1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Denisov, A.Y. McManus, F.P. Noronha, A.M. Wilds, C.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C7 H16 100.202 HEPTANE non-polymer UK Org.Biomol.Chem. 1477-0539 15 8361 8370 10.1039/c7ob02093g 28937154 Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase. 2017 10.2210/pdb2lzw/pdb pdb_00002lzw 3373.222 DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3') 2 syn polymer 100.202 HEPTANE 1 syn non-polymer no no (DC)(DG)(DA)(DA)(DA)(DG)(DT)(DT)(DT)(DC)(DG) CGAAAGTTTCG A,B polydeoxyribonucleotide n n n n n n n n n n n 18.773 1 19 A 1 B 11 1.920 A_DC1:DG11_B 1 -4.259 0.245 -0.992 -0.271 -8.010 1 19 A 2 B 10 8.691 A_DG2:DC10_B 2 -14.898 -0.635 -0.728 -0.276 10.390 1 20 A 3 B 9 1.066 A_DA3:DT9_B 3 -12.119 -0.083 -0.239 -0.360 8.177 1 20 A 4 B 8 7.887 A_DA4:DT8_B 4 -12.783 -0.058 -0.313 -0.331 18.549 1 20 A 5 B 7 -1.271 A_DA5:DT7_B 5 -3.904 -0.082 0.528 -0.285 -17.669 1 20 A 7 B 5 -1.047 A_DT7:DA5_B 6 -4.146 0.082 0.484 -0.286 -7.983 1 20 A 8 B 4 7.737 A_DT8:DA4_B 7 -12.659 0.074 -0.315 -0.333 -10.176 1 20 A 9 B 3 1.057 A_DT9:DA3_B 8 -11.975 0.099 -0.236 -0.365 8.203 1 19 A 10 B 2 8.547 A_DC10:DG2_B 9 -14.860 0.643 -0.723 -0.285 -18.486 1 19 A 11 B 1 1.892 A_DG11:DC1_B 10 -4.212 -0.236 -0.969 -0.284 3.544 33.509 A A 1 2 37.090 B B 11 10 4.788 20.023 0.307 -0.573 AA_DC1DG2:DC10DG11_BB 1 0.171 -0.316 27.007 -5.675 -0.492 2.837 34.086 A A 2 3 14.716 B B 10 9 2.708 8.506 -0.560 0.646 AA_DG2DA3:DT9DC10_BB 2 -5.277 9.130 32.625 -0.071 0.227 2.840 34.597 A A 3 4 24.194 B B 9 8 3.330 13.999 0.142 -0.552 AA_DA3DA4:DT8DT9_BB 3 -0.585 1.011 31.713 -3.059 -0.328 2.902 35.679 A A 4 5 13.856 B B 8 7 3.009 8.388 -0.604 -0.356 AA_DA4DA5:DT7DT8_BB 4 -5.028 8.306 34.355 -1.701 0.314 2.926 35.774 A A 7 8 13.943 B B 5 4 3.034 8.464 0.599 -0.342 AA_DT7DT8:DA4DA5_BB 5 4.782 -7.878 34.469 -1.689 -0.335 2.842 34.550 A A 8 9 24.133 B B 4 3 3.331 13.946 -0.139 -0.553 AA_DT8DT9:DA3DA4_BB 6 0.606 -1.049 31.683 -3.060 0.326 2.837 34.004 A A 9 10 14.794 B B 3 2 2.710 8.529 0.559 0.642 AA_DT9DC10:DG2DA3_BB 7 5.339 -9.260 32.523 -0.085 -0.216 3.546 33.618 A A 10 11 36.963 B B 2 1 4.783 20.027 -0.305 -0.577 AA_DC10DG11:DC1DG2_BB 8 -0.280 0.517 27.140 -5.644 0.462 citation pdbx_entity_src_syn citation database_2 pdbx_nmr_software struct_conn struct_site pdbx_database_status repository Initial release Database references Source and taxonomy Data collection Database references Derived calculations Other 1 0 2013-10-16 1 1 2017-10-04 1 2 2022-08-24 1 3 2023-06-14 _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.title _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _pdbx_database_status.status_code_nmr_data BMRB Y RCSB 2012-10-11 REL REL REL REL HP6 HEPTANE 32630 synthetic construct sample structures with the least restraint violations and the lowest energy 20 11 2D NOESY 2D TOCSY 2D DQF-COSY 2D 1H-31P HSQC 2D NOESY 1 mM 1 mM 0.1 7.5 ambient 298 K 0.1 7.5 ambient 273 K simulated annealing 1 minimized average structure 1 mM DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3'), 100% D2O 100% D2O 1 mM DNA (5'-D(*CP*GP*AP*AP*AP*GP*TP*TP*TP*CP*G)-3'), 90% H2O/10% D2O 90% H2O/10% D2O Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 1.2 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Johnson, One Moon Scientific data analysis NMRView Varian collection VnmrJ 500 Varian Unity Inova Varian Unity Inova 800 Varian Unity Inova Varian Unity Inova 500 Varian VNMRS Varian VNMRS HP6 12 2 HP6 HP6 101 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DA 3 n 3 DA 3 A DA 4 n 4 DA 4 A DA 5 n 5 DA 5 A DG 6 n 6 DG 6 A DT 7 n 7 DT 7 A DT 8 n 8 DT 8 A DT 9 n 9 DT 9 A DC 10 n 10 DC 10 A DG 11 n 11 DG 11 A DC 1 n 1 DC 1 B DG 2 n 2 DG 2 B DA 3 n 3 DA 3 B DA 4 n 4 DA 4 B DA 5 n 5 DA 5 B DG 6 n 6 DG 6 B DT 7 n 7 DT 7 B DT 8 n 8 DT 8 B DT 9 n 9 DT 9 B DC 10 n 10 DC 10 B DG 11 n 11 DG 11 B author_defined_assembly 2 dimeric 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 A A C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 1 B B C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 2 A A C6 O6 DG DG 6 6 0.137 0.009 1.237 1.374 N 2 B B C6 O6 DG DG 6 6 0.136 0.009 1.237 1.373 N 3 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 3 B B C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 4 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 4 B B C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 5 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 5 B B C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 6 A A C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 6 B B C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 7 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 7 B B C6 O6 DG DG 6 6 0.136 0.009 1.237 1.373 N 8 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 8 B B C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 9 A A C6 O6 DG DG 6 6 0.133 0.009 1.237 1.370 N 9 B B C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 10 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 10 B B C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N 11 A A C6 O6 DG DG 6 6 0.135 0.009 1.237 1.372 N 11 B B C6 O6 DG DG 6 6 0.134 0.009 1.237 1.371 N minimized average structure, model 1 minimized average DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link 1 N N 1 N N 2 N N covale 1.428 none A DG 6 A O6 DG 6 1_555 B HP6 101 C C20 HP6 1_555 covale 1.427 none B DG 6 B O6 DG 6 1_555 B HP6 101 C C26 HP6 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 9 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 7 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 4 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 4 B N6 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 1 B N4 DC 1 1_555 DNA INTERSTRAND CROSS-LINK, DNA 2LZW PDB 1 2LZW 1 11 2LZW 1 11 2LZW A 1 1 11 1 11 2LZW 1 11 2LZW B 1 1 11 BINDING SITE FOR RESIDUE HP6 B 101 B HP6 101 Software 2 A DG 6 A DG 6 2 1_555 B DG 6 B DG 6 2 1_555