1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Peterson, L.A. Vu, C. Hingerty, B.E. Broyde, S. Cosman, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C19 H23 N6 O8 P 494.395 n O6-[4-oxo-4-(3-pyridyl)butyl]-2'-deoxyguanosine-5'-monophosphate DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H Y 144 N C Y 145 N C Y 146 N C Y 147 N N Y 148 N C N 149 N N N 150 N C N 151 N O N 152 N C N 153 N C Y 154 N N N 155 N C Y 156 N C Y 157 N C N 158 N P N 159 N O N 160 N O N 161 N O N 162 N C N 163 R C N 164 N O N 165 S C N 166 N O N 167 N C N 168 R C Y 169 N N Y 170 N N Y 171 N C Y 172 N C Y 173 N C Y 174 N N Y 175 N C N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N O N 200 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing Y 162 N sing Y 163 N sing Y 164 N sing Y 165 N doub N 166 N sing Y 167 N doub Y 168 N doub Y 169 N sing Y 170 N sing Y 171 N sing Y 172 N doub N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing Y 180 N doub Y 181 N sing Y 182 N sing Y 183 N doub Y 184 N doub Y 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing US Biochemistry BICHAW 0033 0006-2960 42 13134 13144 10.1021/bi035217v 14609323 Solution structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11 mer DNA duplex: evidence for formation of a base triplex. 2003 10.2210/pdb1pyj/pdb pdb_00001pyj 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M x-ray 1 1.0 3441.336 5'-D(*CP*CP*AP*TP*AP*TP*GP*GP*CP*CP*C)-3' 1 syn polymer 3414.234 5'-D*GP*GP*GP*CP*CP*AP*TP*AP*TP*GP*G)-3' 1 syn polymer no yes (DC)(DC)(DA)(DT)(DA)(DT)(XPB)(DG)(DC)(DC)(DC) CCATATXGCCC A polydeoxyribonucleotide no no (DG)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG) GGGCCATATGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software struct_conn repository Initial release Version format compliance Version format compliance Non-polymer description Data collection Database references Derived calculations 1 0 2004-04-20 1 1 2008-04-29 1 2 2011-07-13 1 3 2014-08-06 1 4 2024-05-01 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag RCSB Y RCSB 2003-07-09 REL REL This structure was determined using standard 2D homonuclear techniques 1 2D NOESY 0.1 M NaCl 7.00 ambient 298 K The structures are based on a total of 325 restraints (271 DNA-DNA, 22 POB-DNA, 5 POB-POB, 29 H-bonds). molecular mechanics in torsion angle space minimized average structure 1 mM [POB]dG-dC 11mer duplex adduct in 600 ul 10 mM sodium phosphate, 0.1 M NaCl, 0.1 mM EDTA, pH7.0 100% D2O and 90% H2O, 10% D2O Varian collection VNMR 6.1C Acceryls data analysis Felix 97 Hingerty and Broyde structure solution DUPLEX Hingerty and Broyde refinement DUPLEX 600 Varian INOVA C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A T 6 n 6 DT 6 A +G 7 n 7 XPB 7 A G 8 n 8 DG 8 A C 9 n 9 DC 9 A C 10 n 10 DC 10 A C 11 n 11 DC 11 A G 12 n 1 DG 12 B G 13 n 2 DG 13 B G 14 n 3 DG 14 B C 15 n 4 DC 15 B C 16 n 5 DC 16 B A 17 n 6 DA 17 B T 18 n 7 DT 18 B A 19 n 8 DA 19 B T 20 n 9 DT 20 B G 21 n 10 DG 21 B G 22 n 11 DG 22 B author_defined_assembly 2 dimeric A XPB 7 A XPB 7 DG 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 -10.25 1.50 119.60 109.35 A A A OP1 P OP2 DC DC DC 2 2 2 N 1 -10.27 1.50 119.60 109.33 A A A OP1 P OP2 DA DA DA 3 3 3 N 1 -10.26 1.50 119.60 109.34 A A A OP1 P OP2 DT DT DT 4 4 4 N 1 -10.22 1.50 119.60 109.38 A A A OP1 P OP2 DA DA DA 5 5 5 N 1 -10.21 1.50 119.60 109.39 A A A OP1 P OP2 DT DT DT 6 6 6 N 1 -10.29 1.50 119.60 109.31 A A A OP1 P OP2 DG DG DG 8 8 8 N 1 -3.81 0.40 110.80 106.99 A A A C4 C5 N7 DG DG DG 8 8 8 N 1 3.69 0.50 104.30 107.99 A A A C5 N7 C8 DG DG DG 8 8 8 N 1 -3.09 0.50 113.10 110.01 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -10.24 1.50 119.60 109.36 A A A OP1 P OP2 DC DC DC 9 9 9 N 1 -10.26 1.50 119.60 109.34 A A A OP1 P OP2 DC DC DC 10 10 10 N 1 -10.23 1.50 119.60 109.37 A A A OP1 P OP2 DC DC DC 11 11 11 N 1 -3.77 0.40 110.80 107.03 B B B C4 C5 N7 DG DG DG 12 12 12 N 1 3.73 0.50 104.30 108.03 B B B C5 N7 C8 DG DG DG 12 12 12 N 1 -3.16 0.50 113.10 109.94 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 -10.23 1.50 119.60 109.37 B B B OP1 P OP2 DG DG DG 13 13 13 N 1 -3.81 0.40 110.80 106.99 B B B C4 C5 N7 DG DG DG 13 13 13 N 1 3.68 0.50 104.30 107.98 B B B C5 N7 C8 DG DG DG 13 13 13 N 1 -3.13 0.50 113.10 109.97 B B B N7 C8 N9 DG DG DG 13 13 13 N 1 -10.23 1.50 119.60 109.37 B B B OP1 P OP2 DG DG DG 14 14 14 N 1 -3.78 0.40 110.80 107.02 B B B C4 C5 N7 DG DG DG 14 14 14 N 1 3.73 0.50 104.30 108.03 B B B C5 N7 C8 DG DG DG 14 14 14 N 1 -3.13 0.50 113.10 109.97 B B B N7 C8 N9 DG DG DG 14 14 14 N 1 -10.26 1.50 119.60 109.34 B B B OP1 P OP2 DC DC DC 15 15 15 N 1 -10.25 1.50 119.60 109.35 B B B OP1 P OP2 DC DC DC 16 16 16 N 1 -10.26 1.50 119.60 109.34 B B B OP1 P OP2 DA DA DA 17 17 17 N 1 -10.27 1.50 119.60 109.33 B B B OP1 P OP2 DT DT DT 18 18 18 N 1 -10.24 1.50 119.60 109.36 B B B OP1 P OP2 DA DA DA 19 19 19 N 1 -10.26 1.50 119.60 109.34 B B B OP1 P OP2 DT DT DT 20 20 20 N 1 -10.27 1.50 119.60 109.33 B B B OP1 P OP2 DG DG DG 21 21 21 N 1 -3.79 0.40 110.80 107.01 B B B C4 C5 N7 DG DG DG 21 21 21 N 1 3.74 0.50 104.30 108.04 B B B C5 N7 C8 DG DG DG 21 21 21 N 1 -3.12 0.50 113.10 109.98 B B B N7 C8 N9 DG DG DG 21 21 21 N 1 -10.25 1.50 119.60 109.35 B B B OP1 P OP2 DG DG DG 22 22 22 N 1 -3.84 0.40 110.80 106.96 B B B C4 C5 N7 DG DG DG 22 22 22 N 1 3.70 0.50 104.30 108.00 B B B C5 N7 C8 DG DG DG 22 22 22 N 1 -3.08 0.50 113.10 110.02 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 A A C8 N9 DG DG 8 8 -0.045 0.007 1.374 1.329 N 1 B B C8 N9 DG DG 12 12 -0.043 0.007 1.374 1.331 N 1 B B C8 N9 DG DG 13 13 -0.044 0.007 1.374 1.330 N 1 B B C8 N9 DG DG 14 14 -0.045 0.007 1.374 1.329 N 1 B B C8 N9 DG DG 21 21 -0.043 0.007 1.374 1.331 N 1 B B C8 N9 DG DG 22 22 -0.044 0.007 1.374 1.330 N minimized average Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex 1 N N 2 N N covale 1.599 both A DT 6 A O3' DT 6 1_555 A XPB 7 A P XPB 7 1_555 covale 1.600 both A XPB 7 A O3' XPB 7 1_555 A DG 8 A P DG 8 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 22 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 22 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 22 B N2 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 21 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 21 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 21 B N2 DG 10 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 20 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 20 B O4 DT 9 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 19 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 19 B N6 DA 8 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 18 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 18 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 17 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 17 B N6 DA 6 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 15 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 15 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 15 B N4 DC 4 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 14 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 14 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 14 B N2 DG 3 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 13 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 13 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 13 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 12 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 12 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 12 B N2 DG 1 1_555 DNA DNA Adduct, DNA 1PYJ PDB 1 1 1PYJ CCATAT(XPB)GCCC 1PYJ PDB 2 12 1PYJ GGGCCATATGG 1 11 1PYJ 1 11 1PYJ A 1 1 11 12 22 1PYJ 12 22 1PYJ B 2 1 11 1 P 1