**************************************************************************** 3DNA v2.0 [June 8, 2008] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com) **************************************************************************** 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: str221.pdb Date and time: Mon Apr 2 00:11:51 2012 Number of base-pairs: 12 Number of atoms: 756 **************************************************************************** TITLE 756 SYSTEM IN WATER T= 221.00000 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.042) ....>-:...1_:[.DG]G-----C[.DC]:..24_:-<.... (0.060) | 2 (0.037) ....>-:...2_:[.DC]C-----G[.DG]:..23_:-<.... (0.027) | 3 (0.067) ....>-:...3_:[.DG]G-----C[.DC]:..22_:-<.... (0.031) | 4 (0.050) ....>-:...4_:[.DC]C-----G[.DG]:..21_:-<.... (0.050) | 5 (0.036) ....>-:...5_:[.DA]A-----T[.DT]:..20_:-<.... (0.036) | 6 (0.049) ....>-:...6_:[.DC]C-----G[.DG]:..19_:-<.... (0.034) | 7 (0.050) ....>-:...7_:[.DG]G-----C[.DC]:..18_:-<.... (0.031) | 8 (0.022) ....>-:...8_:[.DT]T-----A[.DA]:..17_:-<.... (0.050) | 9 (0.086) ....>-:...9_:[.DG]G-----C[.DC]:..16_:-<.... (0.060) | 10 (0.056) ....>-:..10_:[.DC]C-----G[.DG]:..15_:-<.... (0.079) | 11 (0.099) ....>-:..11_:[.DG]G-----C[.DC]:..14_:-<.... (0.035) | 12 (0.047) ....>-:..12_:[.DC]C-----G[.DG]:..13_:-<.... (0.078) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 G-----C [3] O6 - N4 2.95 N1 - N3 2.95 N2 - O2 2.80 2 C-----G [3] N4 - O6 2.60 N3 - N1 3.17 O2 - N2 3.58 3 G-----C [3] O6 - N4 3.19 N1 - N3 3.02 N2 - O2 2.85 4 C-----G [3] N4 - O6 2.85 N3 - N1 2.84 O2 - N2 2.76 5 A-----T [2] N6 - O4 3.09 N1 - N3 2.99 6 C-----G [3] N4 - O6 3.15 N3 - N1 2.83 O2 - N2 2.68 7 G-----C [3] O6 - N4 3.08 N1 - N3 2.98 N2 - O2 2.76 8 T-----A [2] O4 - N6 2.73 N3 - N1 2.90 9 G-----C [3] O6 - N4 2.99 N1 - N3 2.95 N2 - O2 2.98 10 C-----G [3] N4 - O6 2.86 N3 - N1 2.88 O2 - N2 2.81 11 G-----C [3] O6 - N4 2.90 N1 - N3 2.87 N2 - O2 2.85 12 C-----G [3] N4 - O6 2.87 N3 - N1 3.03 O2 - N2 3.22 **************************************************************************** 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 GC/GC 5.82( 3.85) 0.00( 0.00) 0.00( 0.00) 4.61( 2.47) 10.43( 6.32) 2 CG/CG 1.09( 0.00) 0.00( 0.00) 0.25( 0.00) 0.00( 0.00) 1.35( 0.00) 3 GC/GC 4.63( 2.34) 0.00( 0.00) 0.00( 0.00) 5.77( 3.58) 10.40( 5.92) 4 CA/TG 2.75( 1.24) 0.00( 0.00) 0.01( 0.00) 0.28( 0.00) 3.04( 1.24) 5 AC/GT 6.41( 3.66) 0.00( 0.00) 0.00( 0.00) 4.25( 0.62) 10.66( 4.28) 6 CG/CG 0.00( 0.00) 0.00( 0.00) 6.72( 3.79) 0.00( 0.00) 6.72( 3.79) 7 GT/AC 7.25( 2.15) 0.00( 0.00) 0.00( 0.00) 6.22( 3.66) 13.47( 5.80) 8 TG/CA 4.34( 1.98) 0.00( 0.00) 0.00( 0.00) 2.57( 0.65) 6.90( 2.64) 9 GC/GC 0.59( 0.00) 0.28( 0.00) 0.00( 0.00) 1.53( 0.00) 2.41( 0.00) 10 CG/CG 1.69( 0.06) 0.00( 0.00) 0.88( 0.00) 3.43( 1.21) 6.01( 1.27) 11 GC/GC 3.84( 1.58) 0.00( 0.00) 0.00( 0.00) 5.73( 2.74) 9.57( 4.32) **************************************************************************** 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 56.94 23.48 30.13 -0.93 -0.31 -0.19 2 C-G 54.37 22.54 29.57 -0.92 -0.28 -0.26 3 G-C 50.41 22.24 29.28 -0.91 -0.38 -0.19 4 C-G 47.70 20.76 28.79 -0.96 -0.16 -0.25 5 A-T 43.94 21.45 28.79 -0.98 0.06 -0.19 6 C-G 41.16 23.56 28.49 -0.98 0.12 -0.14 7 G-C 37.17 26.35 28.98 -0.99 0.10 -0.11 8 T-A 33.64 28.51 29.54 -0.97 0.15 -0.17 9 G-C 30.78 28.64 27.69 -0.87 -0.00 -0.50 10 C-G 27.54 28.21 27.23 -0.85 -0.01 -0.53 11 G-C 24.75 28.35 25.23 -0.85 -0.18 -0.49 12 C-G 22.10 27.36 22.84 -0.84 -0.36 -0.41 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C 0.08 0.02 -0.33 -14.27 3.98 0.56 2 C-G -0.05 0.06 0.09 9.57 -3.22 -13.28 3 G-C -0.38 0.03 -0.58 -3.89 -3.14 3.96 4 C-G 0.25 -0.16 0.02 5.23 -10.16 -0.37 5 A-T 0.19 0.07 0.07 -9.52 -7.81 -0.29 6 C-G 0.24 -0.03 -0.30 12.75 14.39 6.10 7 G-C -0.81 -0.14 -0.38 -14.61 -3.08 3.00 8 T-A -0.07 -0.14 -0.42 -22.40 -5.57 -5.42 9 G-C 0.42 0.07 -0.11 -17.21 -12.29 -0.07 10 C-G 0.56 -0.23 -0.56 6.54 12.33 -1.68 11 G-C 0.27 -0.14 -0.49 8.43 -9.51 0.96 12 C-G 0.19 -0.05 -0.33 2.20 0.91 -5.88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.07 -0.05 -0.28 -3.10 -1.93 -1.03 s.d. 0.37 0.11 0.24 12.08 8.51 5.17 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GC/GC 0.06 -0.12 2.79 -2.08 -4.22 13.11 2 CG/CG 1.08 0.53 3.80 7.13 0.10 47.24 3 GC/GC -0.57 -0.41 3.05 -7.78 11.10 25.31 4 CA/TG 0.81 -0.88 3.63 4.44 12.41 27.59 5 AC/GT 1.51 -1.06 2.97 4.17 1.40 26.98 6 CG/CG 0.40 -2.50 4.19 0.17 -2.20 29.82 7 GT/AC -1.00 -1.74 3.67 2.60 3.81 30.43 8 TG/CA 0.74 -0.22 3.33 0.49 21.86 20.37 9 GC/GC -0.34 1.29 3.02 1.36 1.42 41.84 10 CG/CG -0.46 -0.31 3.39 -2.32 9.73 21.36 11 GC/GC -0.37 -0.77 3.60 1.78 10.90 34.54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.17 -0.56 3.40 0.91 6.03 28.96 s.d. 0.79 1.03 0.42 4.01 7.81 9.67 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GC/GC 2.98 -1.95 2.66 -17.76 8.76 13.93 2 CG/CG 0.65 -0.66 3.91 0.12 -8.83 47.74 3 GC/GC -3.18 -0.50 2.70 23.31 16.33 28.66 4 CA/TG -4.33 -0.59 3.05 24.33 -8.71 30.52 5 AC/GT -2.58 -2.24 3.11 2.97 -8.86 27.33 6 CG/CG -4.24 -0.72 4.36 -4.27 -0.32 29.90 7 GT/AC -4.07 2.43 3.34 7.20 -4.92 30.77 8 TG/CA -5.00 -1.33 2.14 47.51 -1.07 29.80 9 GC/GC 1.66 0.61 3.05 1.99 -1.91 41.88 10 CG/CG -4.10 0.33 3.00 24.58 5.85 23.56 11 GC/GC -2.87 0.86 3.20 17.81 -2.91 36.21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -2.28 -0.34 3.14 11.62 -0.60 30.94 s.d. 2.74 1.34 0.60 17.97 8.02 8.91 **************************************************************************** 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 G-C 57.6 56.6 10.7 9.1 10.0 2 C-G 49.0 48.5 11.3 9.4 10.0 3 G-C 53.2 61.9 10.7 9.1 10.0 4 C-G 57.0 52.8 10.6 8.9 9.8 5 A-T 54.9 54.4 10.8 9.1 10.0 6 C-G 58.5 55.9 10.5 8.9 9.9 7 G-C 49.6 59.5 10.6 8.9 9.9 8 T-A 51.7 56.7 10.5 8.8 9.6 9 G-C 55.3 53.1 10.8 9.1 10.0 10 C-G 60.2 48.3 10.7 9.0 9.8 11 G-C 55.8 53.1 10.7 9.0 9.9 12 C-G 50.1 50.8 11.0 9.2 10.0 **************************************************************************** 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 GC/GC -4.05 9.12 -1.51 -1.02 8.24 -4.15 2 CG/CG -2.24 8.83 0.29 -1.71 8.83 0.32 B 3 GC/GC -4.06 9.10 -0.65 -6.93 8.67 2.77 B 4 CA/TG -3.22 9.18 0.30 -7.45 8.28 4.02 5 AC/GT -3.17 9.21 1.03 -5.69 9.14 1.49 6 CG/CG -3.38 8.33 1.93 -7.49 8.45 1.33 7 GT/AC -3.58 8.97 0.80 -7.40 8.81 1.83 8 TG/CA -4.26 8.76 -0.67 -9.08 6.51 5.89 9 GC/GC -2.30 8.70 -0.08 -0.73 8.70 0.21 B 10 CG/CG -3.74 9.22 -0.75 -7.66 8.74 2.97 B 11 GC/GC -2.90 9.03 0.30 -5.61 8.55 2.92 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 GC/GC --- --- --- --- 2 CG/CG --- --- --- --- 3 GC/GC 14.9 --- 20.1 --- 4 CA/TG 16.3 15.8 17.8 16.9 5 AC/GT 13.3 12.8 23.8 23.5 6 CG/CG 10.9 10.2 26.3 26.3 7 GT/AC 13.4 12.4 22.1 22.1 8 TG/CA 16.7 16.0 19.9 19.2 9 GC/GC 16.5 --- 19.2 --- 10 CG/CG --- --- --- --- 11 GC/GC --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.29(0.78) **************************************************************************** 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 --- --- 63.2 123.4 -170.2 -92.9 -87.7 2 C -56.0 159.8 41.3 131.4 -76.9 128.1 -79.0 3 G -82.5 155.6 42.7 144.7 -156.9 -84.9 -108.8 4 C -81.4 153.6 53.7 81.2 -163.9 -79.2 -135.5 5 A -75.8 167.7 75.0 87.4 -171.7 -85.1 -158.2 6 C 126.4 -165.0 -154.0 138.9 179.9 -106.6 -133.6 7 G -50.9 169.4 57.4 116.3 -155.6 -74.4 -167.8 8 T -67.2 -178.3 35.0 133.8 -156.2 -76.7 -125.0 9 G -92.5 165.5 36.7 134.1 -71.5 137.7 -99.9 10 C -65.1 -174.9 0.3 147.8 -173.9 -87.6 -91.3 11 G -80.7 144.1 91.4 96.7 -173.6 -82.2 -138.4 12 C -61.1 -177.6 50.8 118.8 --- --- -117.9 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -78.1 174.8 --- --- --- --- -84.7 2 G -81.5 158.8 45.6 142.7 -162.5 -80.9 -103.2 3 C -64.3 -175.6 25.0 136.8 -81.2 146.1 -84.4 4 G -102.4 180.0 70.1 128.6 -155.7 -97.1 -122.9 5 T -62.0 -171.5 56.1 130.4 -174.3 -87.7 -113.0 6 G -63.9 -171.7 42.3 116.3 176.6 -89.2 -137.0 7 C -70.2 145.7 95.2 97.2 -170.0 -86.8 -159.2 8 A -75.4 176.1 41.0 137.9 -178.7 -119.4 -78.7 9 C -72.2 162.1 24.4 148.7 -175.3 -82.7 -95.4 10 G -56.3 169.6 1.8 144.8 -73.0 139.6 -85.0 11 C -70.2 168.3 70.9 134.1 -142.9 -73.6 -136.6 12 G --- --- 56.7 71.4 -157.5 -71.3 -169.7 **************************************************************************** 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 -26.7 32.6 -27.1 13.5 7.9 32.2 147.2 C2'-endo 2 C -44.3 48.8 -30.6 6.1 23.6 47.2 130.4 C1'-exo 3 G -20.9 33.6 -33.6 22.9 -1.4 34.9 163.7 C2'-endo 4 C -32.9 8.0 17.9 -39.1 45.0 44.3 66.2 C4'-exo 5 A -31.1 5.4 19.0 -36.8 44.4 42.7 63.6 C4'-exo 6 C -21.8 35.5 -32.8 21.7 -0.3 34.8 160.7 C2'-endo 7 G -31.6 25.8 -13.2 -4.4 23.1 30.6 115.5 C1'-exo 8 T -32.8 35.9 -27.2 9.1 15.1 36.4 138.2 C1'-exo 9 G -47.5 50.7 -35.2 9.0 24.2 51.0 133.7 C1'-exo 10 C 23.5 -1.6 -18.7 33.5 -35.8 36.0 238.7 C4'-endo 11 G -41.4 32.2 -12.0 -12.5 35.0 41.2 106.9 O4'-endo 12 C -44.3 37.4 -19.8 -4.5 30.2 42.7 117.6 C1'-exo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C --- --- --- --- --- 10000.0 180.0 C3'-exo 2 G -18.7 33.7 -34.3 24.9 -4.3 35.1 167.6 C2'-endo 3 C -28.7 35.0 -29.5 14.9 8.3 34.8 147.8 C2'-endo 4 G -38.5 42.4 -29.8 8.7 18.5 41.9 135.3 C1'-exo 5 T -30.7 40.2 -33.7 17.9 7.7 39.1 149.7 C2'-endo 6 G -30.4 31.9 -22.7 4.6 17.2 33.3 133.0 C1'-exo 7 C -44.8 29.1 -5.2 -20.4 41.3 44.4 96.8 O4'-endo 8 A -29.5 39.4 -33.0 17.8 7.0 38.1 150.2 C2'-endo 9 C 0.2 16.7 -24.4 26.4 -17.7 26.0 200.2 C3'-exo 10 G -39.1 49.2 -38.0 16.2 14.5 47.3 143.5 C1'-exo 11 C -36.4 39.9 -30.8 10.5 16.7 40.8 138.9 C1'-exo 12 G -11.0 -17.0 36.2 -43.7 34.3 43.1 32.9 C3'-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 G/C --- 4.2 1 C/G 7.0 4.8 2 C/G 6.4 5.4 2 G/C 6.3 5.4 3 G/C 7.0 4.6 3 C/G 6.7 5.1 4 C/A 6.1 5.1 4 G/T 6.8 5.3 5 A/C 6.7 5.4 5 T/G 6.4 5.3 6 C/G 7.6 5.2 6 G/C 7.1 6.3 7 G/T 6.7 5.7 7 C/A 6.8 4.4 8 T/G 6.6 5.0 8 A/C 6.8 5.0 9 G/C 6.2 5.8 9 C/G 6.3 5.3 10 C/G 6.8 4.2 10 G/C 6.8 5.2 11 G/C 7.0 5.5 11 C/G --- 5.6 **************************************************************************** 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 GC/GC 6.6 3.1 3.4 10.0 7.2 7.2 2 CG/CG 8.2 5.7 5.1 9.8 6.8 6.3 3 GC/GC 10.3 7.9 7.0 11.9 8.8 8.1 4 CA/TG 10.6 8.7 8.1 11.7 9.5 8.7 5 AC/GT 9.2 6.5 5.9 12.5 10.0 9.2 6 CG/CG 10.5 9.0 8.3 12.1 9.7 9.0 7 GT/AC 14.0 11.0 10.3 9.2 7.4 6.8 8 TG/CA 11.1 8.7 7.8 11.3 9.7 8.6 9 GC/GC 9.3 6.4 6.0 8.2 5.5 4.9 10 CG/CG 11.1 8.9 8.1 12.2 9.1 8.3 11 GC/GC 11.4 8.7 8.0 9.1 7.7 7.0 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 GC/GC 55.67 24.80 26.80 -0.75 -0.57 -0.34 2 CG/CG 52.44 22.58 28.60 -0.96 -0.26 -0.11 3 GC/GC 47.53 24.21 29.32 -0.70 -0.33 -0.63 4 CA/TG 46.57 25.22 28.34 -0.80 0.08 -0.60 5 AC/GT 43.64 23.50 25.67 -0.94 0.20 -0.28 6 CG/CG 39.79 26.51 24.93 -0.98 0.18 -0.09 7 GT/AC 36.29 29.85 25.48 -0.97 0.01 -0.22 8 TG/CA 34.32 25.68 25.13 -0.79 -0.61 0.03 9 GC/GC 28.90 30.03 27.74 -0.86 -0.05 -0.50 10 CG/CG 26.19 24.26 25.88 -0.99 -0.00 -0.11 11 GC/GC 23.76 25.12 24.80 -0.97 -0.17 -0.20