This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA v2.1 (c) 2012 Dr. Xiang-Jun Lu (http://x3dna.org) **************************************************************************** 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: modified.pdb Date and time: Mon Feb 27 17:27:06 2012 Number of base-pairs: 14 Number of atoms: 1001 **************************************************************************** **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.096) ....>-:...1_:[..A]A-**-xT[..T]:..31_:-<.... (0.044) | 2 (0.079) ....>-:...2_:[..A]A----xT[..T]:..30_:-<.... (0.071) | 3 (0.045) ....>-:...3_:[..T]T----xA[ADE]:..29_:-<.... (0.095) | 4 (0.049) ....>-:...4_:[..T]T----xA[..A]:..28_:-<.... (0.092) | 5 (0.041) ....>-:...5_:[..T]T----xA[..A]:..27_:-<.... (0.078) | 6 (0.066) ....>-:...6_:[..T]T----xA[ADE]:..26_:-<.... (0.090) | 7 (0.081) ....>-:...7_:[..T]T----xA[..A]:..25_:-<.... (0.110) | 8 (0.070) ....>-:...8_:[..T]T----xA[..A]:..24_:-<.... (0.097) | 9 (0.057) ....>-:...9_:[..T]T----xA[ADE]:..23_:-<.... (0.139) | 10 (0.076) ....>-:..10_:[..T]T----xA[..A]:..22_:-<.... (0.091) | 11 (0.130) ....>-:..11_:[..A]A----xT[..T]:..21_:-<.... (0.074) | 12 (0.073) ....>-:..12_:[..T]T----xA[..A]:..20_:-<.... (0.080) | 13 (0.069) ....>-:..13_:[..T]T----xA[ADE]:..19_:-<.... (0.069) | 14 (0.090) ....>-:..14_:[..T]T-----A[..A]:..18_:-<.... (0.074) | Note: This structure contains 1[1] non-Watson-Crick base-pair. **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 A-**--T [2] N7 - N3 3.18 N6 - O2 2.94 2 A-----T [2] N6 - O4 2.72 N1 - N3 3.03 3 T-----A [2] O4 - N6 2.81 N3 - N1 2.94 4 T-----A [2] O4 - N6 2.79 N3 - N1 3.02 5 T-----A [2] O4 - N6 2.78 N3 - N1 2.87 6 T-----A [2] O4 - N6 2.81 N3 - N1 2.85 7 T-----A [2] O4 - N6 3.27 N3 - N1 2.78 8 T-----A [2] O4 - N6 2.86 N3 - N1 2.84 9 T-----A [2] O4 - N6 2.98 N3 - N1 2.87 10 T-----A [2] O4 - N6 3.10 N3 - N1 2.91 11 A-----T [2] N6 - O4 3.21 N1 - N3 3.04 12 T-----A [2] O4 - N6 2.84 N3 - N1 2.93 13 T-----A [2] O4 - N6 2.91 N3 - N1 2.97 14 T-----A [2] O4 - N6 3.25 N3 - N1 2.97 **************************************************************************** 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 AA/TT 3.35( 2.04) 0.00( 0.00) 0.00( 0.00) 1.72( 0.02) 5.07( 2.06) 2 AT/AT 5.21( 1.50) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.21( 1.50) 3 TT/AA 5.41( 0.66) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.41( 0.66) 4 TT/AA 5.99( 0.70) 0.00( 0.00) 0.00( 0.00) 2.36( 1.18) 8.34( 1.88) 5 TT/AA 4.24( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.24( 0.00) 6 TT/AA 4.58( 0.24) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.58( 0.24) 7 TT/AA 2.88( 0.00) 0.00( 0.00) 0.00( 0.00) 3.87( 2.58) 6.75( 2.58) 8 TT/AA 2.46( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 2.46( 0.00) 9 TT/AA 5.43( 1.10) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.43( 1.10) 10 TA/TA 2.70( 1.01) 0.00( 0.00) 0.37( 0.17) 0.58( 0.00) 3.65( 1.18) 11 AT/AT 1.82( 0.09) 0.00( 0.00) 0.00( 0.00) 6.92( 3.93) 8.74( 4.02) 12 TT/AA 2.10( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 2.10( 0.00) 13 TT/AA 5.45( 0.20) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.45( 0.20) **************************************************************************** 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 A-T 48.69 -90.49 23.00 -0.76 0.61 0.21 2 A-T 44.51 -90.77 20.60 -0.87 0.48 -0.07 3 T-A 41.69 -89.16 20.06 -0.85 0.53 -0.07 4 T-A 38.55 -88.12 19.81 -0.87 0.49 -0.03 5 T-A 35.41 -86.80 20.46 -0.89 0.46 0.05 6 T-A 31.93 -85.30 20.73 -0.85 0.52 -0.13 7 T-A 28.88 -83.17 21.19 -0.88 0.46 -0.10 8 T-A 24.94 -81.48 21.94 -0.93 0.37 -0.03 9 T-A 21.83 -79.86 23.02 -0.97 0.25 0.09 10 T-A 19.01 -77.95 22.94 -0.97 0.25 0.07 11 A-T 16.50 -76.79 21.84 -0.98 0.14 -0.14 12 T-A 13.59 -74.65 21.89 -0.97 0.23 -0.11 13 T-A 10.57 -73.71 20.29 -0.93 0.35 -0.02 14 T-A 7.25 -72.30 19.93 -0.97 0.23 0.05 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 A-T -4.44 -2.46 -0.40 -8.79 -37.30 -89.72 2 A-T 0.16 0.08 -0.32 20.97 -17.18 -11.72 3 T-A -0.34 -0.06 -0.64 13.84 -23.32 -10.26 4 T-A -0.14 0.04 -0.84 15.00 -9.23 -9.13 5 T-A 0.02 -0.09 -0.74 14.15 -11.58 -1.94 6 T-A -0.24 -0.09 -0.12 11.77 -8.50 -3.25 7 T-A -0.23 0.03 -0.05 -2.37 -25.88 9.08 8 T-A -0.12 -0.00 -0.52 -20.28 5.06 -1.09 9 T-A -0.31 -0.04 0.61 -17.02 -19.46 -3.62 10 T-A 0.77 -0.18 0.57 -9.30 -10.79 -0.97 11 A-T -0.19 0.22 0.41 5.40 -2.47 -2.13 12 T-A -0.28 -0.02 0.12 8.74 -16.78 -10.64 13 T-A -0.89 -0.09 0.54 12.73 -28.19 -8.70 14 T-A -0.22 0.08 0.53 10.93 -11.19 -0.35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.46 -0.18 -0.06 3.98 -15.49 -10.32 s.d. 1.20 0.66 0.53 13.10 10.96 23.52 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 AA/TT 2.75 -2.42 3.14 15.27 11.11 60.11 2 AT/AT -0.16 -0.26 3.28 -1.92 -2.67 27.66 3 TT/AA 0.17 -0.70 3.24 1.43 3.05 32.91 4 TT/AA 0.52 -0.47 3.39 3.44 4.13 35.49 5 TT/AA -0.04 -0.58 3.76 -10.59 -3.49 38.36 6 TT/AA 0.42 -0.86 3.62 1.86 -3.43 31.68 7 TT/AA -0.65 -0.81 4.23 0.43 -7.18 40.54 8 TT/AA -0.74 -0.85 3.48 -5.13 -8.66 37.84 9 TT/AA 0.05 -1.19 3.20 0.64 1.03 25.84 10 TA/TA 0.45 -1.11 2.72 1.23 13.39 17.88 11 AT/AT -1.59 -0.37 3.22 1.50 -5.16 32.52 12 TT/AA -0.06 -1.39 3.27 -5.89 -7.36 31.58 13 TT/AA -0.53 -0.16 3.58 0.67 8.22 28.81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.04 -0.86 3.39 0.23 0.23 33.94 s.d. 1.00 0.59 0.36 6.00 7.28 9.87 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 AA/TT -2.83 -1.95 3.24 10.81 -14.86 62.74 2 AT/AT 0.11 -0.14 3.30 -5.56 3.99 27.85 3 TT/AA -1.74 -0.07 3.16 5.36 -2.51 33.08 4 TT/AA -1.38 -0.34 3.35 6.72 -5.60 35.88 5 TT/AA -0.38 -1.36 3.68 -5.19 15.71 39.88 6 TT/AA -0.86 -0.37 3.71 -6.25 -3.40 31.91 7 TT/AA -0.13 0.99 4.30 -10.27 -0.61 41.14 8 TT/AA -0.12 0.43 3.65 -13.07 7.74 39.10 9 TT/AA -2.94 0.06 3.15 2.30 -1.44 25.87 10 TA/TA -6.49 -0.82 1.55 37.03 -3.41 22.35 11 AT/AT 0.20 3.05 3.16 -9.13 -2.66 32.94 12 TT/AA -1.14 -0.94 3.45 -13.16 10.53 32.92 13 TT/AA -2.16 1.18 3.40 16.10 -1.31 29.95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -1.53 -0.02 3.32 1.21 0.17 35.05 s.d. 1.83 1.27 0.62 14.25 7.78 9.96 **************************************************************************** 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 A-T --- --- --- 7.4 6.7 2 A-T --- --- --- 9.3 10.0 3 T-A --- --- --- 9.2 --- 4 T-A --- --- --- 9.3 10.0 5 T-A --- --- --- 9.1 9.9 6 T-A --- --- --- 9.0 --- 7 T-A --- --- --- 8.9 10.1 8 T-A --- --- --- 9.0 10.0 9 T-A --- --- --- 9.0 --- 10 T-A --- --- --- 9.0 9.9 11 A-T --- --- --- 9.4 10.3 12 T-A --- --- --- 9.3 10.0 13 T-A --- --- --- 9.1 --- 14 T-A --- --- --- 9.1 10.2 **************************************************************************** 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 AA/TT --- --- --- --- --- --- --- 2 AT/AT --- --- --- --- --- --- --- 3 TT/AA --- --- --- --- --- --- --- 4 TT/AA --- --- --- --- --- --- --- 5 TT/AA --- --- --- --- --- --- --- 6 TT/AA --- --- --- --- --- --- --- 7 TT/AA --- --- --- --- --- --- --- 8 TT/AA --- --- --- --- --- --- --- 9 TT/AA --- --- --- --- --- --- --- 10 TA/TA --- --- --- --- --- --- --- 11 AT/AT --- --- --- --- --- --- --- 12 TT/AA --- --- --- --- --- --- --- 13 TT/AA --- --- --- --- --- --- --- **************************************************************************** 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 AA/TT --- --- --- --- 2 AT/AT --- --- --- --- 3 TT/AA --- --- --- --- 4 TT/AA --- --- --- --- 5 TT/AA --- --- --- --- 6 TT/AA --- --- --- --- 7 TT/AA --- --- --- --- 8 TT/AA --- --- --- --- 9 TT/AA --- --- --- --- 10 TA/TA --- --- --- --- 11 AT/AT --- --- --- --- 12 TT/AA --- --- --- --- 13 TT/AA --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.51(0.50) Helix: -0.914 0.405 -0.038 HETATM 9998 XS X X 999 47.717 -91.324 21.874 HETATM 9999 XE X X 999 5.748 -72.745 20.129 Average and standard deviation of helix radius: P: 9.78(0.96), O4': 8.31(1.97), C1': 6.25(0.87) 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 A-T --- --- --- --- 2 A-T --- --- --- --- 3 T-A --- --- --- --- 4 T-A --- --- --- --- 5 T-A --- --- --- --- 6 T-A --- --- --- --- 7 T-A --- --- --- --- 8 T-A --- --- --- --- 9 T-A --- --- --- --- 10 T-A --- --- --- --- 11 A-T --- --- --- --- 12 T-A --- --- --- --- 13 T-A --- --- --- --- 14 T-A --- --- --- --- **************************************************************************** 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 A --- --- 59.3 135.7 -177.2 -88.7 -130.2 2 A -61.2 179.8 66.6 146.1 -174.5 -90.7 -89.6 3 T -75.8 168.2 58.2 117.3 174.1 -92.7 -102.9 4 T -74.0 179.5 58.5 122.9 169.6 -95.3 -100.2 5 T -65.4 -174.9 64.9 129.3 175.5 -105.9 -93.4 6 T -56.5 160.4 63.5 138.1 -167.9 -104.9 -111.3 7 T -81.6 162.3 73.9 109.5 -178.2 -87.9 -142.4 8 T -68.1 177.7 60.7 145.4 -155.9 -127.5 -127.0 9 T -72.4 178.8 49.3 134.0 -172.3 -101.9 -125.6 10 T -61.8 163.6 70.6 127.4 -145.1 -88.2 -138.9 11 A -101.9 175.9 34.3 142.2 -72.3 103.6 -91.2 12 T -104.4 155.2 64.5 134.4 -173.4 -92.5 -145.7 13 T -60.4 177.5 56.0 126.2 -160.5 -86.6 -119.9 14 T -73.7 173.3 50.8 143.6 -175.7 -101.3 -97.0 Strand II base alpha beta gamma delta epsilon zeta chi 1 T --- --- --- --- --- --- --- 2 T --- --- --- --- --- --- --- 3 A --- --- --- --- --- --- --- 4 A --- --- --- --- --- --- --- 5 A --- --- --- --- --- --- --- 6 A --- --- --- --- --- --- --- 7 A --- --- --- --- --- --- --- 8 A --- --- --- --- --- --- --- 9 A --- --- --- --- --- --- --- 10 A --- --- --- --- --- --- --- 11 T --- --- --- --- --- --- --- 12 A --- --- --- --- --- --- --- 13 A --- --- --- --- --- --- --- 14 A --- --- --- --- --- --- --- **************************************************************************** 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 A -34.3 47.3 -39.9 19.4 8.4 46.0 150.1 C2'-endo 2 A -17.3 35.2 -38.4 28.1 -7.8 38.8 172.0 C2'-endo 3 T -41.3 38.7 -23.1 -0.0 26.7 41.6 123.7 C1'-exo 4 T -34.0 38.4 -29.1 10.2 15.1 38.4 139.2 C1'-exo 5 T -20.6 33.5 -32.4 22.5 -1.8 33.8 163.4 C2'-endo 6 T -33.2 40.9 -32.0 14.1 11.8 39.6 144.0 C1'-exo 7 T -37.2 24.6 -5.0 -16.2 33.5 36.6 97.8 O4'-endo 8 T -22.6 39.8 -39.7 28.5 -3.8 40.8 166.2 C2'-endo 9 T -26.8 34.6 -28.6 12.9 9.3 34.2 146.7 C2'-endo 10 T -40.5 41.2 -24.4 1.9 24.4 41.7 125.8 C1'-exo 11 A -34.4 42.1 -33.1 13.4 13.5 41.4 143.1 C1'-exo 12 T -30.5 33.7 -24.2 7.2 15.3 33.8 135.9 C1'-exo 13 T -32.6 41.3 -33.8 14.3 11.6 41.0 145.7 C2'-endo 14 T -43.5 51.9 -39.7 18.6 16.0 49.9 142.7 C1'-exo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 T --- --- --- --- --- --- --- --- 2 T --- --- --- --- --- --- --- --- 3 A --- --- --- --- --- --- --- --- 4 A --- --- --- --- --- --- --- --- 5 A --- --- --- --- --- --- --- --- 6 A --- --- --- --- --- --- --- --- 7 A --- --- --- --- --- --- --- --- 8 A --- --- --- --- --- --- --- --- 9 A --- --- --- --- --- --- --- --- 10 A --- --- --- --- --- --- --- --- 11 T --- --- --- --- --- --- --- --- 12 A --- --- --- --- --- --- --- --- 13 A --- --- --- --- --- --- --- --- 14 A --- --- --- --- --- --- --- --- **************************************************************************** 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 A/A --- 5.2 1 T/T --- --- 2 A/T 7.2 4.7 2 T/A --- --- 3 T/T 7.1 5.1 3 A/A --- --- 4 T/T 6.8 5.0 4 A/A --- --- 5 T/T 6.8 5.0 5 A/A --- --- 6 T/T 7.1 4.8 6 A/A --- --- 7 T/T 7.1 5.9 7 A/A --- --- 8 T/T 7.2 5.7 8 A/A --- --- 9 T/T 6.8 4.7 9 A/A --- --- 10 T/A 6.9 5.1 10 A/T --- --- 11 A/T 6.4 5.2 11 T/A --- --- 12 T/T 7.0 5.2 12 A/A --- --- 13 T/T 6.9 5.3 13 A/A --- --- **************************************************************************** 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 AA/TT 6.7 5.3 5.0 ---- 8.6 ---- 2 AT/AT 9.5 6.1 5.7 ---- 6.9 ---- 3 TT/AA 10.4 7.3 6.7 ---- 9.3 ---- 4 TT/AA 9.6 6.8 6.3 ---- 10.7 ---- 5 TT/AA 8.4 5.4 4.9 ---- 10.2 ---- 6 TT/AA 9.7 6.5 5.9 ---- 10.5 ---- 7 TT/AA 10.1 7.2 6.5 ---- 9.2 ---- 8 TT/AA 9.6 6.6 6.1 ---- 8.7 ---- 9 TT/AA 11.1 8.2 7.5 ---- 11.6 ---- 10 TA/TA 13.0 10.4 9.5 ---- 14.0 ---- 11 AT/AT 12.2 9.4 8.8 ---- 7.5 ---- 12 TT/AA 9.3 6.2 5.7 ---- 11.0 ---- 13 TT/AA 11.7 8.6 7.9 ---- 10.1 ---- **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 AA/TT 45.99 -93.16 23.15 -0.92 0.33 0.21 2 AT/AT 43.18 -89.82 20.37 -0.85 0.49 -0.19 3 TT/AA 39.84 -89.09 21.52 -0.82 0.57 0.02 4 TT/AA 37.42 -87.00 21.32 -0.81 0.59 0.07 5 TT/AA 34.04 -85.05 19.81 -0.96 0.25 -0.13 6 TT/AA 30.86 -83.52 20.66 -0.84 0.53 -0.01 7 TT/AA 27.26 -81.84 22.28 -0.86 0.51 0.07 8 TT/AA 23.58 -80.31 22.49 -0.86 0.45 0.21 9 TT/AA 20.13 -79.45 20.18 -0.98 0.21 0.06 10 TA/TA 17.93 -81.57 17.54 -0.90 -0.35 0.27 11 AT/AT 16.06 -74.27 19.53 -0.94 0.21 -0.28 12 TT/AA 11.35 -75.04 21.96 -0.85 0.44 -0.29 13 TT/AA 7.97 -75.19 20.27 -0.88 0.40 0.26