0.040453 0.000000 0.000000 0.000000 0.024618 0.000000 0.000000 0.000000 0.015218 0.00000 0.00000 0.00000 0000-0002-3484-3589 Troisi, R. 0000-0001-5682-3100 Tito, G. 0000-0001-9385-2429 Ferraro, G. 0000-0003-4501-4476 Sica, F. 0000-0002-1045-7720 Merlino, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.720 40.620 65.710 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 H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer Pt 2 195.078 PLATINUM (II) ION non-polymer 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 N 144 N O N 145 N H N 146 N H N 147 N MG N 148 N PT 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 To Be Published 0353 10.1016/j.inoche.2026.117829 To Be Published 0000-0002-3484-3589 0000-0001-5682-3100 0000-0001-9385-2429 0000-0003-4501-4476 0000-0002-1045-7720 10.2210/pdb32ut/pdb pdb_000032ut 100 1 N PIXEL 2022-06-14 DECTRIS PILATUS 6M M SINGLE WAVELENGTH M x-ray 1 1.0000 1.0 11.2C ELETTRA 1.0000 SYNCHROTRON ELETTRA BEAMLINE 11.2C 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 195.078 PLATINUM (II) ION 5 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 9 nat water no no (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.25 45.37 VAPOR DIFFUSION, HANGING DROP 6.5 MPD 14 % v/v, MgCl2 20 mM, spermine tetrahydrochloride 80 mM, sodium cacodylate 60 mM, pH 6.5. Equilibrated against a reservoir containing MPD 60 % v/v 293 6.071 1 19 A 1 B 24 -0.480 A_DC1:DG24_B 1 -14.564 0.108 -0.137 -0.189 -3.178 1 19 A 2 B 23 -5.527 A_DG2:DC23_B 2 -10.413 -0.195 0.034 -0.363 -1.097 1 19 A 3 B 22 -1.375 A_DC3:DG22_B 3 -3.645 0.016 -0.014 -0.207 11.705 1 19 A 4 B 21 0.606 A_DG4:DC21_B 4 -11.816 -0.360 0.117 -0.142 7.055 1 20 A 5 B 20 2.620 A_DA5:DT20_B 5 -19.013 -0.027 0.214 -0.135 -1.127 1 20 A 6 B 19 2.229 A_DA6:DT19_B 6 -16.169 0.216 -0.057 -0.140 0.378 1 20 A 7 B 18 4.027 A_DT7:DA18_B 7 -18.122 0.105 0.065 -0.121 -3.225 1 20 A 8 B 17 3.232 A_DT8:DA17_B 8 -14.862 0.036 -0.019 -0.223 -12.705 1 19 A 9 B 16 0.028 A_DC9:DG16_B 9 -9.258 0.241 0.086 -0.130 0.150 1 19 A 10 B 15 -0.748 A_DG10:DC15_B 10 -4.287 -0.413 -0.111 -0.196 7.091 1 19 A 11 B 14 -4.449 A_DC11:DG14_B 11 -16.432 -0.032 0.257 -0.134 12.395 1 19 A 12 B 13 -2.157 A_DG12:DC13_B 12 -0.107 -0.414 0.639 -0.218 3.622 36.558 A A 1 2 9.073 B B 24 23 3.615 5.668 -0.421 0.214 AA_DC1DG2:DC23DG24_BB 1 -1.729 2.768 36.090 -0.529 0.406 3.220 37.114 A A 2 3 -3.467 B B 23 22 3.246 -2.206 0.614 0.547 AA_DG2DC3:DG22DC23_BB 2 0.731 -1.149 37.044 1.151 -0.869 3.204 29.996 A A 3 4 15.441 B B 22 21 3.095 7.901 -0.256 0.864 AA_DC3DG4:DC21DG22_BB 3 0.895 -1.749 28.946 0.073 0.676 3.360 39.517 A A 4 5 1.723 B B 21 20 3.354 1.165 -0.018 0.272 AA_DG4DA5:DT20DC21_BB 4 -1.033 1.529 39.487 0.261 -0.098 3.350 37.991 A A 5 6 4.390 B B 20 19 3.388 2.855 -0.180 -0.338 AA_DA5DA6:DT19DT20_BB 5 0.861 -1.324 37.878 -0.894 0.390 3.164 31.593 A A 6 7 -3.608 B B 19 18 3.135 -1.963 0.115 -0.588 AA_DA6DT7:DA18DT19_BB 6 -0.220 0.404 31.533 -0.729 -0.251 3.299 36.365 A A 7 8 0.239 B B 18 17 3.305 0.149 -0.027 -0.163 AA_DT7DT8:DA17DA18_BB 7 1.863 -2.987 36.318 -0.283 0.305 3.463 40.039 A A 8 9 -1.558 B B 17 16 3.462 -1.067 -0.130 -0.101 AA_DT8DC9:DG16DA17_BB 8 -0.029 0.042 40.025 -0.018 0.187 3.301 27.767 A A 9 10 11.025 B B 16 15 3.188 5.259 0.429 0.990 AA_DC9DG10:DC15DG16_BB 9 -0.902 1.892 27.260 0.795 -1.110 3.064 43.825 A A 10 11 -14.940 B B 15 14 3.192 -11.011 -1.181 0.662 AA_DG10DC11:DG14DC15_BB 10 -5.849 7.936 42.098 1.911 1.038 3.166 35.144 A A 11 12 5.250 B B 14 13 3.184 3.165 0.689 0.246 AA_DC11DG12:DC13DG14_BB 11 -1.359 2.253 34.980 -0.052 -1.338 citation repository Initial release Database references 1 0 2026-11-04 1 1 2026-11-11 _citation.pdbx_database_id_DOI _citation.title Not funded antonello.merlino@unina.it 0000-0002-1045-7720 Antonello Merlino principal investigator/group leader Crystal structure of carboplatinplatin/B-DNA adduct Crystal structure of oxaliplatin/B-DNA adduct N PDBE Y PDBE 2026-07-27 REL REL PT PT SUBJECT OF INVESTIGATION PT PLATINUM (II) ION MG MAGNESIUM ION HOH water 32630 synthetic construct sample 1 12 Y N 3U2N PDB experimental model PT 101 2 PT PT 101 A PT 102 2 PT PT 102 A MG 103 3 MG MG 103 A PT 101 2 PT PT 101 B PT 102 2 PT PT 102 B PT 103 2 PT PT 103 B HOH 201 4 HOH HOH 201 A HOH 204 4 HOH HOH 202 A HOH 205 4 HOH HOH 203 A HOH 202 4 HOH HOH 204 A HOH 203 4 HOH HOH 205 A HOH 202 4 HOH HOH 201 B HOH 203 4 HOH HOH 202 B HOH 204 4 HOH HOH 203 B HOH 201 4 HOH HOH 204 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DC 3 n 3 DC 3 A DG 4 n 4 DG 4 A DA 5 n 5 DA 5 A DA 6 n 6 DA 6 A DT 7 n 7 DT 7 A DT 8 n 8 DT 8 A DC 9 n 9 DC 9 A DG 10 n 10 DG 10 A DC 11 n 11 DC 11 A DG 12 n 12 DG 12 A DC 13 n 1 DC 13 B DG 14 n 2 DG 14 B DC 15 n 3 DC 15 B DG 16 n 4 DG 16 B DA 17 n 5 DA 17 B DA 18 n 6 DA 18 B DT 19 n 7 DT 19 B DT 20 n 8 DT 20 B DC 21 n 9 DC 21 B DG 22 n 10 DG 22 B DC 23 n 11 DC 23 B DG 24 n 12 DG 24 B author_and_software_defined_assembly PISA 2 dimeric none A HOH 201 I O HOH 1_555 A MG 103 E MG MG 1_555 A HOH 204 I O HOH 1_555 71.4 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 1 2.12 0.30 108.30 110.42 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -5.09 0.80 102.40 97.31 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 -6.42 0.90 105.70 99.28 B B B O5' P OP1 DA DA DA 17 17 17 N 1 2.46 0.30 108.30 110.76 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 2.07 0.30 108.30 110.37 B B B O4' C1' N9 DG DG DG 24 24 24 N 39.226 3.26 0.00 0.00 1.75 0.00 -5.02 0.957 0.950 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 0.23765 0.20428 0.20608 2.50 34.58 137 2368 5.5 99.25 9.533 0.210 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.612 0.279 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.50 34.58 9 501 6 486 0 0.005 0.011 544 1.875 1.790 836 0.091 0.200 94 0.012 0.020 252 4.555 3.890 544 9.508 47.29 931 0.326 0.301 2.565 12 162 20 98.86 2.50 40.62 32UT 2521 1.0 1 6.7 9.5 99.6 2.50 2.61 2.2 293 1.0 1 9.6 99.4 data reduction MOSFLM data scaling Aimless phasing PHASER refinement REFMAC 5.8.0430 data extraction PDB_EXTRACT N Crystal structure of iodoplatin/B-DNA adduct 1 N N 1 N N 2 N N 2 N N 3 N N 2 N N 2 N N 2 N N 4 N N 4 N N metalc 2.638 A DG 4 A N7 DG 4 1_555 A PT 101 C PT PT 1_555 metalc 2.186 A DG 10 A N7 DG 10 1_555 A PT 102 D PT PT 1_555 metalc 2.376 A MG 103 E MG MG 1_555 A HOH 201 I O HOH 1_555 metalc 2.398 A MG 103 E MG MG 1_555 A HOH 204 I O HOH 1_555 metalc 2.338 B DG 14 B N7 DG 2 1_555 B PT 102 G PT PT 1_555 metalc 2.355 B DG 16 B N7 DG 4 1_555 B PT 101 F PT PT 1_555 metalc 2.367 B DG 22 B N7 DG 10 1_555 B PT 103 H PT PT 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 DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 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 DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 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 DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 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 DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA DNA dodecamer, Dickerson duplex, platination, iodoplatin, Pt-DNA adduct, DNA 32UT PDB 1 1 32UT 1 12 32UT 1 12 32UT A 1 1 12 13 24 32UT 13 24 32UT B 1 1 12 19 P 21 21 21