**************************************************************************** File name: 2ms0.pdb no. of peptide chains: 2 [A=55,C=56] no. of DNA/RNA chains: 1 [B=71] no. of amino acids: 111 no. of nucleotides: 71 no. of atoms: 4046 no. of waters: 0 no. of metals: 2 [Zn=2] **************************************************************************** List of 3 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'-GGCUC-3' bp-type ||||| strand-2 3'-CCGAG-5' helix-form AAAA 1 B.G1 B.C72 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C71 G-C WC 19-XIX cWW cW-W 3 B.C3 B.G70 C-G WC 19-XIX cWW cW-W 4 B.U4 B.A69 U-A WC 20-XX cWW cW-W 5 B.C5 B.G68 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=8 strand-1 5'-GGACCCGG-3' bp-type |..||||| strand-2 3'-CUUGGGCC-5' helix-form .xxAAA. 1 B.G19 B.C56 G-C WC 19-XIX cWW cW-W 2 B.G18 B.U55 G+U rWobble 27-XXVII tWW tW+W 3 B.A58 B.U54 A-U rHoogsteen 24-XXIV tHW tM-W 4 B.C61 B.G53 C-G WC 19-XIX cWW cW-W 5 B.C62 B.G52 C-G WC 19-XIX cWW cW-W 6 B.C63 B.G51 C-G WC 19-XIX cWW cW-W 7 B.G64 B.C50 G-C WC 19-XIX cWW cW-W 8 B.G65 B.C49 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[0] bps=12 strand-1 5'-GCGAGAGUCUAG-3' bp-type |||||||||... strand-2 3'-CGCUCUUAGUAC-5' helix-form .A...x.A..x 1 B.G39 B.C31 G-C WC 19-XIX cWW cW-W 2 B.C40 B.G30 C-G WC 19-XIX cWW cW-W 3 B.G41 B.C29 G-C WC 19-XIX cWW cW-W 4 B.A42 B.U28 A-U WC 20-XX cWW cW-W 5 B.G43 B.C27 G-C WC 19-XIX cWW cW-W 6 B.A44 B.U26 A-U WC 20-XX cWW cW-W 7 B.G10 B.U25 G-U Wobble 28-XXVIII cWW cW-W 8 B.U11 B.A24 U-A WC 20-XX cWW cW-W 9 B.C12 B.G23 C-G WC 19-XIX cWW cW-W 10 B.U13 B.U22 U-U -- 16-XVI cWW cW-W 11 B.A14 B.A21 A-A -- -- c.W c.-W 12 B.G15 B.C48 G+C rWC 22-XXII tWW tW+W **************************************************************************** List of 50 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2ms0 G-tyr B.G6 A.TYR28 10.01 -23.68 0.33 10.00 0.26 19.43 13.53 -0.16 2 2ms0 G-lys B.G6 A.LYS41 9.99 36.76 7.64 6.15 1.87 35.41 -9.34 3.27 3 2ms0 U-tyr B.U7 A.TYR28 -8.60 94.20 3.49 6.67 -4.16 9.71 10.52 93.36 4 2ms0 U-ala B.U7 A.ALA36 -8.05 71.02 -5.64 5.12 -2.61 31.27 -41.26 50.42 5 2ms0 U-lys B.U7 A.LYS42 -6.90 65.80 1.60 1.50 -6.54 -43.92 40.36 29.16 6 2ms0 U-arg B.U8 A.ARG17 6.80 83.63 -1.65 3.15 5.79 1.36 -3.20 83.57 7 2ms0 U-arg B.U8 A.ARG18 4.50 95.56 0.21 2.69 3.59 26.28 35.06 87.18 8 2ms0 U-ser B.U8 A.SER19 4.90 117.43 4.54 -1.31 1.32 24.69 -76.71 94.19 9 2ms0 U-leu B.U8 A.LEU21 10.08 155.22 6.33 -6.27 4.71 -21.95 24.03 154.16 10 2ms0 U-ala B.U8 A.ALA27 -8.49 -35.50 2.33 8.00 -1.63 -4.36 9.04 -34.09 11 2ms0 U-lys B.U8 A.LYS30 -9.80 114.56 7.63 -2.13 -5.77 -63.74 -29.74 97.22 12 2ms0 G-leu B.G9 A.LEU21 -7.39 86.54 -6.83 2.49 -1.34 -59.35 -37.80 54.03 13 2ms0 G-asp B.G9 A.ASP22 -7.32 -129.10 -0.74 -6.23 -3.78 -40.94 46.12 -119.93 14 2ms0 G-arg B.G9 A.ARG23 6.30 126.69 -2.14 4.90 3.34 16.73 -56.31 118.03 15 2ms0 G-gln B.G9 A.GLN25 -4.91 90.53 -3.35 -2.34 2.73 67.61 -41.74 47.55 16 2ms0 G-cys B.G9 A.CYS26 -3.46 143.02 -2.31 -2.09 -1.50 7.95 7.37 142.85 17 2ms0 G-ala B.G9 A.ALA27 -4.00 -127.86 -1.16 -1.50 -3.53 72.38 -50.38 -104.54 18 2ms0 G-trp B.G9 A.TRP35 3.78 146.24 -1.92 -1.27 3.01 67.15 36.30 136.66 19 2ms0 G-ala B.G9 A.ALA36 5.07 98.25 3.07 -3.99 0.63 -12.89 35.70 92.42 20 2ms0 G-gln B.G15 A.GLN9 9.77 -141.82 -3.67 8.94 1.46 -41.66 74.13 -127.32 21 2ms0 G-val B.G16 C.VAL103 8.28 -80.86 -7.43 -0.63 -3.60 36.48 72.16 -0.74 22 2ms0 A-tyr B.A34 C.TYR128 7.48 94.63 -1.11 7.39 -0.22 85.41 1.06 45.37 23 2ms0 A-cys B.A34 C.CYS129 4.65 -38.70 -1.92 2.18 3.64 36.38 -12.03 -5.52 24 2ms0 A-lys B.A34 C.LYS141 8.00 176.15 1.28 -6.82 3.98 -38.39 64.36 175.15 25 2ms0 G-tyr B.G35 C.TYR128 -8.32 139.13 5.46 4.02 -4.83 7.02 -10.05 138.89 26 2ms0 G-ala B.G35 C.ALA136 -5.42 123.43 -1.28 -0.20 -5.26 52.98 -43.53 110.02 27 2ms0 G-lys B.G35 C.LYS137 -4.79 61.77 0.33 -1.35 -4.58 -5.65 19.38 58.69 28 2ms0 G-lys B.G35 C.LYS142 -9.59 81.97 6.73 2.71 -6.27 -51.48 -8.08 65.66 29 2ms0 G-arg B.G36 C.ARG117 7.67 97.37 -0.45 7.65 0.13 61.84 -31.31 73.24 30 2ms0 G-ala B.G36 C.ALA127 -8.88 -34.32 4.19 7.83 -0.06 -30.34 -15.93 -2.01 31 2ms0 G-leu B.G37 C.LEU121 -7.42 76.08 -6.82 2.80 -0.85 -56.57 -25.75 46.27 32 2ms0 G-asp B.G37 C.ASP122 7.39 -134.08 -1.63 -6.15 -3.75 -52.12 47.48 -122.94 33 2ms0 G-arg B.G37 C.ARG123 6.14 111.01 -1.52 4.87 3.42 -1.85 -32.92 107.60 34 2ms0 G-asp B.G37 C.ASP124 6.76 57.05 -5.44 -1.90 3.53 -37.29 15.45 41.20 35 2ms0 G-gln B.G37 C.GLN125 4.84 70.44 -3.14 -1.58 3.33 39.01 -29.25 52.48 36 2ms0 G-cys B.G37 C.CYS126 3.17 146.06 -2.36 -2.08 -0.35 -13.98 38.00 143.75 37 2ms0 G-ala B.G37 C.ALA127 -3.85 111.42 1.61 -3.23 -1.34 40.82 72.35 82.36 38 2ms0 G-trp B.G37 C.TRP135 3.99 125.52 -0.57 0.24 3.94 48.53 54.03 110.77 39 2ms0 G-ala B.G37 C.ALA136 5.22 104.91 3.34 -3.60 1.79 -43.17 51.93 85.72 40 2ms0 U-lys B.U38 C.LYS137 -6.48 -74.27 -1.72 -3.26 -5.34 -44.45 56.74 -19.30 41 2ms0 C-gln B.C49 A.GLN12 -6.20 -62.70 1.14 3.91 -4.67 -54.18 29.91 -10.59 42 2ms0 C-gly B.C49 A.GLY13 -5.30 -168.50 -1.84 0.94 -4.89 3.98 56.90 -166.90 43 2ms0 C-gly B.C49 A.GLY14 -8.18 -139.95 -7.33 2.36 -2.77 -53.53 -12.60 -134.59 44 2ms0 C-glu B.C49 A.GLU15 -8.63 -109.20 -6.09 -2.18 -5.72 24.89 36.37 -102.65 45 2ms0 U-gln B.U60 A.GLN9 6.19 -120.36 4.16 3.76 2.63 5.02 -65.03 -107.64 46 2ms0 U-gln B.U60 A.GLN12 -3.89 -90.15 3.64 -1.37 -0.10 83.42 19.53 -31.25 47 2ms0 U-gly B.U60 A.GLY13 -5.36 141.37 3.79 -3.63 -1.11 26.50 35.01 138.21 48 2ms0 U-val B.U60 C.VAL103 8.70 52.44 -6.39 4.82 3.41 -3.72 38.51 36.10 49 2ms0 G-gln B.G65 A.GLN12 6.63 -166.52 4.16 2.82 4.32 4.29 -49.35 -165.15 50 2ms0 G-arg B.G68 A.ARG17 -11.28 108.24 5.46 9.87 -0.08 -63.73 57.67 73.54 **************************************************************************** List of 6 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2ms0 GC-gln B.G15 B.C48 A.GLN9 11.56 142.36 7.40 8.86 -0.65 -24.18 -73.94 131.02 2 2ms0 GC-gln B.G65 B.C49 A.GLN12 6.41 -168.58 4.00 1.99 4.59 17.00 -52.33 -167.12 3 2ms0 GC-gly B.G65 B.C49 A.GLY13 5.41 -62.04 1.68 -1.63 4.88 56.31 13.56 -23.26 4 2ms0 GC-gly B.G65 B.C49 A.GLY14 8.16 -63.13 2.83 -7.07 2.91 -17.46 -41.50 -45.46 5 2ms0 GC-glu B.G65 B.C49 A.GLU15 8.51 -94.83 -1.80 -5.25 6.46 30.32 33.36 -85.78 6 2ms0 GC-arg B.G68 B.C5 A.ARG17 -11.23 111.26 5.06 10.03 0.13 -60.83 60.81 78.92 **************************************************************************** List of 18 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 2ms0 OP1@B.G9 NH1@A.ARG18 2.80 po4:sidechain:salt-bridge 2 2ms0 O5'@B.G9 NH1@A.ARG18 2.99 po4:sidechain 3 2ms0 OP1@B.U11 NH1@A.ARG18 2.81 po4:sidechain:salt-bridge 4 2ms0 OP1@B.U11 NH2@A.ARG18 2.84 po4:sidechain:salt-bridge 5 2ms0 O3'@B.G10 NH2@A.ARG23 2.83 po4:sidechain 6 2ms0 OP1@B.C12 NH1@A.ARG11 2.79 po4:sidechain:salt-bridge 7 2ms0 OP1@B.C12 NH2@A.ARG11 2.82 po4:sidechain:salt-bridge 8 2ms0 OP2@B.U13 NH1@A.ARG11 2.78 po4:sidechain:salt-bridge 9 2ms0 O3'@B.C12 NE2@C.GLN112 2.88 po4:sidechain 10 2ms0 OP1@B.A14 N@A.GLN9 2.97 po4:backbone 11 2ms0 OP2@B.A14 NE2@A.GLN9 2.76 po4:sidechain 12 2ms0 OP1@B.G15 NE2@A.GLN7 3.39 po4:sidechain 13 2ms0 O3'@B.A14 NE2@A.GLN7 3.43 po4:sidechain 14 2ms0 OP1@B.U33 OH@C.TYR128 3.82 po4:sidechain 15 2ms0 OP2@B.U38 NH1@C.ARG118 2.75 po4:sidechain:salt-bridge 16 2ms0 OP2@B.G68 NH2@A.ARG17 2.77 po4:sidechain:salt-bridge 17 2ms0 O3'@B.C67 NE@A.ARG17 3.25 po4:sidechain 18 2ms0 O5'@B.G68 NE@A.ARG17 3.16 po4:sidechain **************************************************************************** List of 12 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 2ms0 O2'@B.G6 NZ@A.LYS30 2.85 sugar:sidechain 2 2ms0 O2'@B.G9 NH2@A.ARG23 2.87 sugar:sidechain 3 2ms0 O2'@B.G10 NH1@A.ARG23 2.88 sugar:sidechain 4 2ms0 O2'@B.G10 NH2@A.ARG23 3.07 sugar:sidechain 5 2ms0 O2'@B.C12 NE2@C.GLN112 3.16 sugar:sidechain 6 2ms0 O2'@B.U32 OH@C.TYR128 3.71 sugar:sidechain 7 2ms0 O2'@B.U32 NZ@C.LYS142 3.14 sugar:sidechain 8 2ms0 O4'@B.G36 NH1@C.ARG117 3.06 sugar:sidechain 9 2ms0 O2'@B.G37 NE@C.ARG123 3.12 sugar:sidechain 10 2ms0 O2'@B.G37 NH2@C.ARG123 2.90 sugar:sidechain 11 2ms0 O2'@B.C49 O@A.GLU15 3.13 sugar:backbone 12 2ms0 O2'@B.A59 O@A.GLY13 3.56 sugar:backbone **************************************************************************** List of 17 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 2ms0 N7@B.G6 NZ@A.LYS41 2.96 base:sidechain 2 2ms0 O6@B.G6 NZ@A.LYS41 2.90 base:sidechain 3 2ms0 O2@B.U7 NZ@A.LYS42 2.80 base:sidechain 4 2ms0 O4@B.U8 NZ@A.LYS30 2.82 base:sidechain 5 2ms0 O6@B.G9 N@A.ALA27 3.04 base:backbone 6 2ms0 O6@B.G9 N@A.ALA36 2.93 base:backbone 7 2ms0 N1@B.G9 O@A.GLN25 2.83 base:backbone 8 2ms0 N2@B.G9 O@A.ASP22 2.69 base:backbone 9 2ms0 N2@B.G9 O@A.GLN25 2.79 base:backbone 10 2ms0 O6@B.G15 NE2@A.GLN9 3.83 base:sidechain 11 2ms0 N7@B.G35 NZ@C.LYS142 2.91 base:sidechain 12 2ms0 O6@B.G37 N@C.ALA127 3.01 base:backbone 13 2ms0 O6@B.G37 N@C.ALA136 2.86 base:backbone 14 2ms0 N1@B.G37 O@C.GLN125 2.89 base:backbone 15 2ms0 N2@B.G37 O@C.ASP122 2.71 base:backbone 16 2ms0 N2@B.G37 O@C.GLN125 2.74 base:backbone 17 2ms0 N3@B.U60 OE1@A.GLN12 2.92 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 2ms0 G-gln B.G15 A.GLN9 1.73 58 2 2ms0 U-gln B.U60 A.GLN12 0.25 39 **************************************************************************** List of 5 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 2ms0 U-tyr B.U7 A.TYR28 3.98 40 2 2ms0 G-trp B.G9 A.TRP35 3.50 15 3 2ms0 A-tyr B.A34 C.TYR128 4.75 39 4 2ms0 G-trp B.G37 C.TRP135 3.75 17 5 2ms0 G-arg B.G68 A.ARG17 4.13 41 **************************************************************************** List of 3 additional files 1 -- 2ms0-baseAA-pairs.pdb 2 -- 2ms0-baseAA-stacks.pdb 3 -- 2ms0-pairs.pdb