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/pdb1pgc/pdb pdb_00001pgc 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 -0.439 1 19 A 1 B 24 2.540 A_DC1:DG24_B 1 0.346 0.270 0.014 -0.242 -3.208 1 19 A 2 B 23 3.727 A_DC2:DG23_B 2 2.806 -0.003 0.004 -0.135 -3.418 1 20 A 3 B 22 -2.180 A_DT3:DA22_B 3 -4.560 -0.145 0.198 -0.274 -6.331 1 19 A 4 B 21 -6.588 A_DC4:DG21_B 4 -6.254 -0.198 0.018 -0.147 2.239 1 20 A 5 B 20 -0.961 A_DA5:DT20_B 5 -5.830 -0.064 0.010 -0.278 10.120 1 19 A 6 B 19 2.449 A_DG6:DC19_B 6 -8.227 -0.373 0.101 -0.337 -2.964 1 19 A 7 B 18 4.774 A_DG7:DC18_B 7 3.173 -0.597 0.028 -0.314 -1.012 1 19 A 8 B 17 -2.947 A_DC8:DG17_B 8 -3.804 0.276 -0.072 -0.208 -4.045 1 19 A 9 B 16 -5.254 A_DC9:DG16_B 9 -1.321 0.249 -0.080 -0.162 3.079 1 20 A 10 B 15 -1.954 A_DT10:DA15_B 10 1.817 0.109 -0.048 -0.302 1.945 1 19 A 11 B 14 3.320 A_DC11:DG14_B 11 -0.429 -0.084 -0.004 -0.128 1.037 1 19 A 12 B 13 2.431 A_DC12:DG13_B 12 -0.644 0.114 0.099 -0.253 3.457 33.445 A A 1 2 36.994 B B 24 23 3.944 19.926 -0.148 0.441 AA_DC1DC2:DG23DG24_BB 1 -2.131 3.956 26.915 -3.391 -0.187 2.905 27.047 A A 2 3 29.852 B B 23 22 3.557 13.363 -1.277 -0.522 AA_DC2DT3:DA22DG23_BB 2 -1.228 2.744 23.537 -4.712 2.399 3.029 37.895 A A 3 4 7.331 B B 22 21 3.093 4.744 0.052 -0.292 AA_DT3DC4:DG21DA22_BB 3 3.166 -4.893 37.479 -1.021 0.302 2.898 35.496 A A 4 5 6.657 B B 21 20 3.057 4.046 0.383 -0.888 AA_DC4DA5:DT20DG21_BB 4 -3.040 5.002 35.145 -1.998 -1.036 3.067 24.358 A A 5 6 10.135 B B 20 19 3.340 4.241 0.118 -1.016 AA_DA5DG6:DC19DT20_BB 5 -3.433 8.203 23.748 -3.727 -1.347 1.228 38.550 A A 6 7 55.670 B B 19 18 3.639 31.604 0.897 -1.033 AA_DG6DG7:DC18DC19_BB 6 -2.574 4.534 22.210 -5.334 -1.665 3.808 33.842 A A 7 8 -2.400 B B 18 17 3.922 -1.396 -1.112 1.062 AA_DG7DC8:DG17DC18_BB 7 1.940 -3.336 33.760 2.091 2.280 3.464 36.995 A A 8 9 -4.546 B B 17 16 3.393 -2.882 0.265 -1.091 AA_DC8DC9:DG16DG17_BB 8 -0.194 0.306 36.886 -1.313 -0.446 3.507 28.320 A A 9 10 -18.011 B B 16 15 3.345 -8.675 0.666 -1.018 AA_DC9DT10:DA15DG16_BB 9 0.477 -0.990 26.980 0.074 -1.244 3.052 39.463 A A 10 11 15.388 B B 15 14 3.207 10.255 1.021 -0.601 AA_DT10DC11:DG14DA15_BB 10 4.842 -7.266 37.860 -2.073 -0.954 3.457 36.183 A A 11 12 35.455 B B 14 13 3.638 20.749 -0.772 0.746 AA_DC11DC12:DG13DG14_BB 11 -1.400 2.392 29.774 -2.302 1.007 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) structures with the lowest energy 20 15 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 15 lowest energy 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 Molecular 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 92.5 A DG 6 A N7 DG 6 1_555 A 1PT 77 C PT 1PT 1_555 A 1PT 77 C N2 1PT 1_555 178.1 A 1PT 77 C N1 1PT 1_555 A 1PT 77 C PT 1PT 1_555 A 1PT 77 C N2 1PT 1_555 85.6 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 89.8 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 92.0 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 1.47 1 A B O2 H21 DC DG 12 13 1.52 1 A B O2 H21 DC DG 1 24 1.54 1 A B H21 O2 DG DC 6 19 1.56 1 A B O2 H21 DC DG 2 23 1.58 2 A B H21 O2 DG DC 7 18 1.48 2 A B O2 H21 DC DG 12 13 1.53 2 A B O2 H21 DC DG 1 24 1.54 2 A B O2 H21 DC DG 2 23 1.55 2 A B O2 H21 DC DG 11 14 1.59 3 A B H21 O2 DG DC 7 18 1.48 3 A B O2 H21 DC DG 12 13 1.54 3 A B O2 H21 DC DG 1 24 1.56 3 A B O2 H21 DC DG 11 14 1.57 3 A B O2 H21 DC DG 2 23 1.60 4 A B H21 O2 DG DC 7 18 1.46 4 A B O2 H21 DC DG 12 13 1.52 4 A B O2 H21 DC DG 1 24 1.54 4 A B O2 H21 DC DG 11 14 1.60 4 A B O2 H21 DC DG 2 23 1.60 5 A B H21 O2 DG DC 7 18 1.46 5 A B O2 H21 DC DG 12 13 1.52 5 A B O2 H21 DC DG 1 24 1.55 5 A B O2 H21 DC DG 11 14 1.60 5 A B O2 H21 DC DG 2 23 1.60 6 A B H21 O2 DG DC 7 18 1.48 6 A B O2 H21 DC DG 12 13 1.53 6 A B O2 H21 DC DG 2 23 1.55 6 A B O2 H21 DC DG 1 24 1.55 6 A B H21 O2 DG DC 6 19 1.55 6 A B O2 H21 DC DG 11 14 1.60 7 A B H21 O2 DG DC 7 18 1.45 7 A B O2 H21 DC DG 12 13 1.52 7 A B O2 H21 DC DG 2 23 1.54 7 A B O2 H21 DC DG 1 24 1.57 7 A B H21 O2 DG DC 6 19 1.58 7 A B O2 H21 DC DG 11 14 1.59 8 A B H21 O2 DG DC 7 18 1.47 8 A B O2 H21 DC DG 12 13 1.53 8 A B O2 H21 DC DG 1 24 1.55 8 A B O2 H21 DC DG 2 23 1.55 9 A B H21 O2 DG DC 7 18 1.45 9 A B O2 H21 DC DG 12 13 1.53 9 A B O2 H21 DC DG 1 24 1.54 9 A B H21 O2 DG DC 6 19 1.56 9 A B O2 H21 DC DG 2 23 1.59 9 A B O2 H21 DC DG 11 14 1.60 10 A B H21 O2 DG DC 7 18 1.49 10 A B O2 H21 DC DG 12 13 1.53 10 A B O2 H21 DC DG 2 23 1.55 10 A B O2 H21 DC DG 1 24 1.56 10 A B O2 H21 DC DG 11 14 1.60 11 A B H21 O2 DG DC 7 18 1.49 11 A B O2 H21 DC DG 12 13 1.53 11 A B O2 H21 DC DG 2 23 1.55 11 A B O2 H21 DC DG 1 24 1.55 11 A B O2 H21 DC DG 11 14 1.60 12 A B H21 O2 DG DC 7 18 1.46 12 A B O2 H21 DC DG 12 13 1.52 12 A B O2 H21 DC DG 1 24 1.56 12 A B H21 O2 DG DC 6 19 1.59 12 A B O2 H21 DC DG 11 14 1.59 12 A B O2 H21 DC DG 2 23 1.60 13 A B H21 O2 DG DC 7 18 1.48 13 A B O2 H21 DC DG 12 13 1.52 13 A B O2 H21 DC DG 1 24 1.55 13 A B O2 H21 DC DG 2 23 1.56 13 A B H21 O2 DG DC 6 19 1.56 14 A B H21 O2 DG DC 7 18 1.49 14 A B O2 H21 DC DG 12 13 1.52 14 A B O2 H21 DC DG 1 24 1.55 14 A B O2 H21 DC DG 2 23 1.57 14 A B O2 H21 DC DG 11 14 1.60 15 A B H21 O2 DG DC 7 18 1.48 15 A B O2 H21 DC DG 12 13 1.52 15 A B O2 H21 DC DG 1 24 1.55 15 A B O2 H21 DC DG 2 23 1.56 15 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 2.012 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 1PGC PDB 1 1PGC 1PGC PDB 2 1PGC 1 12 1PGC 1 12 1PGC A 1 1 12 13 24 1PGC 13 24 1PGC B 2 1 12 BINDING SITE FOR RESIDUE 1PT A 77 A 1PT 77 Software 3 A DA 5 A DA 5 3 1_555 A DG 6 A DG 6 3 1_555 A DG 7 A DG 7 3 1_555