( 2.75) 8 TC/GA 2.45( 0.00) 0.00( 0.00) 0.00( 0.00) 4.63( 1.66) 7.08( 1.66) 9 CG/CG 4.97( 1.14) 0.00( 0.00) 0.07( 0.00) 2.02( 0.00) 7.06( 1.14) 10 GC/GC 0.43( 0.00) 0.00( 0.00) 0.00( 0.00) 5.36( 2.23) 5.79( 2.23) 11 CG/CG 3.25( 0.43) 0.00( 0.00) 0.37( 0.00) 0.10( 0.00) 3.72( 0.43) **************************************************************************** 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 C-G 16.043 25.944 26.569 -0.091 -0.503 -0.860 2 G-C 16.491 24.267 23.107 -0.181 -0.367 -0.912 3 C-G 15.724 23.617 19.777 -0.162 -0.464 -0.871 4 G-C 15.666 22.244 16.926 -0.231 -0.288 -0.929 5 A-T 15.242 21.243 13.693 -0.184 -0.212 -0.960 6 A-T 14.658 20.521 10.671 -0.158 -0.263 -0.952 7 T-A 14.659 20.303 7.074 -0.156 -0.258 -0.954 8 T-A 14.215 19.761 4.001 -0.088 -0.220 -0.971 9 C-G 13.849 19.002 0.607 -0.095 -0.200 -0.975 10 G-C 12.631 18.392 -2.209 -0.237 -0.249 -0.939 11 C-G 13.288 18.519 -5.945 -0.027 -0.107 -0.994 12 G-C 12.557 18.674 -9.322 -0.019 -0.122 -0.992 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 C-G 0.45 -0.09 -0.22 13.84 -19.92 4.78 2 G-C -0.17 -0.13 0.18 -8.67 -6.67 -3.95 3 C-G 0.28 -0.22 0.20 -5.69 -4.34 -4.02 4 G-C -0.20 -0.18 -0.32 5.05 -8.65 1.74 5 A-T 0.01 -0.18 -0.49 2.36 -16.53 4.55 6 A-T 0.21 0.04 0.12 4.95 -18.39 4.77 7 T-A -0.12 -0.06 0.34 -2.43 -19.30 2.82 8 T-A 0.06 -0.10 -0.12 2.10 -16.61 0.37 9 C-G 0.17 -0.15 -0.01 -9.83 -12.15 1.38 10 G-C -0.08 -0.13 0.30 5.42 -5.75 0.09 11 C-G 0.21 -0.22 0.57 1.47 -22.04 -4.05 12 G-C -0.26 -0.16 0.32 4.36 -0.44 -2.80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.04 -0.13 0.07 1.08 -12.57 0.47 s.d. 0.22 0.07 0.31 6.73 7.18 3.47 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 CG/CG -0.88 0.40 3.75 -5.54 8.13 41.32 2 GC/GC 0.81 0.21 3.38 1.75 -5.88 36.86 3 CG/CG -0.12 0.58 3.11 4.88 10.25 25.95 4 GA/TC 0.07 0.31 3.40 0.84 5.34 40.53 5 AA/TT -0.04 -0.04 3.16 -3.17 0.92 37.76 6 AT/AT 0.23 -0.89 3.48 0.34 0.03 29.89 7 TT/AA -0.21 -0.07 3.14 4.52 0.25 36.41 8 TC/GA 0.03 0.04 3.50 -0.51 -1.10 42.84 9 CG/CG 0.42 0.59 3.04 -4.37 7.69 25.23 10 GC/GC -1.32 0.44 3.53 -4.72 -14.19 41.50 11 CG/CG 0.81 0.26 3.35 0.68 -0.72 34.23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.02 0.17 3.35 -0.48 0.97 35.68 s.d. 0.64 0.42 0.22 3.58 6.98 6.21 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 CG/CG -0.42 0.56 3.84 11.32 7.72 42.43 2 GC/GC 1.13 -1.03 3.34 -9.22 -2.74 37.35 3 CG/CG -1.15 1.36 3.04 21.55 -10.26 28.29 4 GA/TC -0.16 -0.01 3.41 7.66 -1.21 40.88 5 AA/TT -0.17 -0.34 3.15 1.41 4.89 37.90 6 AT/AT -1.74 -0.38 3.49 0.06 -0.66 29.89 7 TT/AA -0.15 0.93 3.10 0.40 -7.20 36.68 8 TC/GA 0.18 -0.09 3.49 -1.51 0.70 42.86 9 CG/CG -0.62 -1.98 2.98 16.96 9.62 26.71 10 GC/GC 2.04 1.28 3.34 -19.28 6.41 44.00 11 CG/CG 0.56 -1.26 3.36 -1.22 -1.16 34.25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.05 -0.09 3.32 2.56 0.56 36.47 s.d. 1.04 1.07 0.25 11.53 6.18 6.05 **************************************************************************** Structure classification: This is a right-handed nucleic acid structure **************************************************************************** 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 C-G 56.6 55.0 10.5 8.9 9.9 2 G-C 49.4 49.6 10.9 9.0 9.9 3 C-G 50.8 52.1 10.8 8.9 9.8 4 G-C 55.0 54.5 10.6 8.9 9.8 5 A-T 54.5 55.9 10.4 8.8 9.8 6 A-T 55.2 53.8 10.6 8.9 10.0 7 T-A 54.0 56.4 10.5 8.9 9.9 8 T-A 53.7 52.6 10.6 8.9 9.9 9 C-G 54.6 53.8 10.6 8.9 9.8 10 G-C 56.6 52.6 10.6 8.9 9.9 11 C-G 50.2 50.9 10.8 9.0 9.8 12 G-C 50.7 50.5 10.9 9.0 9.9 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like; intermediate of A and B, or other cases step Xp Yp Zp XpH YpH ZpH Form 1 CG/CG -2.52 8.96 -0.17 -2.93 8.83 1.52 B 2 GC/GC -2.54 9.29 -0.25 -1.45 9.15 -1.66 B 3 CG/CG -2.51 9.15 -0.15 -3.66 8.58 3.19 B 4 GA/TC -2.83 8.79 -0.47 -3.00 8.78 0.63 B 5 AA/TT -3.29 9.02 -0.68 -3.41 9.03 -0.49 B 6 AT/AT -3.49 9.24 -0.21 -5.17 9.24 -0.20 B 7 TT/AA -2.97 9.12 -0.31 -3.09 9.12 -0.26 B 8 TC/GA -2.58 8.80 -0.01 -2.42 8.80 -0.23 B 9 CG/CG -2.71 9.06 -0.30 -3.44 8.75 2.44 B 10 GC/GC -2.35 9.11 -0.10 -0.38 8.63 -2.91 B 11 CG/CG -2.57 9.00 -0.17 -2.02 8.99 -0.37 B **************************************************************************** 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 (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 CG/CG --- --- --- --- 2 GC/GC --- --- --- --- 3 CG/CG 14.0 --- 17.2 --- 4 GA/TC 12.3 12.3 17.9 17.8 5 AA/TT 11.0 10.9 17.1 17.0 6 AT/AT 10.3 10.3 16.2 15.8 7 TT/AA 9.7 9.7 17.4 17.4 8 TC/GA 10.6 10.5 19.1 19.1 9 CG/CG 11.6 --- 17.3 --- 10 GC/GC --- --- --- --- 11 CG/CG --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.30(0.44) Helix: -0.074 -0.290 -0.954 HETATM 9998 XS X X 999 16.576 25.937 25.876 HETATM 9999 XE X X 999 13.901 15.375 -8.827 Average and standard deviation of helix radius: P: 9.46(1.08), O4': 6.48(1.08), C1': 5.93(1.08) Global parameters based on C1'-C1' vectors: disp.: displacement of the middle C1'-C1' point from the helix angle: inclination between C1'-C1' vector and helix (subtracted from 90) twist: helical twist angle between consecutive C1'-C1' vectors rise: helical rise by projection of the vector connecting consecutive C1'-C1' middle points onto the helical axis bp disp. angle twist rise 1 C-G 2.12 7.18 44.69 2.71 2 G-C 2.94 7.20 34.64 3.11 3 C-G 2.58 7.38 29.46 3.99 4 G-C 3.51 5.14 39.01 3.22 5 A-T 3.50 -0.72 36.74 3.23 6 A-T 3.38 -3.52 31.31 3.12 7 T-A 2.98 -4.74 35.97 3.36 8 T-A 3.12 -4.70 41.62 2.88 9 C-G 2.94 -6.58 27.96 4.19 10 G-C 2.48 -7.57 39.38 2.89 11 C-G 2.45 -12.81 37.77 3.67 12 G-C 1.95 -7.83 --- --- **************************************************************************** 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 C --- -165.7 166.1 140.6 -114.9 -166.4 -94.0 2 G -60.4 155.4 28.8 138.0 -166.2 -106.1 -108.7 3 C -51.0 149.2 57.5 88.0 -174.7 -89.6 -140.7 4 G -58.7 176.0 52.9 141.5 -175.7 -114.3 -99.5 5 A -52.9 167.4 55.0 135.2 -170.0 -93.7 -112.5 6 A -65.0 177.1 52.9 130.3 -177.6 -91.5 -108.5 7 T -58.0 169.9 54.0 103.5 -172.8 -93.8 -135.9 8 T -55.3 172.2 52.1 131.4 173.6 -104.2 -107.3 9 C -44.4 -172.3 36.9 142.5 -159.7 -94.0 -100.6 10 G -58.0 161.2 41.3 140.8 -101.1 149.4 -92.2 11 C -75.8 140.8 55.5 137.7 -158.5 -87.4 -117.8 12 G -69.0 174.9 38.1 135.0 --- --- -96.1 Strand II base alpha beta gamma delta epsilon zeta chi 1 G -69.4 171.4 42.4 86.8 --- --- -137.0 2 C -65.4 142.4 28.6 136.0 -172.1 -107.5 -101.7 3 G -51.3 162.5 46.6 144.8 -89.0 161.0 -93.1 4 C -57.2 -166.2 37.5 137.8 -167.9 -107.3 -91.9 5 T -49.6 174.9 41.0 132.8 -176.4 -101.8 -103.8 6 T -52.3 161.5 58.6 115.2 -171.3 -97.3 -135.8 7 A -51.1 178.5 41.3 136.0 -173.1 -107.2 -106.7 8 A -52.9 -175.6 47.7 141.6 -178.8 -95.2 -110.7 9 G -57.0 171.9 61.9 140.5 173.2 -102.7 -103.2 10 C -58.8 156.3 57.3 84.0 -179.7 -83.8 -138.3 11 G -49.8 179.5 47.0 138.1 -172.7 -95.5 -103.4 12 C --- -130.7 47.0 139.4 -176.3 -114.3 -116.9 **************************************************************************** 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: the amplitude of pucker P: the phase angle of pseudorotation Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 C -39.9 48.8 -39.4 17.5 13.8 48.1 145.0 C2'-endo 2 G -18.7 31.2 -31.3 21.0 -1.5 32.6 164.2 C2'-endo 3 C -42.1 19.4 7.7 -31.9 47.2 46.3 80.4 O4'-endo 4 G -16.2 30.3 -32.1 23.4 -4.5 32.6 169.3 C2'-endo 5 A -19.6 31.3 -30.7 19.9 -0.2 32.3 161.9 C2'-endo 6 A -25.3 34.1 -29.7 15.6 6.1 33.9 151.4 C2'-endo 7 T -49.3 35.9 -11.5 -16.4 41.5 47.9 103.9 O4'-endo 8 T -29.4 37.9 -31.8 15.7 8.4 37.3 148.5 C2'-endo 9 C -13.8 28.2 -31.2 24.0 -6.4 31.4 173.2 C2'-endo 10 G -39.2 48.3 -39.0 17.6 13.2 47.5 145.3 C2'-endo 11 C -21.7 33.1 -31.7 19.9 1.0 33.7 159.8 C2'-endo 12 G -31.5 39.7 -32.7 15.2 10.1 39.1 146.7 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 G 3.8 -26.2 36.9 -35.3 19.9 37.8 12.5 C3'-endo 2 C -26.9 37.3 -33.3 18.3 5.4 37.2 153.4 C2'-endo 3 G -34.3 45.6 -39.2 20.7 8.3 44.9 150.8 C2'-endo 4 C -14.7 26.6 -27.8 19.8 -3.2 28.4 167.9 C2'-endo 5 T -30.5 38.7 -32.5 15.9 8.9 38.3 148.2 C2'-endo 6 T -45.1 40.9 -23.1 -2.3 30.0 44.9 121.0 C1'-exo 7 A -23.3 34.2 -31.8 18.8 2.8 34.5 157.0 C2'-endo 8 A -13.9 28.9 -32.1 24.5 -6.7 32.3 173.3 C2'-endo 9 G -15.4 30.6 -33.2 24.9 -6.0 33.6 171.6 C2'-endo 10 C -25.6 1.3 21.3 -36.6 39.8 39.8 57.6 C4'-exo 11 G -13.2 26.1 -28.5 21.5 -5.2 28.8 171.9 C2'-endo 12 C -16.7 30.6 -32.2 22.9 -3.9 32.9 168.3 C2'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II step P--P C1'--C1' step P--P C1'--C1' 1 C/G 7.21 5.55 1 G/C 6.66 4.92 2 G/C 6.76 4.42 2 C/G 6.59 5.12 3 C/G 6.54 5.31 3 G/C 6.35 4.69 4 G/A 6.95 4.95 4 C/T 6.78 5.32 5 A/A 7.00 5.04 5 T/T 6.90 5.06 6 A/T 6.99 4.70 6 T/A 6.78 4.84 7 T/T 6.56 5.16 7 A/A 6.87 4.76 8 T/C 7.10 5.12 8 A/G 7.17 4.95 9 C/G 6.55 4.59 9 G/C 6.58 5.25 10 G/C 6.62 5.24 10 C/G 6.76 4.29 11 C/G 7.05 4.92 11 G/C 6.16 5.34 **************************************************************************** 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 CG/CG 9.81 7.19 6.44 8.81 6.37 5.61 2 GC/GC 8.42 4.87 4.39 10.11 6.92 6.55 3 CG/CG 10.43 8.34 7.44 8.28 5.81 4.90 4 GA/TC 9.19 6.60 5.92 9.37 6.45 5.94 5 AA/TT 9.33 6.23 5.64 9.98 6.78 6.23 6 AT/AT 10.35 7.02 6.54 10.83 7.64 7.14 7 TT/AA 10.53 7.36 6.74 8.74 5.64 5.10 8 TC/GA 9.04 6.01 5.65 9.22 6.41 5.88 9 CG/CG 8.19 5.06 4.30 10.82 8.78 7.85 10 GC/GC 9.78 6.55 6.40 7.51 4.00 3.67 11 CG/CG 8.31 5.06 4.50 10.21 7.43 6.88 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 CG/CG 15.70 24.80 24.92 0.05 -0.33 -0.94 2 GC/GC 17.40 23.31 21.27 -0.32 -0.43 -0.84 3 CG/CG 14.48 24.06 17.83 0.18 -0.24 -0.95 4 GA/TC 15.56 21.85 15.26 -0.10 -0.32 -0.94 5 AA/TT 15.16 20.60 12.21 -0.24 -0.27 -0.93 6 AT/AT 16.06 19.42 8.93 -0.15 -0.27 -0.95 7 TT/AA 15.24 20.38 5.36 -0.06 -0.34 -0.94 8 TC/GA 13.96 19.55 2.27 -0.07 -0.20 -0.98 9 CG/CG 11.49 19.54 -0.23 -0.27 0.09 -0.96 10 GC/GC 15.11 18.00 -3.71 0.06 -0.44 -0.90 11 CG/CG 13.86 19.51 -7.80 -0.05 -0.13 -0.99