1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Wu, Y. Pradhan, P. Havener, J. Chaney, S.G. Campbel, S.L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C6 H14 N2 Pt 2 309.267 CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) OXALIPLATIN non-polymer 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 341 1251 1269 10.1016/j.jmb.2004.06.066 15321720 NMR solution structure of an oxaliplatin 1,2-d(GG) intrastrand cross-link in a DNA dodecamer duplex 2004 10.2210/pdb1pg9/pdb pdb_00001pg9 G6 and G7 are Cross-Linked by a cis-Pt compound, residue 1PT 3559.319 5'-D(*CP*CP*TP*CP*AP*GP*GP*CP*CP*TP*CP*C)-3' 1 syn polymer 3768.453 5'-D(*GP*GP*AP*GP*GP*CP*CP*TP*GP*AP*GP*G)-3' 1 syn polymer 309.267 CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) 1 syn non-polymer no no (DC)(DC)(DT)(DC)(DA)(DG)(DG)(DC)(DC)(DT)(DC)(DC) CCTCAGGCCTCC A polydeoxyribonucleotide no no (DG)(DG)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG)(DG) GGAGGCCTGAGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n 0.145 1 19 A 1 B 24 1.662 A_DC1:DG24_B 1 -0.010 0.506 -0.026 -0.330 -3.048 1 19 A 2 B 23 2.725 A_DC2:DG23_B 2 1.579 0.281 -0.064 -0.240 -4.488 1 20 A 3 B 22 -2.255 A_DT3:DA22_B 3 -6.001 0.048 0.090 -0.307 -6.419 1 19 A 4 B 21 -1.396 A_DC4:DG21_B 4 -5.475 -0.140 0.044 -0.177 2.218 1 20 A 5 B 20 -1.235 A_DA5:DT20_B 5 -4.377 -0.122 -0.031 -0.279 10.590 1 19 A 6 B 19 2.498 A_DG6:DC19_B 6 -9.921 -0.513 0.122 -0.361 -5.649 1 19 A 7 B 18 6.423 A_DG7:DC18_B 7 -0.508 -0.667 -0.007 -0.254 -1.703 1 19 A 8 B 17 -2.309 A_DC8:DG17_B 8 -4.115 0.302 -0.033 -0.238 -5.072 1 19 A 9 B 16 -5.200 A_DC9:DG16_B 9 -2.410 0.272 -0.020 -0.165 2.492 1 20 A 10 B 15 -2.235 A_DT10:DA15_B 10 0.288 0.112 -0.013 -0.299 1.697 1 19 A 11 B 14 3.440 A_DC11:DG14_B 11 -1.252 -0.080 0.005 -0.124 0.988 1 19 A 12 B 13 2.258 A_DC12:DG13_B 12 -0.581 0.079 0.098 -0.255 4.165 29.877 A A 1 2 18.603 B B 24 23 4.222 9.427 0.012 0.517 AA_DC1DC2:DG23DG24_BB 1 -2.047 4.040 28.311 -1.577 -0.584 2.973 28.288 A A 2 3 22.284 B B 23 22 3.556 10.624 -1.011 -1.067 AA_DC2DT3:DA22DG23_BB 2 -2.022 4.241 26.178 -4.742 1.581 2.985 35.880 A A 3 4 11.357 B B 22 21 3.115 6.953 0.054 -0.394 AA_DT3DC4:DG21DA22_BB 3 1.547 -2.527 35.189 -1.577 0.121 3.158 31.470 A A 4 5 16.655 B B 21 20 3.406 8.910 0.651 -0.251 AA_DC4DA5:DT20DG21_BB 4 -1.963 3.670 30.150 -2.170 -1.576 3.119 22.906 A A 5 6 10.192 B B 20 19 3.378 4.015 0.198 -0.873 AA_DA5DG6:DC19DT20_BB 5 -3.096 7.861 22.345 -3.631 -1.604 1.434 38.274 A A 6 7 49.177 B B 19 18 3.606 28.702 0.986 -1.260 AA_DG6DG7:DC18DC19_BB 6 -2.448 4.195 25.472 -5.311 -1.792 3.654 36.423 A A 7 8 2.381 B B 18 17 3.638 1.488 -1.375 0.991 AA_DG7DC8:DG17DC18_BB 7 0.544 -0.870 36.390 1.356 2.283 3.230 36.277 A A 8 9 0.736 B B 17 16 3.244 0.458 0.184 -1.100 AA_DC8DC9:DG16DG17_BB 8 -0.159 0.256 36.274 -1.831 -0.318 3.425 28.343 A A 9 10 -16.277 B B 16 15 3.254 -7.868 0.614 -1.018 AA_DC9DT10:DA15DG16_BB 9 0.885 -1.831 27.236 -0.185 -1.041 3.093 39.480 A A 10 11 12.057 B B 15 14 3.155 8.070 1.103 -0.572 AA_DT10DC11:DG14DA15_BB 10 5.134 -7.671 38.348 -1.769 -1.047 3.408 36.409 A A 11 12 36.169 B B 14 13 3.591 21.242 -0.832 0.750 AA_DC11DC12:DG13DG14_BB 11 -1.559 2.655 29.702 -2.309 1.073 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2004-07-06 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2003-05-28 REL REL 1PT CYCLOHEXANE-1(R),2(R)-DIAMINE-PLATINUM(II) closest to the average 20 1 2D NOESY 2D TOCSY DQF-COSY 2D NOESY 100mM NaCl, 5mM NaPi 7.0 1 atm 275 K 100mM NaCl, 5mM NaPi 7.0 1 atm 298 K simulated annealing 1 closest to the average 100mM NaCl,5mM NaPi buffer, 95% H2O, 5% D2O 95% H2O/5% D2O 100mM NaCl,5mM NaPi buffer, 100% D2O 100% D2O Brunger structure solution CNS 1.0 molecualr Simulations Inc. data analysis Felix 2000 Delaglio processing NMRPipe 2.1 Brunger refinement CNS 1.0 600 Varian UNITYPLUS 800 Varian UNITYPLUS 1PT 77 3 1PT 1PT 77 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A T 3 n 3 DT 3 A C 4 n 4 DC 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A G 7 n 7 DG 7 A C 8 n 8 DC 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A C 11 n 11 DC 11 A C 12 n 12 DC 12 A G 13 n 1 DG 13 B G 14 n 2 DG 14 B A 15 n 3 DA 15 B G 16 n 4 DG 16 B G 17 n 5 DG 17 B C 18 n 6 DC 18 B C 19 n 7 DC 19 B T 20 n 8 DT 20 B G 21 n 9 DG 21 B A 22 n 10 DA 22 B G 23 n 11 DG 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric A DG 6 A N7 DG 6 1_555 A 1PT 77 C PT 1PT 1_555 A 1PT 77 C N1 1PT 1_555 91.9 A DG 6 A N7 DG 6 1_555 A 1PT 77 C PT 1PT 1_555 A 1PT 77 C N2 1PT 1_555 177.6 A 1PT 77 C N1 1PT 1_555 A 1PT 77 C PT 1PT 1_555 A 1PT 77 C N2 1PT 1_555 85.7 A DG 6 A N7 DG 6 1_555 A 1PT 77 C PT 1PT 1_555 A DG 7 A N7 DG 7 1_555 90.6 A 1PT 77 C N1 1PT 1_555 A 1PT 77 C PT 1PT 1_555 A DG 7 A N7 DG 7 1_555 177.6 A 1PT 77 C N2 1PT 1_555 A 1PT 77 C PT 1PT 1_555 A DG 7 A N7 DG 7 1_555 91.9 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 B H21 O2 DG DC 7 18 1.45 1 A B O2 H21 DC DG 12 13 1.52 1 A B O2 H21 DC DG 2 23 1.54 1 A B O2 H21 DC DG 1 24 1.56 1 A B H21 O2 DG DC 6 19 1.60 1 A B O2 H21 DC DG 11 14 1.60 NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex 1 N N 2 N N 3 N N metalc 2.008 A DG 6 A N7 DG 6 1_555 A 1PT 77 C PT 1PT 1_555 metalc 2.013 A DG 7 A N7 DG 7 1_555 A 1PT 77 C PT 1PT 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 23 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 23 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 23 B N2 DG 11 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 22 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 22 B N6 DA 10 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 21 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 21 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 21 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 19 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 19 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 19 B N4 DC 7 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 18 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 18 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 18 B N4 DC 6 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 17 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 17 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 17 B N2 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 15 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 15 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 13 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 13 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 13 B N2 DG 1 1_555 DNA DEOXYRIBONUCLEIC ACID; OXALIPLATIN; DNA; DUPLEX; DODECAMER; NMR, DNA 1PG9 PDB 1 1PG9 1PG9 PDB 2 1PG9 1 12 1PG9 1 12 1PG9 A 1 1 12 13 24 1PG9 13 24 1PG9 B 2 1 12 BINDING SITE FOR RESIDUE 1PT A 77 A 1PT 77 Software 2 A DG 6 A DG 6 2 1_555 A DG 7 A DG 7 2 1_555