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 C9 H13 N2 O8 P 308.182 y 2'-DEOXYURIDINE-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/pdb2lzv/pdb pdb_00002lzv 3334.183 DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3') 2 syn polymer 100.202 HEPTANE 1 syn non-polymer no no (DC)(DG)(DA)(DA)(DA)(DU)(DT)(DT)(DT)(DC)(DG) CGAAAUTTTCG A,B polydeoxyribonucleotide n n n n n n n n n n n 7.521 1 19 A 1 B 11 -11.915 A_DC1:DG11_B 1 17.724 -0.480 -1.124 -0.455 -1.369 1 19 A 2 B 10 3.618 A_DG2:DC10_B 2 -5.625 -0.117 -0.595 -0.253 -1.331 1 20 A 3 B 9 7.713 A_DA3:DT9_B 3 -3.277 -0.189 -0.279 -0.264 7.129 1 20 A 4 B 8 3.253 A_DA4:DT8_B 4 -3.478 0.079 -0.186 -0.300 15.164 1 20 A 5 B 7 -6.125 A_DA5:DT7_B 5 -10.143 -0.062 0.006 -0.145 -15.103 1 20 A 7 B 5 -6.254 A_DT7:DA5_B 6 -9.968 0.066 0.013 -0.143 -7.118 1 20 A 8 B 4 3.231 A_DT8:DA4_B 7 -3.382 -0.065 -0.184 -0.300 1.303 1 20 A 9 B 3 7.490 A_DT9:DA3_B 8 -3.174 0.204 -0.276 -0.272 1.486 1 19 A 10 B 2 3.567 A_DC10:DG2_B 9 -5.664 0.127 -0.581 -0.266 -7.103 1 19 A 11 B 1 -11.829 A_DG11:DC1_B 10 17.822 0.481 -1.104 -0.470 2.524 36.238 A A 1 2 46.211 B B 11 10 4.121 25.930 0.956 -0.485 AA_DC1DG2:DC10DG11_BB 1 -2.056 3.664 25.452 -5.181 -1.885 2.642 35.858 A A 2 3 20.374 B B 10 9 3.009 12.290 0.303 -0.479 AA_DG2DA3:DT9DC10_BB 2 -3.052 5.060 33.616 -2.353 -0.884 2.675 33.795 A A 3 4 20.833 B B 9 8 2.975 11.865 -0.541 -0.395 AA_DA3DA4:DT8DT9_BB 3 -1.031 1.809 31.685 -2.394 0.782 3.014 37.530 A A 4 5 9.834 B B 8 7 2.949 6.296 -1.286 0.222 AA_DA4DA5:DT7DT8_BB 4 -2.206 3.445 36.954 -0.410 1.733 3.016 37.603 A A 7 8 9.845 B B 5 4 2.950 6.314 1.289 0.218 AA_DT7DT8:DA4DA5_BB 5 2.271 -3.540 37.021 -0.418 -1.729 2.676 33.795 A A 8 9 20.826 B B 4 3 2.977 11.861 0.536 -0.397 AA_DT8DT9:DA3DA4_BB 6 1.070 -1.879 31.685 -2.398 -0.768 2.646 35.805 A A 9 10 20.157 B B 3 2 3.009 12.147 -0.298 -0.484 AA_DT9DC10:DG2DA3_BB 7 3.020 -5.012 33.613 -2.349 0.874 2.517 36.276 A A 10 11 46.135 B B 2 1 4.111 25.922 -0.949 -0.491 AA_DC10DG11:DC1DG2_BB 8 2.105 -3.746 25.511 -5.164 1.880 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 0.5 mM 0.5 mM 0.1 7.5 ambient 298 K 0.1 7.5 ambient 273 K simulated annealing 1 minimized average structure 0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 100% D2O 100% D2O 0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*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 DU 6 n 6 DU 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 DU 6 n 6 DU 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 C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 1 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 2 A A C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 2 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 3 A A C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 3 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 4 A A C4 O4 DU DU 6 6 0.142 0.008 1.232 1.374 N 4 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 5 A A C4 O4 DU DU 6 6 0.143 0.008 1.232 1.375 N 5 B B C4 O4 DU DU 6 6 0.143 0.008 1.232 1.375 N 6 A A C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 6 B B C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 7 A A C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 7 B B C4 O4 DU DU 6 6 0.139 0.008 1.232 1.371 N 8 A A C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 8 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 9 A A C4 O4 DU DU 6 6 0.142 0.008 1.232 1.374 N 9 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 10 A A C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 10 B B C4 O4 DU DU 6 6 0.140 0.008 1.232 1.372 N 11 A A C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N 11 B B C4 O4 DU DU 6 6 0.141 0.008 1.232 1.373 N minimized average structure, model 1 minimized average DNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link 1 N N 1 N N 2 N N covale 1.430 none A DU 6 A O4 DU 6 1_555 B HP6 101 C C20 HP6 1_555 covale 1.429 none B DU 6 B O4 DU 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 2LZV PDB 1 2LZV 1 11 2LZV 1 11 2LZV A 1 1 11 1 11 2LZV 1 11 2LZV B 1 1 11 BINDING SITE FOR RESIDUE HP6 B 101 B HP6 101 Software 2 A DU 6 A DU 6 2 1_555 B DU 6 B DU 6 2 1_555