0.027937 0.016129 0.000000 0.000000 0.032259 0.000000 0.000000 0.000000 0.016389 0.00000 0.00000 0.00000 0000-0002-5682-3685 Kondo, J. Kosugi, K. Sugawara, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 35.795 35.795 61.015 C10 H16 N3 O7 P S 353.289 4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-3-methoxy-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2-thione RNA linking Au 1 196.967 GOLD ION 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 N 1 R C N 2 N C N 3 R C N 4 R C N 5 N C N 6 R C N 7 N C N 8 N C N 9 N C N 10 N C N 11 N N N 12 N N N 13 N N N 14 N O N 15 N O N 16 N O N 17 N O N 18 N O N 19 N O N 20 N P N 21 N S N 22 N H 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 H N 39 N AU N 40 N O N 41 N P N 42 N O N 43 N O N 44 N O N 45 N C N 46 R C N 47 N O N 48 S C N 49 N O N 50 N C N 51 R C Y 52 N N Y 53 N C Y 54 N N Y 55 N C Y 56 N C N 57 N N Y 58 N N Y 59 N C Y 60 N N Y 61 N C 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 H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N O N 77 N P N 78 N O N 79 N O N 80 N O N 81 N C N 82 R C N 83 N O N 84 S C N 85 N O N 86 N C N 87 R C N 88 N N N 89 N C N 90 N O N 91 N N N 92 N C N 93 N N N 94 N C N 95 N C 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 H N 109 N H N 110 N O N 111 N P N 112 N O N 113 N O N 114 N O N 115 N C N 116 R C N 117 N O N 118 S C N 119 N O N 120 N C N 121 R C Y 122 N N Y 123 N C Y 124 N N Y 125 N C N 126 N C N 127 N O N 128 N N N 129 N C N 130 N N N 131 N N Y 132 N C 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 H N 145 N H N 146 N H N 147 N O N 148 N P N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 S C N 156 N O N 157 N C N 158 R C N 159 N N N 160 N C N 161 N O N 162 N N N 163 N C N 164 N O N 165 N C N 166 N C N 167 N C N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N doub N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub 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 doub 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 Y 63 N sing Y 64 N sing Y 65 N doub N 66 N sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N doub N 72 N sing N 73 N sing Y 74 N sing Y 75 N doub N 76 N sing Y 77 N sing N 78 N sing N 79 N sing N 80 N doub 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 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 doub N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub 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 Y 136 N sing Y 137 N sing Y 138 N doub N 139 N sing Y 140 N sing N 141 N sing Y 142 N doub N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing GE Chembiochem 1439-7633 26 e202500565 e202500565 10.1002/cbic.202500565 41078110 Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold. 2025 0000-0002-5682-3685 10.2210/pdb9uyt/pdb pdb_00009uyt 100 1 N PIXEL 2024-10-14 DECTRIS PILATUS3 S 6M SINGLE WAVELENGTH M x-ray 1 1.03932 1.0 BL-5A Photon Factory 1.03932 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 3715.552 DNA (5'-D(*GP*GP*AP*GP*TP*XP*XP*AP*CP*TP*CP*C)-3') 2 syn polymer 196.967 GOLD ION 2 syn non-polymer no yes (DG)(DG)(DA)(DG)(DT)(A1L9Q)(A1L9Q)(DA)(DC)(DT)(DC)(DC) GGAGTXXACTCC A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.59 52.45 VAPOR DIFFUSION, SITTING DROP MOPs, Spermine,KNO3,MPD 293 -9.234 1 19 A 1 B 12 -4.897 A_DG1:DC12_B 1 -14.573 -0.236 -0.095 -0.236 -8.956 1 19 A 2 B 11 0.304 A_DG2:DC11_B 2 -12.736 -0.254 0.012 -0.240 4.015 1 20 A 3 B 10 3.854 A_DA3:DT10_B 3 -14.931 0.401 0.264 -0.151 4.211 1 19 A 4 B 9 -1.027 A_DG4:DC9_B 4 -8.976 -0.161 0.334 -0.103 -0.613 1 20 A 5 B 8 6.858 A_DT5:DA8_B 5 -14.790 -0.480 0.148 -0.078 0.825 1 20 A 8 B 5 3.990 A_DA8:DT5_B 6 -6.792 0.205 0.075 -0.171 2.141 1 19 A 9 B 4 3.236 A_DC9:DG4_B 7 -2.015 0.294 0.282 -0.228 14.535 1 20 A 10 B 3 -4.618 A_DT10:DA3_B 8 -3.372 -0.061 -0.255 -0.258 13.795 1 19 A 11 B 2 -4.976 A_DC11:DG2_B 9 -1.744 0.146 -0.686 -0.162 11.495 1 19 A 12 B 1 -5.642 A_DC12:DG1_B 10 -5.055 0.375 -0.436 -0.326 3.113 35.915 A A 1 2 6.620 B B 12 11 3.281 4.071 -0.476 -1.576 AA_DG1DG2:DC11DC12_BB 1 -2.492 4.053 35.607 -3.127 0.422 3.082 32.472 A A 2 3 -0.068 B B 11 10 3.082 -0.038 -0.007 -0.875 AA_DG2DA3:DT10DC11_BB 2 -0.852 1.524 32.461 -1.558 -0.128 2.896 31.480 A A 3 4 11.534 B B 10 9 3.215 6.213 0.022 -1.293 AA_DA3DG4:DC9DT10_BB 3 -2.267 4.208 30.795 -3.479 -0.440 2.478 30.442 A A 4 5 24.327 B B 9 8 3.408 12.418 -0.116 -1.613 AA_DG4DT5:DA8DC9_BB 4 0.128 -0.250 27.848 -5.411 0.244 2.859 31.599 A A 8 9 15.742 B B 5 4 3.328 8.470 0.422 -1.272 AA_DA8DC9:DG4DT5_BB 5 -1.324 2.462 30.443 -3.850 -1.012 2.563 27.323 A A 9 10 12.994 B B 4 3 3.058 6.077 -0.644 -1.543 AA_DC9DT10:DA3DG4_BB 6 2.903 -6.208 26.495 -4.586 1.993 3.311 35.069 A A 10 11 3.261 B B 3 2 3.391 1.962 -0.366 -1.690 AA_DT10DC11:DG2DA3_BB 7 -2.487 4.132 34.930 -3.107 0.224 3.357 31.653 A A 11 12 6.392 B B 2 1 3.523 3.476 -0.225 -1.423 AA_DC11DC12:DG1DG2_BB 8 -2.701 4.967 31.353 -3.288 -0.114 citation repository Initial release Database references 1 0 2025-11-12 1 1 2025-11-19 _citation.journal_volume Japan Japan Agency for Medical Research and Development (AMED) j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ N PDBJ 2025-05-15 REL REL AU AU SUBJECT OF INVESTIGATION AU GOLD ION 32630 synthetic construct sample 1 12 Y N AU 2 2 AU AU 101 A AU 1 2 AU AU 101 B DG 1 n 1 DG 1 A DG 2 n 2 DG 2 A DA 3 n 3 DA 3 A DG 4 n 4 DG 4 A DT 5 n 5 DT 5 A TCY 6 n 6 A1L9Q 6 A TCY 7 n 7 A1L9Q 7 A DA 8 n 8 DA 8 A DC 9 n 9 DC 9 A DT 10 n 10 DT 10 A DC 11 n 11 DC 11 A DC 12 n 12 DC 12 A DG 1 n 1 DG 1 B DG 2 n 2 DG 2 B DA 3 n 3 DA 3 B DG 4 n 4 DG 4 B DT 5 n 5 DT 5 B TCY 6 n 6 A1L9Q 6 B TCY 7 n 7 A1L9Q 7 B DA 8 n 8 DA 8 B DC 9 n 9 DC 9 B DT 10 n 10 DT 10 B DC 11 n 11 DC 11 B DC 12 n 12 DC 12 B author_and_software_defined_assembly PISA 2 dimeric none 1470 -18 4340 A A1L9Q 6 A N3 A1L9Q 6 1_555 B AU 101 D AU AU 1_555 A A1L9Q 6 A S2 A1L9Q 6 1_555 60.3 A A1L9Q 6 A N3 A1L9Q 6 1_555 B AU 101 D AU AU 1_555 B A1L9Q 7 B S2 A1L9Q 7 1_555 154.9 A A1L9Q 6 A S2 A1L9Q 6 1_555 B AU 101 D AU AU 1_555 B A1L9Q 7 B S2 A1L9Q 7 1_555 142.9 A A1L9Q 7 A S2 A1L9Q 7 1_555 A AU 101 C AU AU 1_555 B A1L9Q 6 B N3 A1L9Q 6 1_555 157.8 A A1L9Q 7 A S2 A1L9Q 7 1_555 A AU 101 C AU AU 1_555 B A1L9Q 6 B S2 A1L9Q 6 1_555 139.7 B A1L9Q 6 B N3 A1L9Q 6 1_555 A AU 101 C AU AU 1_555 B A1L9Q 6 B S2 A1L9Q 6 1_555 59.4 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 0.2075 0.1738 0.1771 2.51 31.00 579 5925 9.77 99.51 0.11 1 FREE R-VALUE 2.00 SAD 33.30 0.90 1.10 ML FLAT BULK SOLVENT MODEL 2.51 31.00 0 490 2 488 0 0.009 544 1.064 834 16.567 208 0.039 94 0.005 24 0.3568 0.3384 2.77 152 1346 100.00 0.3672 0.2761 3.17 138 1316 100.00 0.2284 0.1812 3.98 150 1346 99.00 0.1352 0.1149 31.00 139 1338 100.00 2.51 31.0 9UYT 5946 1.0 0.031 0.034 1 31.27 5.2 99.9 0.321 2.51 2.58 456 0.947 0.36 1 0.187 2.58 2.65 402 0.98 0.21 1 0.175 2.65 2.73 440 0.988 0.194 1 0.131 2.73 2.81 400 0.993 0.145 1 0.1 2.81 2.9 378 0.996 0.111 1 0.085 2.90 3.0 392 0.998 0.094 1 0.043 3.00 3.12 358 0.999 0.048 1 0.034 3.12 3.25 388 1.0 0.037 1 0.026 3.25 3.39 298 1.0 0.029 1 0.027 3.39 3.56 345 0.999 0.031 1 0.026 3.56 3.75 294 1.0 0.029 1 0.026 3.75 3.98 313 1.0 0.029 1 0.023 3.98 4.25 230 1.0 0.025 1 0.025 4.25 4.59 268 0.999 0.028 1 0.027 4.59 5.03 248 0.999 0.03 1 0.028 5.03 5.62 196 0.998 0.031 1 0.026 5.62 6.49 192 0.999 0.029 1 0.025 6.49 7.95 168 0.999 0.028 1 0.026 7.95 11.24 114 0.999 0.029 1 0.025 11.24 31.0 66 0.999 0.028 1 refinement PHENIX (1.20.1_4487: ???) data scaling XSCALE data extraction PDB_EXTRACT phasing AutoSol N DNA duplex containing gold-mediated 2-thio-cytosine base pairs 1 N N 1 N N 2 N N 2 N N covale 1.598 one A DT 5 A O3' DT 5 1_555 A A1L9Q 6 A P A1L9Q 6 1_555 covale 1.605 none A A1L9Q 6 A O3' A1L9Q 6 1_555 A A1L9Q 7 A P A1L9Q 7 1_555 covale 1.609 one A A1L9Q 7 A O3' A1L9Q 7 1_555 A DA 8 A P DA 8 1_555 covale 1.602 one B DT 5 B O3' DT 5 1_555 B A1L9Q 6 B P A1L9Q 6 1_555 covale 1.607 none B A1L9Q 6 B O3' A1L9Q 6 1_555 B A1L9Q 7 B P A1L9Q 7 1_555 covale 1.599 one B A1L9Q 7 B O3' A1L9Q 7 1_555 B DA 8 B P DA 8 1_555 metalc 2.788 A A1L9Q 6 A N3 A1L9Q 6 1_555 B AU 101 D AU AU 1_555 metalc 2.344 A A1L9Q 6 A S2 A1L9Q 6 1_555 B AU 101 D AU AU 1_555 metalc 2.316 A A1L9Q 7 A S2 A1L9Q 7 1_555 A AU 101 C AU AU 1_555 metalc 2.796 A AU 101 C AU AU 1_555 B A1L9Q 6 B N3 A1L9Q 6 1_555 metalc 2.355 A AU 101 C AU AU 1_555 B A1L9Q 6 B S2 A1L9Q 6 1_555 metalc 2.442 B A1L9Q 7 B S2 A1L9Q 7 1_555 B AU 101 D AU AU 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 12 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 12 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 12 B N4 DC 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 11 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 10 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 10 B O4 DT 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 8 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 8 B N6 DA 8 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 5 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 5 B O4 DT 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 1 B N2 DG 1 1_555 DNA DNA, gold 9UYT PDB 1 1 9UYT 1 12 9UYT 1 12 9UYT A 1 1 12 1 12 9UYT 1 12 9UYT B 1 1 12 144 P 31