**************************************************************************** File name: 8hio.pdb no. of peptide chains: 2 [A=567,D=152] no. of DNA/RNA chains: 1 [B=47] no. of amino acids: 719 no. of nucleotides: 47 no. of atoms: 6681 no. of waters: 0 no. of metals: 2 [Mg=1,Zn=1] **************************************************************************** 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=11 strand-1 5'-GCCCGCCAAGA-3' bp-type ||||||||||. strand-2 3'-CGGGCGGUUCG-5' helix-form AAAxAA.AAA 1 B.G-27 B.C-12 G-C WC 19-XIX cWW cW-W 2 B.C-26 B.G-13 C-G WC 19-XIX cWW cW-W 3 B.C-25 B.G-14 C-G WC 19-XIX cWW cW-W 4 B.C-24 B.G-15 C-G WC 19-XIX cWW cW-W 5 B.G-7 B.C-16 G-C WC 19-XIX cWW cW-W 6 B.C-6 B.G-17 C-G WC 19-XIX cWW cW-W 7 B.C-5 B.G-18 C-G WC 19-XIX cWW cW-W 8 B.A-4 B.U-19 A-U WC 20-XX cWW cW-W 9 B.A-3 B.U-20 A-U WC 20-XX cWW cW-W 10 B.G-2 B.C-21 G-C WC 19-XIX cWW cW-W 11 B.A-1 B.G-22 A-G Imino 08-VIII cWW cW-W **************************************************************************** List of 62 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 8hio C-trp B.C-31 A.TRP440 5.53 152.14 -2.31 -2.05 4.59 61.14 -13.88 147.25 2 8hio C-ala B.C-31 A.ALA441 2.40 -165.24 1.40 0.30 1.93 13.63 -0.34 -165.14 3 8hio C-ser B.C-31 A.SER444 6.32 169.09 2.39 -5.84 -0.09 -81.03 23.87 165.25 4 8hio C-leu B.C-31 A.LEU445 6.51 -167.96 -4.72 2.40 3.79 -7.37 15.71 -167.82 5 8hio C-gln B.C-31 D.GLN172 -6.94 -174.12 1.06 -3.48 -5.91 6.62 37.38 -173.78 6 8hio C-lys B.C-31 D.LYS177 -8.16 108.00 2.59 7.65 -1.16 -43.41 16.66 100.46 7 8hio A-leu B.A-30 A.LEU445 -7.02 -76.35 3.41 5.94 -1.55 -3.74 -7.13 -75.99 8 8hio A-lys B.A-30 A.LYS448 -5.07 -81.57 5.02 0.13 0.69 14.47 50.09 -65.10 9 8hio A-gln B.A-30 A.GLN449 -4.79 -88.73 0.57 -0.30 -4.75 10.63 -42.70 -79.10 10 8hio A-gln B.A-30 A.GLN452 -7.23 -76.36 2.85 -6.05 -2.74 30.28 11.70 -70.09 11 8hio G-gln B.G-27 A.GLN452 9.97 179.90 3.76 8.57 -3.42 61.44 -16.00 179.88 12 8hio A-his B.A-23 A.HIS12 -5.37 155.34 0.98 4.09 -3.34 0.84 34.75 154.14 13 8hio A-arg B.A-23 A.ARG245 4.83 63.82 -2.15 2.12 3.77 46.07 40.50 18.55 14 8hio A-pro B.A-23 A.PRO265 -4.46 -168.32 3.34 -2.93 -0.33 -51.10 49.05 -165.65 15 8hio A-val B.A-23 A.VAL266 5.76 -146.17 0.08 -5.74 0.48 -29.82 4.81 -144.92 16 8hio A-gln B.A-23 A.GLN267 6.44 125.70 -0.22 1.04 6.35 -77.60 -36.23 103.05 17 8hio G-thr B.G-22 A.THR8 -8.57 -159.03 -3.68 -0.38 -7.73 -63.36 12.49 -155.14 18 8hio G-gln B.G-22 A.GLN267 -10.13 103.33 5.72 7.37 3.95 -34.16 81.22 60.69 19 8hio G-his B.G-22 A.HIS269 -6.27 69.66 5.43 2.61 -1.72 -28.24 42.37 49.22 20 8hio U-asp B.U-20 A.ASP466 -10.07 -63.46 -8.77 4.92 -0.66 24.07 -57.67 -11.67 21 8hio G-ala B.G-11 A.ALA289 6.28 -160.75 5.19 -2.96 1.95 -30.46 39.23 -158.77 22 8hio G-ile B.G-11 A.ILE291 -7.51 -144.86 -0.10 -6.18 -4.26 -13.00 -67.92 -136.99 23 8hio G-arg B.G-11 A.ARG447 5.32 -68.52 1.60 2.23 4.56 63.51 -19.11 -18.25 24 8hio G-lys B.G-11 A.LYS448 5.01 83.62 2.96 0.62 4.00 50.99 16.30 66.81 25 8hio G-ala B.G-11 A.ALA451 4.69 109.94 -0.84 -4.19 1.92 40.57 73.68 78.75 26 8hio A-tyr B.A-9 A.TYR13 8.78 85.50 7.26 1.13 4.81 81.30 10.22 26.92 27 8hio C-arg B.C-5 A.ARG241 13.41 88.96 11.39 5.96 3.82 37.96 -14.94 80.86 28 8hio A-arg B.A-4 A.ARG241 12.49 69.00 12.15 2.89 0.46 31.32 -33.30 53.15 29 8hio A-arg B.A-3 A.ARG237 11.14 51.35 9.74 5.40 0.41 11.60 -46.22 19.71 30 8hio G-arg B.G-2 A.ARG237 10.57 -50.26 9.44 4.14 -2.33 -9.15 -48.29 -10.85 31 8hio G-asp B.G-2 A.ASP466 -9.74 166.28 -2.29 8.89 -3.25 41.63 -30.52 164.75 32 8hio C-his B.C0 A.HIS269 4.67 121.78 -2.97 -3.15 -1.76 -26.20 37.77 116.20 33 8hio C-arg B.C0 A.ARG270 4.76 108.31 0.22 -4.26 2.11 -30.77 -34.37 100.94 34 8hio G-met B.G1 A.MET4 -4.44 -126.55 -1.64 1.88 -3.68 -8.47 -41.50 -122.34 35 8hio G-val B.G1 A.VAL6 -7.94 -127.69 -7.89 -0.20 -0.88 -35.95 -57.93 -115.69 36 8hio G-val B.G2 A.VAL6 -8.99 -128.74 -6.98 5.40 -1.68 -48.89 -34.09 -120.21 37 8hio G-his B.G2 A.HIS161 9.42 135.43 -3.98 3.46 7.80 -23.32 -60.35 126.66 38 8hio G-glu B.G2 A.GLU282 -11.48 -94.50 -10.85 0.49 -3.72 -65.06 -12.97 -71.63 39 8hio G-arg B.G4 A.ARG168 -7.85 -63.91 6.41 3.73 -2.56 -44.29 30.68 -35.76 40 8hio A-gln B.A5 A.GLN453 -7.79 -109.47 4.10 5.28 -3.99 -44.94 -44.91 -94.46 41 8hio A-glu B.A5 A.GLU454 -7.44 -136.62 0.42 3.94 -6.30 53.51 -3.74 -131.07 42 8hio A-arg B.A5 A.ARG457 -9.17 -139.56 -3.73 7.02 -4.57 -55.74 -54.87 -127.09 43 8hio U-arg B.U6 A.ARG182 9.84 -178.51 -4.15 -8.91 -0.47 -42.26 73.87 -177.97 44 8hio G-arg B.G7 A.ARG182 7.93 -173.53 0.84 -7.78 -1.29 -47.02 69.52 -171.30 45 8hio A-arg B.A8 A.ARG182 -4.93 -155.91 2.14 -2.79 -3.47 -35.03 57.99 -150.88 46 8hio A-his B.A8 A.HIS183 -6.33 -145.56 -3.61 -4.05 -3.26 -77.23 -39.56 -131.93 47 8hio G-arg B.G10 A.ARG185 -8.64 103.26 4.69 6.51 -3.21 -62.22 -63.56 59.13 48 8hio U-asn B.U11 A.ASN30 -4.77 128.51 -4.37 1.89 -0.25 36.53 -62.23 114.98 49 8hio U-asp B.U11 A.ASP34 -4.13 92.73 0.80 -2.91 -2.82 -63.24 41.25 58.44 50 8hio G-glu B.G12 A.GLU19 7.34 170.64 -6.46 3.41 0.72 5.16 31.21 170.27 51 8hio G-arg B.G12 A.ARG22 7.71 -174.73 1.88 -6.26 4.09 47.01 -8.27 -174.24 52 8hio G-gln B.G12 A.GLN23 -6.01 154.26 -1.73 3.67 -4.44 40.55 46.67 149.91 53 8hio G-trp B.G12 A.TRP26 -8.57 169.81 2.35 8.19 -0.91 -13.29 21.35 169.56 54 8hio C-arg B.C13 A.ARG22 -5.75 -169.04 1.98 -5.23 1.31 55.81 -40.21 -166.71 55 8hio C-phe B.C13 A.PHE186 -11.40 -52.54 -7.67 6.32 -5.58 -35.01 14.50 -37.08 56 8hio G-arg B.G14 A.ARG287 11.70 -65.10 5.40 7.51 7.17 -8.85 -53.91 -36.85 57 8hio G-arg B.G14 A.ARG379 -9.71 -125.77 8.90 -2.26 -3.17 52.38 1.46 -118.94 58 8hio G-gln B.G14 A.GLN419 -6.76 -123.73 -3.43 2.09 -5.43 -7.56 18.66 -122.76 59 8hio G-ala B.G14 A.ALA422 -6.76 -139.77 -1.32 -4.40 -4.96 25.75 75.08 -126.91 60 8hio G-phe B.G14 A.PHE443 -7.38 137.91 -6.09 4.13 0.59 -16.79 -36.59 135.03 61 8hio G-trp B.G14 A.TRP450 5.81 127.51 -2.39 -4.72 2.39 -20.58 -0.79 126.58 62 8hio C-his B.C15 A.HIS426 -10.10 -44.71 4.04 7.98 -4.69 -20.84 39.51 -2.04 **************************************************************************** List of 10 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 8hio GC-gln B.G-27 B.C-12 A.GLN452 9.92 176.44 3.85 8.55 -3.23 67.27 -16.97 175.68 2 8hio GC-arg B.G-18 B.C-5 A.ARG241 -13.16 108.63 -5.36 -11.36 -3.93 16.57 -44.55 100.81 3 8hio AU-arg B.A-4 B.U-19 A.ARG241 12.64 73.65 12.22 2.98 1.27 32.97 -39.08 54.91 4 8hio AU-arg B.A-3 B.U-20 A.ARG237 11.23 46.66 9.95 5.20 0.02 8.94 -42.75 16.83 5 8hio AU-asp B.A-3 B.U-20 A.ASP466 10.14 -165.75 5.29 -8.65 0.23 -54.65 23.69 -163.56 6 8hio GC-arg B.G-2 B.C-21 A.ARG237 10.55 -49.02 9.37 4.41 -2.04 -3.94 -47.77 -10.60 7 8hio GC-asp B.G-2 B.C-21 A.ASP466 -9.80 169.86 -2.29 8.96 -3.25 43.11 -34.02 168.57 8 8hio AG-thr B.A-1 B.G-22 A.THR8 9.33 -61.83 0.28 -4.04 8.40 13.82 -58.17 -16.54 9 8hio AG-gln B.A-1 B.G-22 A.GLN267 10.76 144.96 -7.82 -6.45 -3.63 -80.35 31.98 131.19 10 8hio AG-his B.A-1 B.G-22 A.HIS269 6.74 144.22 -2.88 -5.79 1.91 -40.70 28.87 140.39 **************************************************************************** List of 31 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 8hio OP2@B.A-28 NZ@D.LYS101 2.68 po4:sidechain:salt-bridge 2 8hio OP1@B.C-26 NH2@A.ARG371 4.00 po4:sidechain:salt-bridge 3 8hio OP1@B.C-21 NH1@A.ARG293 3.11 po4:sidechain:salt-bridge 4 8hio OP1@B.U-19 NH1@A.ARG368 3.47 po4:sidechain:salt-bridge 5 8hio OP2@B.U-19 NZ@A.LYS459 2.20 po4:sidechain:salt-bridge 6 8hio OP1@B.C-12 NE@D.ARG182 2.66 po4:sidechain:salt-bridge 7 8hio OP2@B.G-11 NZ@A.LYS448 2.54 po4:sidechain:salt-bridge 8 8hio O3'@B.C-12 NZ@A.LYS448 2.68 po4:sidechain 9 8hio OP1@B.G-7 NZ@A.LYS14 2.11 po4:sidechain:salt-bridge 10 8hio OP2@B.G-7 OH@A.TYR13 2.23 po4:sidechain 11 8hio OP1@B.C-6 NH1@A.ARG245 3.02 po4:sidechain:salt-bridge 12 8hio OP2@B.C-6 NH2@A.ARG245 3.31 po4:sidechain:salt-bridge 13 8hio OP1@B.C-5 OG@A.SER238 2.95 po4:sidechain 14 8hio OP2@B.C-5 NH1@A.ARG241 2.20 po4:sidechain:salt-bridge 15 8hio OP2@B.A-3 NE@A.ARG237 2.35 po4:sidechain:salt-bridge 16 8hio OP2@B.A-3 NH2@A.ARG237 3.17 po4:sidechain:salt-bridge 17 8hio OP2@B.G-2 NH2@A.ARG237 3.25 po4:sidechain:salt-bridge 18 8hio OP1@B.C0 NH1@A.ARG532 3.22 po4:sidechain:salt-bridge 19 8hio OP1@B.C0 NH2@A.ARG532 3.16 po4:sidechain:salt-bridge 20 8hio OP1@B.G1 NH1@A.ARG532 2.85 po4:sidechain:salt-bridge 21 8hio OP2@B.G1 NH2@A.ARG270 3.15 po4:sidechain:salt-bridge 22 8hio O3'@B.G2 NZ@A.LYS295 3.52 po4:sidechain 23 8hio OP1@B.A8 OG@A.SER417 3.02 po4:sidechain 24 8hio OP1@B.A8 NE2@A.GLN419 2.80 po4:sidechain 25 8hio OP1@B.G9 NH2@A.ARG185 2.90 po4:sidechain:salt-bridge 26 8hio O3'@B.A8 NE@A.ARG185 3.20 po4:sidechain 27 8hio O3'@B.A8 NH2@A.ARG185 2.50 po4:sidechain 28 8hio OP1@B.G14 O@A.ASP187 2.76 po4:backbone 29 8hio OP1@B.G14 OH@A.TYR292 3.52 po4:sidechain 30 8hio OP2@B.G14 O@A.PHE186 3.27 po4:backbone 31 8hio OP1@B.C15 OG@A.SER423 3.13 po4:sidechain **************************************************************************** List of 7 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 8hio O2'@B.U-29 NZ@D.LYS101 2.85 sugar:sidechain 2 8hio O2'@B.G-27 NE2@A.GLN452 2.91 sugar:sidechain 3 8hio O2'@B.C-26 ND2@A.ASN455 3.56 sugar:sidechain 4 8hio O2'@B.C-24 OH@A.TYR13 2.83 sugar:sidechain 5 8hio O2'@B.A-23 NH2@A.ARG245 2.38 sugar:sidechain 6 8hio O2'@B.A-23 OE1@A.GLN267 3.31 sugar:sidechain 7 8hio O4'@B.G1 N@A.VAL6 3.76 sugar:backbone **************************************************************************** List of 13 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 8hio O2@B.C-31 NZ@D.LYS177 3.40 base:sidechain 2 8hio N3@B.C-31 NE2@D.GLN172 3.20 base:sidechain 3 8hio N4@B.C-31 OG@A.SER444 2.16 base:sidechain 4 8hio N3@B.G-27 NE2@A.GLN452 2.87 base:sidechain 5 8hio N7@B.G-2 NH2@A.ARG237 3.34 base:sidechain 6 8hio N2@B.G-2 OD1@A.ASP466 3.77 base:sidechain 7 8hio N3@B.C0 NE2@A.HIS269 3.31 base:sidechain 8 8hio N7@B.G4 NH1@A.ARG168 2.78 base:sidechain 9 8hio O6@B.G4 NH1@A.ARG168 2.96 base:sidechain 10 8hio O6@B.G4 NH2@A.ARG168 2.84 base:sidechain 11 8hio N1@B.G12 OE1@A.GLN23 2.97 base:sidechain 12 8hio N2@B.G12 OE2@A.GLU19 3.26 base:sidechain 13 8hio O6@B.G14 NH2@A.ARG379 3.04 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 8hio G-arg B.G-2 A.ARG237 2.26 48 2 8hio G-asp B.G-2 A.ASP466 0.60 50 3 8hio C-his B.C0 A.HIS269 0.43 38 4 8hio G-arg B.G14 A.ARG379 1.09 44 **************************************************************************** List of 7 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 8hio A-his B.A-23 A.HIS12 3.13 4 2 8hio A-arg B.A-23 A.ARG245 3.19 12 3 8hio G-his B.G-22 A.HIS269 3.81 27 4 8hio C-arg B.C0 A.ARG270 3.45 38 5 8hio G-arg B.G10 A.ARG185 4.34 34 6 8hio G-trp B.G12 A.TRP26 3.84 40 7 8hio G-trp B.G14 A.TRP450 3.14 13 **************************************************************************** List of 2 interface stacks with 3+ planar moieties Note: an interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default). 1 size=3 CGH B.C-21,B.G-22,A.HIS269 2 size=4 GACR B.G-2,B.A-1,B.C0,A.ARG270 **************************************************************************** List of 3 additional files 1 -- 8hio-baseAA-pairs.pdb 2 -- 8hio-baseAA-stacks.pdb 3 -- 8hio-pairs.pdb