**************************************************************************** File name: 5j2j.pdb no. of peptide chains: 1 [A=327] no. of DNA/RNA chains: 3 [D=5,P=10,T=16] no. of amino acids: 326 no. of nucleotides: 32 no. of atoms: 3665 no. of waters: 385 no. of metals: 4 [Na=2,Mg=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 DUP-u 1 A.DUP401 **************************************************************************** List of 2 helices 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=11 strand-1 5'-ATCGCATCAGC-3' bp-type |.||||||||| strand-2 3'-uGGCGTAGTCG-5' helix-form x..BBBBBBB 1 T.DA6 A.DUP401 A-u WC 20-XX cWW cW-W 2 T.DT7 P.DG10 T+G -- -- cWH cW+M 3 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 4 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 5 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 6 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 7 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 8 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 9 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 10 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 11 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 11 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5j2j C-his T.DC5 A.HIS34 5.22 -98.86 -2.78 3.34 2.89 73.80 47.35 -51.24 2 5j2j A-lys T.DA6 A.LYS280 -6.11 179.16 2.97 1.76 -5.04 -0.01 -9.78 179.16 3 5j2j A-arg T.DA6 A.ARG283 -9.55 179.74 4.48 8.20 -1.95 -64.29 -46.22 179.67 4 5j2j T-arg T.DT7 A.ARG283 -12.02 160.52 6.04 9.30 -4.64 -79.40 -25.87 153.78 5 5j2j G-lys T.DG9 A.LYS234 -11.02 -46.21 -10.00 3.92 -2.45 31.05 -9.71 -33.27 6 5j2j G-his D.DG1 A.HIS34 -4.94 -100.71 -1.29 2.92 -3.77 -70.88 -35.03 -68.37 7 5j2j G-lys D.DG1 A.LYS35 -6.22 -129.17 -3.61 1.16 -4.93 -4.37 1.75 -129.13 8 5j2j G-ala D.DG1 A.ALA38 -6.92 -135.52 -2.43 -4.49 -4.67 20.13 50.79 -129.58 9 5j2j U-tyr A.DUP401 A.TYR271 -8.93 110.09 -3.51 7.91 -2.21 45.43 -57.64 88.79 10 5j2j U-asp A.DUP401 A.ASP276 5.20 34.44 -1.68 3.95 2.93 26.78 21.40 3.44 11 5j2j U-asn A.DUP401 A.ASN279 6.57 -109.62 -0.06 -2.69 6.00 3.04 -89.70 -71.17 **************************************************************************** List of 10 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5j2j AU-tyr T.DA6 A.DUP401 A.TYR271 -8.91 115.74 -8.05 3.50 1.49 54.66 -50.95 95.99 2 5j2j AU-asp T.DA6 A.DUP401 A.ASP276 -5.16 177.50 -3.81 1.52 -3.12 -28.02 -29.01 177.34 3 5j2j AU-asn T.DA6 A.DUP401 A.ASN279 -6.59 -129.87 -2.62 0.35 -6.04 -83.03 1.58 -111.07 4 5j2j AU-lys T.DA6 A.DUP401 A.LYS280 -6.05 178.99 2.79 2.04 -4.96 6.68 -7.71 178.98 5 5j2j AU-arg T.DA6 A.DUP401 A.ARG283 -9.48 178.60 4.40 8.27 -1.47 -57.66 -44.08 178.26 6 5j2j GC-lys T.DG9 P.DC8 A.LYS234 -11.04 -47.18 -9.97 3.87 -2.72 30.23 -11.78 -34.73 7 5j2j GT-arg P.DG10 T.DT7 A.ARG283 -13.42 179.85 6.82 -8.70 -7.62 77.71 -42.53 179.78 8 5j2j GC-his D.DG1 T.DC5 A.HIS34 -5.07 -104.58 -1.51 2.66 -4.05 -77.07 -37.46 -66.92 9 5j2j GC-lys D.DG1 T.DC5 A.LYS35 -6.38 -129.08 -3.53 0.76 -5.26 -8.91 -3.22 -128.89 10 5j2j GC-ala D.DG1 T.DC5 A.ALA38 -7.19 -134.91 -2.30 -4.91 -4.73 15.58 45.83 -130.29 **************************************************************************** List of 20 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5j2j OP1@T.DA6 NZ@A.LYS280 3.39 po4:sidechain:salt-bridge 2 5j2j OP2@T.DA6 NZ@A.LYS280 3.38 po4:sidechain:salt-bridge 3 5j2j OP1@T.DT7 OG1@A.THR292 2.70 po4:sidechain 4 5j2j OP1@T.DC8 ND2@A.ASN294 3.29 po4:sidechain 5 5j2j OP1@T.DG9 OH@A.TYR296 2.67 po4:sidechain 6 5j2j OP1@T.DC10 N@A.THR233 2.93 po4:backbone 7 5j2j OP1@T.DC10 N@A.LYS234 2.96 po4:backbone 8 5j2j O3'@T.DG9 OG1@A.THR233 3.41 po4:sidechain 9 5j2j OP1@T.DA11 N@A.LYS230 3.08 po4:backbone 10 5j2j OP1@P.DC8 N@A.GLY107 3.07 po4:backbone 11 5j2j OP1@P.DC8 N@A.ALA110 2.76 po4:backbone 12 5j2j OP2@P.DC8 N@A.SER109 2.99 po4:backbone 13 5j2j OP1@P.DG9 N@A.GLY105 2.74 po4:backbone 14 5j2j OP1@P.DG10 NH2@A.ARG254 2.51 po4:sidechain:salt-bridge 15 5j2j OP1@D.DG1 NZ@A.LYS68 2.87 po4:sidechain:salt-bridge 16 5j2j OP2@D.DG1 NZ@A.LYS68 2.82 po4:sidechain:salt-bridge 17 5j2j OP1@D.DT2 N@A.GLY66 2.86 po4:backbone 18 5j2j OP1@D.DT2 N@A.ILE69 2.84 po4:backbone 19 5j2j OP2@D.DT2 N@A.LYS68 3.22 po4:backbone 20 5j2j OP1@D.DC3 N@A.GLY64 2.90 po4:backbone **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5j2j O4'@T.DT7 NH1@A.ARG283 2.90 sugar:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5j2j N7@T.DA6 NZ@A.LYS280 2.79 base:sidechain 2 5j2j N3@T.DA6 NH1@A.ARG283 3.22 base:sidechain 3 5j2j N3@T.DG9 NZ@A.LYS234 2.95 base:sidechain 4 5j2j O2@A.DUP401 ND2@A.ASN279 3.01 base:sidechain **************************************************************************** List of 1 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5j2j U-asn A.DUP401 A.ASN279 0.49 47 **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5j2j C-his T.DC5 A.HIS34 3.56 7 **************************************************************************** List of 3 additional files 1 -- 5j2j-baseAA-pairs.pdb 2 -- 5j2j-baseAA-stacks.pdb 3 -- 5j2j-pairs.pdb