0.023635 0.000000 0.000000 0.000000 0.023635 0.000000 0.000000 0.000000 0.041135 0.00000 0.00000 0.00000 Zhang, W. Coronado, G. Huang, Z. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 42.310 42.310 24.310 C11 H17 N2 O8 P Se 415.195 n 5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE) DNA linking 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 H2 O 18.015 WATER 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 N N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N O N 13 N C N 14 N C N 15 R C N 16 N C N 17 R C N 18 N O N 19 R C N 20 R C N 21 N SE N 22 N C N 23 N O 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 H N 38 N H N 39 N H N 40 N H N 41 N O N 42 N P N 43 N O N 44 N O N 45 N O N 46 N C N 47 R C N 48 N O N 49 S C N 50 N O N 51 N C N 52 R C Y 53 N N Y 54 N C Y 55 N N Y 56 N C Y 57 N C N 58 N N Y 59 N N Y 60 N C Y 61 N N Y 62 N C 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 H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N O N 78 N P N 79 N O N 80 N O N 81 N O N 82 N C N 83 R C N 84 N O N 85 S C N 86 N O N 87 N C N 88 R C N 89 N N N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N C N 96 N C 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 H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 N C N 122 R C Y 123 N N Y 124 N C Y 125 N N Y 126 N C N 127 N C N 128 N O N 129 N N N 130 N C N 131 N N N 132 N N Y 133 N C 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 H N 145 N H N 146 N H N 147 N H N 148 N O N 149 N H N 150 N H N 151 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 doub N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N doub N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N doub 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 sing Y 65 N sing Y 66 N sing Y 67 N doub N 68 N sing Y 69 N sing Y 70 N sing Y 71 N doub N 72 N sing Y 73 N doub N 74 N sing N 75 N sing Y 76 N sing Y 77 N doub N 78 N sing Y 79 N sing N 80 N sing N 81 N sing N 82 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub 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 Y 138 N sing Y 139 N sing Y 140 N doub N 141 N sing Y 142 N sing N 143 N sing Y 144 N doub N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing To be Published 0353 DNA octamer D (GTseGTACAC) partially crosslinked with platinum 10.2210/pdb4h5a/pdb pdb_00004h5a 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 99 1 CCD 2012-07-13 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 0.9795 1.0 8.2.2 ALS 0.9795 SYNCHROTRON ALS BEAMLINE 8.2.2 short DNA 8mer with Se modification 2520.592 DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3') 1 syn polymer 195.078 PLATINUM (II) ION 1 syn non-polymer 18.015 water 36 nat water no yes (DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC) GTGGCCAC A polydeoxyribonucleotide n n n n n n n n 5 2.16 43.01 VAPOR DIFFUSION, HANGING DROP 6.8 the platinum was added to the crystallization buffer , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 -20.786 1 19 A 1 A 8 1.784 A_DG1:DC8_A 1 -9.164 -0.381 -0.355 -0.011 -7.576 1 20 A 2 A 7 -1.021 A_2ST2:DA7_A 2 -12.387 -0.169 0.126 -0.105 -5.038 1 19 A 3 A 6 -1.523 A_DG3:DC6_A 3 -11.692 -0.220 0.134 -0.218 -5.367 1 19 A 4 A 5 -0.746 A_DG4:DC5_A 4 -14.376 -0.176 0.099 -0.079 5.367 1 19 A 5 A 4 -0.746 A_DC5:DG4_A 5 -14.375 0.176 0.099 -0.079 5.038 1 19 A 6 A 3 -1.523 A_DC6:DG3_A 6 -11.692 0.220 0.134 -0.218 7.576 1 20 A 7 A 2 -1.021 A_DA7:2ST2_A 7 -12.387 0.169 0.126 -0.105 20.786 1 19 A 8 A 1 1.784 A_DC8:DG1_A 8 -9.164 0.381 -0.355 -0.011 2.660 32.592 A A 1 2 16.935 A A 8 7 3.074 9.366 -0.047 -1.014 AA_DG12ST2:DA7DC8_AA 1 -2.722 4.922 31.136 -3.270 -0.342 2.619 30.493 A A 2 3 17.549 A A 7 6 3.143 9.093 0.599 -1.409 AA_2ST2DG3:DC6DA7_AA 2 1.423 -2.747 29.102 -4.314 -0.883 2.928 35.859 A A 3 4 9.713 A A 6 5 3.224 5.948 0.375 -1.701 AA_DG3DG4:DC5DC6_AA 3 2.924 -4.774 35.261 -3.572 -0.211 2.914 29.538 A A 4 5 9.034 A A 5 4 3.111 4.588 0.000 -1.061 AA_DG4DC5:DG4DC5_AA 4 0.000 0.000 29.187 -2.984 0.000 2.928 35.859 A A 5 6 9.713 A A 4 3 3.224 5.948 -0.375 -1.701 AA_DC5DC6:DG3DG4_AA 5 -2.924 4.774 35.261 -3.572 0.211 2.619 30.493 A A 6 7 17.549 A A 3 2 3.143 9.093 -0.599 -1.409 AA_DC6DA7:2ST2DG3_AA 6 -1.423 2.747 29.102 -4.314 0.883 2.660 32.592 A A 7 8 16.935 A A 2 1 3.074 9.366 0.047 -1.014 AA_DA7DC8:DG12ST2_AA 7 2.722 -4.922 31.136 -3.270 0.342 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Data collection Database references Derived calculations 1 0 2012-10-03 1 1 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Se-DNA without platinum crosslinked RCSB Y RCSB 2012-09-18 REL REL PT PLATINUM (II) ION HOH water PT 1 2 PT PT 101 A HOH 1 3 HOH HOH 201 A HOH 2 3 HOH HOH 202 A HOH 3 3 HOH HOH 203 A HOH 4 3 HOH HOH 204 A HOH 5 3 HOH HOH 205 A HOH 6 3 HOH HOH 206 A HOH 7 3 HOH HOH 207 A HOH 8 3 HOH HOH 208 A HOH 10 3 HOH HOH 209 A HOH 11 3 HOH HOH 210 A HOH 14 3 HOH HOH 211 A HOH 18 3 HOH HOH 212 A HOH 19 3 HOH HOH 213 A HOH 20 3 HOH HOH 214 A HOH 21 3 HOH HOH 215 A HOH 22 3 HOH HOH 216 A HOH 23 3 HOH HOH 217 A HOH 24 3 HOH HOH 218 A HOH 25 3 HOH HOH 219 A HOH 26 3 HOH HOH 220 A HOH 27 3 HOH HOH 221 A HOH 28 3 HOH HOH 222 A HOH 29 3 HOH HOH 223 A HOH 32 3 HOH HOH 224 A HOH 33 3 HOH HOH 225 A HOH 35 3 HOH HOH 226 A HOH 36 3 HOH HOH 227 A HOH 37 3 HOH HOH 228 A HOH 39 3 HOH HOH 229 A HOH 41 3 HOH HOH 230 A HOH 46 3 HOH HOH 231 A HOH 47 3 HOH HOH 232 A HOH 48 3 HOH HOH 233 A HOH 49 3 HOH HOH 234 A HOH 50 3 HOH HOH 235 A HOH 51 3 HOH HOH 236 A G 1 n 1 DG 1 A 2ST 2 n 2 2ST 2 A G 3 n 3 DG 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A author_and_software_defined_assembly PISA 2 dimeric 2210 -30 2880 A 2ST 2 A 2ST 2 DT 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 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_554 -y,-x,-z-1/2 crystal symmetry operation 0.0000000000 0.0000000000 -12.1550000000 1 A HOH 234 C HOH 1 A A O O HOH HOH 209 223 1.79 1 A A OP2 O DG HOH 3 231 1.94 1 A A O O HOH HOH 222 223 2.00 1 A A O O HOH HOH 227 231 2.11 1 A A O3' P 2ST DG 2 3 1.77 1 7.36 1.20 115.70 123.06 A A A C5' C4' C3' DG DG DG 3 3 3 N 1 -10.33 0.70 102.20 91.87 A A A C4' C3' C2' DG DG DG 3 3 3 N 1 2.34 0.30 108.30 110.64 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 5.42 0.50 128.60 134.02 A A A N3 C4 C5 DG DG DG 3 3 3 N 1 -4.13 0.50 104.30 100.17 A A A C5 N7 C8 DG DG DG 3 3 3 N 1 4.68 0.50 113.10 117.78 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -4.15 0.60 126.00 121.85 A A A N3 C4 N9 DG DG DG 3 3 3 N 1 -4.23 0.40 104.50 100.27 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 -4.86 0.70 121.90 117.04 A A A N3 C2 O2 DC DC DC 5 5 5 N 1 -2.40 0.40 104.50 102.10 A A A O4' C4' C3' DC DC DC 6 6 6 N 1 -2.55 0.40 121.90 119.35 A A A N3 C4 C5 DC DC DC 6 6 6 N 1 5.17 0.70 121.90 127.07 A A A N3 C2 O2 DC DC DC 6 6 6 N 1 -2.94 0.40 104.50 101.56 A A A O4' C4' C3' DA DA DA 7 7 7 N 1 4.18 0.60 118.60 122.78 A A A C6 N1 C2 DA DA DA 7 7 7 N 1 -3.95 0.50 129.30 125.35 A A A N1 C2 N3 DA DA DA 7 7 7 N 1 -2.73 0.40 105.80 103.07 A A A N9 C4 C5 DA DA DA 7 7 7 N 1 4.42 0.60 118.60 123.02 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 5.83 0.90 103.10 108.93 A A A C4' C3' C2' DC DC DC 8 8 8 N 1 -6.68 0.70 119.20 112.52 A A A N1 C2 N3 DC DC DC 8 8 8 N 1 5.47 0.50 119.90 125.37 A A A C2 N3 C4 DC DC DC 8 8 8 N 1 4.28 0.70 121.90 126.18 A A A N3 C2 O2 DC DC DC 8 8 8 N 1 A A O3' P 2ST DG 2 3 0.160 0.012 1.607 1.767 Y 1 A A C5 N7 DG DG 3 3 0.044 0.006 1.388 1.432 N 1 A A N3 C4 DC DC 8 8 -0.043 0.007 1.335 1.292 N 1 A A O O HOH HOH 224 232 1.98 1_555 7_655 19.524 -0.02 0.00 0.00 -0.02 0.00 0.03 0.956 0.940 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.23708 0.21187 0.21317 1.42 21.08 206 4265 4.6 99.25 1.458 0.057 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.074 0.074 0.80 0.80 1.40 MAXIMUM LIKELIHOOD MASK 1.42 21.08 36 200 1 163 0 0.027 0.021 180 3.145 3.000 271 0.437 0.200 32 0.029 0.020 84 2.456 3.000 180 3.151 4.500 271 0.457 0.402 1.455 20 293 20 96.01 1.42 21.08 4H5A 4265 0.091 1 17.93 12.5 0.584 1.42 1.47 3.73 1 9.5 99.5 data collection HKL-2000 phasing PHASES refinement REFMAC 5.5.0110 data reduction HKL-2000 data scaling HKL-2000 DNA octamer D (GTseGTACAC) partially crosslinked with platinum 1 N N 2 N N 3 N N covale 1.625 both A DG 1 A O3' DG 1 1_555 A 2ST 2 A P 2ST 2 1_555 covale 1.767 both A 2ST 2 A O3' 2ST 2 1_555 A DG 3 A P DG 3 1_555 metalc 2.175 A DG 4 A N7 DG 4 1_555 A PT 101 B PT PT 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 8 A N3 DC 8 8_554 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 8 A O2 DC 8 8_554 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 8 A N4 DC 8 8_554 hydrog WATSON-CRICK A 2ST 2 A N3 2ST 2 1_555 A DA 7 A N1 DA 7 8_554 hydrog WATSON-CRICK A 2ST 2 A O4 2ST 2 1_555 A DA 7 A N6 DA 7 8_554 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 A DC 6 A N3 DC 6 8_554 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 A DC 6 A O2 DC 6 8_554 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 A DC 6 A N4 DC 6 8_554 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 5 A N3 DC 5 8_554 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 5 A O2 DC 5 8_554 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 5 A N4 DC 5 8_554 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 4 A N1 DG 4 8_554 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 4 A O6 DG 4 8_554 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 4 A N2 DG 4 8_554 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 3 A N1 DG 3 8_554 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 3 A O6 DG 3 8_554 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 3 A N2 DG 3 8_554 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 A 2ST 2 A N3 2ST 2 8_554 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 A 2ST 2 A O4 2ST 2 8_554 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 A DG 1 A N1 DG 1 8_554 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 A DG 1 A O6 DG 1 8_554 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 A DG 1 A N2 DG 1 8_554 DNA selenium modification to facilitate crystallization, DNA 4H5A PDB 1 4H5A 1 8 4H5A 1 8 4H5A A 1 1 8 BINDING SITE FOR RESIDUE PT A 101 A PT 101 Software 2 A DG 4 A DG 4 2 1_555 A HOH 220 C HOH 2 1_555 96 P 43 21 2