**************************************************************************** File name: 7b46.pdb no. of peptide chains: 4 [A=192,B=191,C=189,D=192] no. of DNA/RNA chains: 4 [E=11,F=11,G=12,H=12] no. of amino acids: 764 no. of nucleotides: 46 no. of atoms: 7119 no. of waters: 295 no. of metals: 4 [Zn=4] **************************************************************************** List of 1 helix Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=22 strand-1 5'-GGGCATGCCCGCGGGCATGCCC-3' bp-type |||||||||||||||||||||| strand-2 3'-CCCGTACGGGCGCCCGTACGGG-5' helix-form B.BB.BBB..x..BBB.BB.B 1 F.DG2 E.DC11 G-C WC 19-XIX cWW cW-W 2 F.DG3 E.DC10 G-C WC 19-XIX cWW cW-W 3 F.DG4 E.DC9 G-C WC 19-XIX cWW cW-W 4 F.DC5 E.DG8 C-G WC 19-XIX cWW cW-W 5 F.DA6 E.DT7 A-T WC 20-XX cWW cW-W 6 F.DT7 E.DA6 T-A WC 20-XX cWW cW-W 7 F.DG8 E.DC5 G-C WC 19-XIX cWW cW-W 8 F.DC9 E.DG4 C-G WC 19-XIX cWW cW-W 9 F.DC10 E.DG3 C-G WC 19-XIX cWW cW-W 10 F.DC11 E.DG2 C-G WC 19-XIX cWW cW-W 11 F.DG12 E.DC1 G-C WC 19-XIX cWW cW-W 12 H.DC1 G.DG12 C-G WC 19-XIX cWW cW-W 13 H.DG2 G.DC11 G-C WC 19-XIX cWW cW-W 14 H.DG3 G.DC10 G-C WC 19-XIX cWW cW-W 15 H.DG4 G.DC9 G-C WC 19-XIX cWW cW-W 16 H.DC5 G.DG8 C-G WC 19-XIX cWW cW-W 17 H.DA6 G.DT7 A-T WC 20-XX cWW cW-W 18 H.DT7 G.DA6 T-A WC 20-XX cWW cW-W 19 H.DG8 G.DC5 G-C WC 19-XIX cWW cW-W 20 H.DC9 G.DG4 C-G WC 19-XIX cWW cW-W 21 H.DC10 G.DG3 C-G WC 19-XIX cWW cW-W 22 H.DC11 G.DG2 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 40 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7b46 C-ser E.DC1 A.SER121 8.66 103.81 5.85 6.37 0.43 68.69 -46.25 69.30 2 7b46 G-ser E.DG2 A.SER121 9.32 85.34 5.98 6.20 -3.55 33.92 -60.86 52.77 3 7b46 T-arg E.DT7 B.ARG280 12.52 82.73 8.19 7.88 5.24 44.81 24.59 67.41 4 7b46 G-arg E.DG8 A.ARG248 -14.11 -47.30 -13.75 2.00 2.50 4.25 -45.88 -11.01 5 7b46 G-ala E.DG8 B.ALA276 9.86 -126.47 -7.67 6.18 -0.34 -18.27 85.85 -102.65 6 7b46 G-arg E.DG8 B.ARG280 11.13 58.17 10.10 3.43 3.18 47.87 -1.18 34.04 7 7b46 C-lys E.DC9 B.LYS120 9.52 -148.62 2.38 8.57 3.41 26.26 -17.66 -147.35 8 7b46 C-ala E.DC9 B.ALA276 9.56 -152.72 -4.04 7.66 -4.04 5.15 88.36 -141.55 9 7b46 C-cys E.DC9 B.CYS277 8.53 63.64 8.44 1.11 -0.51 -29.51 -29.11 49.40 10 7b46 C-arg E.DC9 B.ARG280 9.57 -46.31 9.54 0.01 -0.66 44.78 -11.56 -2.55 11 7b46 G-lys F.DG2 B.LYS120 8.53 40.71 5.75 4.93 3.92 -25.05 3.48 32.17 12 7b46 G-lys F.DG3 B.LYS120 -8.73 -38.52 8.10 3.26 0.18 -31.89 20.13 -7.98 13 7b46 G-lys F.DG4 B.LYS120 -9.54 -55.24 8.60 2.04 -3.61 -26.50 30.95 -38.12 14 7b46 G-arg F.DG4 B.ARG280 -9.77 175.61 -0.07 -9.76 0.14 16.46 -37.04 175.32 15 7b46 T-arg F.DT7 A.ARG280 12.26 90.11 8.55 7.34 4.85 53.49 24.56 71.60 16 7b46 G-ala F.DG8 A.ALA276 9.32 83.56 5.57 4.83 5.71 -63.44 -48.33 27.35 17 7b46 G-arg F.DG8 A.ARG280 11.00 67.47 10.43 2.49 2.48 58.19 -0.45 35.75 18 7b46 C-ala F.DC9 A.ALA276 9.11 -83.43 6.14 5.81 3.41 -78.02 -29.28 -4.39 19 7b46 C-cys F.DC9 A.CYS277 8.70 69.17 8.39 0.23 -2.30 -21.90 -45.21 49.19 20 7b46 C-arg F.DC9 A.ARG280 10.56 54.88 10.45 -1.40 -0.71 52.10 -16.81 3.96 21 7b46 G-ser F.DG12 C.SER121 6.96 101.39 3.95 4.86 3.05 43.41 -9.62 93.64 22 7b46 G-arg G.DG4 D.ARG280 -10.00 177.50 0.49 -9.98 0.41 11.22 -41.75 177.32 23 7b46 T-arg G.DT7 C.ARG280 12.37 87.21 8.38 7.75 4.76 48.48 27.71 69.93 24 7b46 G-ala G.DG8 C.ALA276 9.57 92.82 6.42 5.19 4.84 -71.14 -48.42 38.80 25 7b46 G-arg G.DG8 C.ARG280 11.09 61.70 10.56 2.74 1.99 52.13 10.01 32.68 26 7b46 C-lys G.DC9 C.LYS120 9.47 -156.43 3.48 8.53 2.20 19.47 -34.88 -154.90 27 7b46 C-ala G.DC9 C.ALA276 -9.17 -89.93 6.16 5.70 3.70 -86.17 -25.64 -2.53 28 7b46 C-cys G.DC9 C.CYS277 8.45 62.54 8.40 0.16 -0.89 -27.93 -26.19 50.42 29 7b46 C-arg G.DC9 C.ARG280 -9.69 -51.23 9.58 -1.15 -0.83 49.81 -11.42 -3.59 30 7b46 C-ser H.DC1 C.SER121 8.57 98.18 7.86 3.30 -0.89 51.72 -39.35 78.13 31 7b46 G-lys H.DG2 C.LYS120 8.90 64.50 6.72 4.82 3.31 -50.01 -1.34 42.10 32 7b46 G-lys H.DG3 C.LYS120 -9.15 53.53 8.24 3.98 -0.29 -48.55 21.72 6.31 33 7b46 G-lys H.DG4 C.LYS120 -9.46 -59.05 8.62 2.98 -2.52 -45.20 23.75 -30.70 34 7b46 G-arg H.DG4 C.ARG280 -9.77 176.13 0.89 -9.72 0.31 14.52 -40.16 175.85 35 7b46 T-arg H.DT7 D.ARG280 12.39 84.94 8.27 7.72 5.05 47.90 24.48 68.40 36 7b46 G-ala H.DG8 D.ALA276 9.63 95.06 6.24 4.99 5.37 -72.77 -51.84 36.58 37 7b46 G-arg H.DG8 D.ARG280 11.08 59.79 10.32 3.09 2.59 49.95 4.78 33.62 38 7b46 C-ala H.DC9 D.ALA276 9.51 -154.63 -4.15 7.63 -3.88 -2.49 89.79 -143.88 39 7b46 C-cys H.DC9 D.CYS277 8.75 66.46 8.65 0.82 -1.03 -26.96 -29.97 53.98 40 7b46 C-arg H.DC9 D.ARG280 -9.80 -49.11 9.75 -0.29 -0.88 48.14 -9.72 -0.56 **************************************************************************** List of 35 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7b46 GC-ser E.DG2 F.DC11 A.SER121 -9.26 81.43 5.02 6.23 -4.67 28.15 -51.48 59.20 2 7b46 GC-ala E.DG4 F.DC9 A.ALA276 -9.20 -178.22 5.77 6.31 -3.40 -30.14 -76.87 -177.63 3 7b46 GC-cys E.DG4 F.DC9 A.CYS277 -8.89 134.25 -0.17 -8.59 2.29 45.44 20.43 129.24 4 7b46 GC-arg E.DG4 F.DC9 A.ARG280 -10.81 175.09 1.28 -10.71 0.64 15.60 -53.03 174.45 5 7b46 AT-arg E.DA6 F.DT7 A.ARG280 -12.24 111.45 -7.84 -7.88 -5.14 -20.91 -48.53 102.07 6 7b46 GC-arg E.DG8 F.DC5 A.ARG248 -14.24 -49.89 -13.96 1.69 2.29 5.65 -48.70 -9.56 7 7b46 GC-ala E.DG8 F.DC5 B.ALA276 9.78 -123.12 -7.86 5.82 -0.26 -17.35 84.00 -98.91 8 7b46 GC-arg E.DG8 F.DC5 B.ARG280 10.98 59.61 9.74 3.63 3.52 47.47 -3.27 37.00 9 7b46 GC-lys F.DG2 E.DC11 B.LYS120 8.25 44.15 5.80 4.74 3.46 -26.44 9.14 34.50 10 7b46 GC-lys F.DG3 E.DC10 B.LYS120 -8.94 -36.93 8.39 3.08 -0.12 -28.20 22.50 -7.99 11 7b46 GC-lys F.DG4 E.DC9 B.LYS120 -9.53 -50.13 8.58 2.21 -3.51 -22.11 28.55 -35.37 12 7b46 GC-ala F.DG4 E.DC9 B.ALA276 9.50 -91.79 7.70 -3.84 4.02 83.41 5.03 -42.10 13 7b46 GC-cys F.DG4 E.DC9 B.CYS277 -8.52 132.11 -1.11 -8.42 0.64 30.89 34.12 127.67 14 7b46 GC-arg F.DG4 E.DC9 B.ARG280 -9.66 178.99 -0.03 -9.66 0.40 13.97 -40.88 178.92 15 7b46 AT-arg F.DA6 E.DT7 B.ARG280 -12.56 110.17 -8.36 -7.10 -6.12 -17.70 -44.05 102.59 16 7b46 GC-ala F.DG8 E.DC5 A.ALA276 9.23 91.07 5.13 5.45 5.40 -69.45 -51.06 32.81 17 7b46 GC-arg F.DG8 E.DC5 A.ARG280 10.73 62.78 10.09 2.87 2.23 50.79 0.17 38.20 18 7b46 GC-ser F.DG12 E.DC1 A.SER121 -9.00 117.40 -7.52 -4.89 0.69 33.63 -58.33 102.76 19 7b46 GC-ser F.DG12 E.DC1 C.SER121 7.24 116.16 3.79 4.55 4.17 51.76 -19.41 106.71 20 7b46 GC-ala G.DG4 H.DC9 D.ALA276 9.39 -92.44 7.62 -3.94 3.81 86.28 -3.02 -36.92 21 7b46 GC-cys G.DG4 H.DC9 D.CYS277 -8.72 128.20 -0.65 -8.62 1.13 29.80 30.12 124.13 22 7b46 GC-arg G.DG4 H.DC9 D.ARG280 -9.89 179.01 0.39 -9.87 0.65 10.45 -44.94 178.93 23 7b46 AT-arg G.DA6 H.DT7 D.ARG280 -12.43 110.18 -8.44 -7.34 -5.43 -21.28 -42.63 102.55 24 7b46 GC-ala G.DG8 H.DC5 C.ALA276 9.49 -128.41 -7.40 5.93 -0.44 -24.74 83.33 -106.33 25 7b46 GC-arg G.DG8 H.DC5 C.ARG280 10.98 60.86 10.19 2.91 2.85 49.65 1.87 36.31 26 7b46 GC-ser G.DG12 H.DC1 C.SER121 -8.64 118.42 -2.42 -8.23 1.03 40.48 -35.78 109.86 27 7b46 GC-lys H.DG2 G.DC11 C.LYS120 9.03 56.60 7.42 4.02 3.23 -45.25 6.21 34.37 28 7b46 GC-lys H.DG3 G.DC10 C.LYS120 -9.14 48.10 8.33 3.77 0.11 -44.96 16.87 2.75 29 7b46 GC-lys H.DG4 G.DC9 C.LYS120 -9.46 -52.96 8.58 3.23 -2.36 -40.07 21.52 -27.89 30 7b46 GC-ala H.DG4 G.DC9 C.ALA276 9.13 -90.51 7.58 -3.41 3.79 84.41 1.01 -36.24 31 7b46 GC-cys H.DG4 G.DC9 C.CYS277 -8.43 129.98 -0.26 -8.37 1.00 26.88 33.09 126.02 32 7b46 GC-arg H.DG4 G.DC9 C.ARG280 -9.73 179.72 1.03 -9.66 0.57 12.90 -44.96 179.69 33 7b46 AT-arg H.DA6 G.DT7 C.ARG280 -12.40 109.63 -8.35 -7.36 -5.46 -22.79 -45.78 100.60 34 7b46 GC-ala H.DG8 G.DC5 D.ALA276 9.57 -128.71 -7.54 5.85 -0.78 -26.60 80.43 -108.30 35 7b46 GC-arg H.DG8 G.DC5 D.ARG280 11.01 57.11 10.15 3.25 2.75 45.38 1.31 35.60 **************************************************************************** List of 28 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7b46 OP2@E.DG2 N@A.SER121 3.04 po4:backbone 2 7b46 OP2@E.DT7 NH1@B.ARG273 2.82 po4:sidechain:salt-bridge 3 7b46 OP2@E.DT7 NH2@B.ARG273 3.02 po4:sidechain:salt-bridge 4 7b46 O5'@E.DT7 NH2@B.ARG273 3.17 po4:sidechain 5 7b46 OP1@E.DG8 OG@B.SER241 2.71 po4:sidechain 6 7b46 OP2@E.DG8 N@B.ALA276 3.20 po4:backbone 7 7b46 OP2@F.DG2 N@B.LYS120 3.70 po4:backbone 8 7b46 OP2@F.DT7 NH1@A.ARG273 2.99 po4:sidechain:salt-bridge 9 7b46 OP2@F.DT7 NH2@A.ARG273 2.94 po4:sidechain:salt-bridge 10 7b46 O5'@F.DT7 NH2@A.ARG273 3.14 po4:sidechain 11 7b46 OP1@F.DG8 OG@A.SER241 2.62 po4:sidechain 12 7b46 OP2@F.DG8 N@A.ALA276 2.89 po4:backbone 13 7b46 OP2@F.DG12 N@C.THR123 3.28 po4:backbone 14 7b46 OP2@F.DG12 OG1@C.THR123 2.90 po4:sidechain 15 7b46 OP2@G.DT7 NH1@C.ARG273 2.80 po4:sidechain:salt-bridge 16 7b46 OP2@G.DT7 NH2@C.ARG273 2.94 po4:sidechain:salt-bridge 17 7b46 O5'@G.DT7 NH2@C.ARG273 3.19 po4:sidechain 18 7b46 OP1@G.DG8 OG@C.SER241 2.61 po4:sidechain 19 7b46 OP2@G.DG8 N@C.ALA276 2.86 po4:backbone 20 7b46 OP1@G.DC10 NH1@D.ARG248 3.59 po4:sidechain:salt-bridge 21 7b46 OP1@H.DG2 NH2@C.ARG283 3.61 po4:sidechain:salt-bridge 22 7b46 OP2@H.DG2 N@C.LYS120 2.28 po4:backbone 23 7b46 OP2@H.DT7 NH1@D.ARG273 2.82 po4:sidechain:salt-bridge 24 7b46 OP2@H.DT7 NH2@D.ARG273 3.04 po4:sidechain:salt-bridge 25 7b46 O5'@H.DT7 NH2@D.ARG273 3.26 po4:sidechain 26 7b46 OP1@H.DG8 OG@D.SER241 2.48 po4:sidechain 27 7b46 OP2@H.DG8 N@D.ALA276 2.93 po4:backbone 28 7b46 O3'@H.DT7 OG@D.SER241 3.54 po4:sidechain **************************************************************************** List of 15 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7b46 N7@E.DG2 OG@A.SER121 3.70 base:sidechain 2 7b46 N7@E.DG8 NH2@B.ARG280 2.98 base:sidechain 3 7b46 O6@E.DG8 NH1@B.ARG280 2.97 base:sidechain 4 7b46 N7@F.DG3 NZ@B.LYS120 3.37 base:sidechain 5 7b46 O6@F.DG3 NZ@B.LYS120 3.21 base:sidechain 6 7b46 O6@F.DG4 NZ@B.LYS120 2.73 base:sidechain 7 7b46 N7@F.DG8 NH2@A.ARG280 3.07 base:sidechain 8 7b46 O6@F.DG8 NH1@A.ARG280 2.93 base:sidechain 9 7b46 N7@G.DG8 NH2@C.ARG280 2.93 base:sidechain 10 7b46 O6@G.DG8 NH1@C.ARG280 2.90 base:sidechain 11 7b46 N7@H.DG3 NZ@C.LYS120 2.79 base:sidechain 12 7b46 O6@H.DG3 NZ@C.LYS120 3.24 base:sidechain 13 7b46 O6@H.DG4 NZ@C.LYS120 2.58 base:sidechain 14 7b46 N7@H.DG8 NH2@D.ARG280 3.10 base:sidechain 15 7b46 O6@H.DG8 NH1@D.ARG280 2.92 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7b46 G-arg E.DG8 B.ARG280 0.49 23 2 7b46 G-arg F.DG8 A.ARG280 0.36 12 3 7b46 G-arg G.DG8 C.ARG280 0.07 5 4 7b46 G-arg H.DG8 D.ARG280 0.07 19 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7b46 T-arg E.DT7 B.ARG280 3.73 13 2 7b46 T-arg F.DT7 A.ARG280 3.57 9 3 7b46 T-arg G.DT7 C.ARG280 3.59 5 4 7b46 T-arg H.DT7 D.ARG280 3.54 14 **************************************************************************** List of 3 additional files 1 -- 7b46-baseAA-pairs.pdb 2 -- 7b46-baseAA-stacks.pdb 3 -- 7b46-pairs.pdb