0.025786 0.000000 0.000000 0.000000 0.021149 0.000000 0.000000 0.000000 0.015025 0.00000 0.00000 0.00000 0000-0002-5682-3685 Kondo, J. Atsugi, T. 0000-0002-2150-7084 Ono, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 38.781 47.283 66.556 C10 H15 N2 O7 P S 338.274 n 2-thio-thymidine DNA linking C9 H12 Br N2 O8 P 387.078 n 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE 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 Hg 2 200.590 MERCURY (II) ION non-polymer H2 O 18.015 WATER non-polymer N 1 R C N 2 N C N 3 N C N 4 S 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 O N 14 N O N 15 N O N 16 N O N 17 N O N 18 N O N 19 N P N 20 N S N 21 N H 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 O N 35 N H N 36 N H N 37 N N N 38 N C N 39 N N N 40 N C N 41 N C N 42 N C N 43 N O N 44 N O N 45 N BR N 46 R C N 47 N C N 48 S C N 49 R C N 50 N O N 51 N O N 52 N C N 53 N O N 54 N P N 55 N O N 56 N O N 57 N O 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 O N 71 N P N 72 N O N 73 N O N 74 N O N 75 N C N 76 R C N 77 N O N 78 S C N 79 N O N 80 N C N 81 R C Y 82 N N Y 83 N C Y 84 N N Y 85 N C Y 86 N C N 87 N N Y 88 N N Y 89 N C Y 90 N N Y 91 N C N 92 N H N 93 N H 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 O N 107 N P N 108 N O N 109 N O N 110 N O N 111 N C N 112 R C N 113 N O N 114 S C N 115 N O N 116 N C N 117 R C N 118 N N N 119 N C N 120 N O N 121 N N N 122 N C N 123 N N N 124 N C N 125 N C N 126 N H N 127 N H N 128 N H 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 O N 141 N P N 142 N O N 143 N O N 144 N O N 145 N C N 146 R C N 147 N O N 148 S C N 149 N O N 150 N C N 151 R C Y 152 N N Y 153 N C Y 154 N N Y 155 N C N 156 N C N 157 N O N 158 N N N 159 N C N 160 N N N 161 N N Y 162 N C N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H 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 HG N 178 N O N 179 N H N 180 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 doub N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N doub N 13 N sing N 14 N sing N 15 N doub N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N doub 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 doub N 47 N doub 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 N 65 N sing N 66 N sing N 67 N doub N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing 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 Y 95 N sing Y 96 N sing Y 97 N doub N 98 N sing Y 99 N sing Y 100 N sing Y 101 N doub N 102 N sing Y 103 N doub N 104 N sing N 105 N sing Y 106 N sing Y 107 N doub N 108 N sing Y 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 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 doub N 136 N sing N 137 N doub N 138 N sing 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 sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing 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 Y 168 N sing Y 169 N sing Y 170 N doub N 171 N sing Y 172 N sing N 173 N sing Y 174 N doub N 175 N doub N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing To Be Published 0353 DNA-Stabilized Triangular Mercury(II) Nanocluster 0000-0002-5682-3685 0000-0002-2150-7084 10.2210/pdb9vgy/pdb pdb_00009vgy 100 1 N PIXEL 2016-12-10 DECTRIS PILATUS 2M SINGLE WAVELENGTH M x-ray 1 0.91915 1.0 BL-17A Photon Factory 0.91915 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 3751.380 DNA (5'-D(*CP*GP*CP*GP*AP*XP*XP*(BRU)P*CP*GP*CP*G)-3') 4 syn polymer 200.590 MERCURY (II) ION 6 syn non-polymer 18.015 water 62 nat water no yes (DC)(DG)(DC)(DG)(DA)(A1AAZ)(A1AAZ)(BRU)(DC)(DG)(DC)(DG) CGCGAXXUCGCG A,B,C,D polydeoxyribonucleotide n n n n n n n n n n n n 1 1.78 30.93 VAPOR DIFFUSION, HANGING DROP MOPS, Spermine, MPD, NaNO3 293 -4.812 1 19 B 9 A 4 2.030 B_DC9:DG4_A 1 -21.999 0.235 0.057 -0.147 1.028 1 19 B 10 A 3 -3.707 B_DG10:DC3_A 2 -4.161 -0.127 0.157 -0.313 -0.976 1 19 B 11 A 2 0.137 B_DC11:DG2_A 3 -0.669 0.198 0.236 -0.155 -3.306 1 19 C 2 D 11 -0.140 C_DG2:DC11_D 4 -5.026 -0.241 0.200 -0.204 -5.220 1 19 C 3 D 10 -2.354 C_DC3:DG10_D 5 -5.075 0.088 0.271 -0.197 2.460 1 19 C 4 D 9 0.407 C_DG4:DC9_D 6 -18.831 -0.227 0.170 -0.140 -3.760 C 6 D 8 -9.339 C_A1AAZ6:BRU8_D 7 -17.148 1.526 0.199 -0.756 3.659 C 8 D 6 -8.235 C_BRU8:A1AAZ6_D 8 -16.949 -1.349 0.217 -0.905 1.146 1 19 C 9 D 4 0.690 C_DC9:DG4_D 9 -20.743 0.371 0.029 -0.152 2.457 1 19 C 10 D 3 0.991 C_DG10:DC3_D 10 -4.409 -0.370 0.119 -0.147 5.150 1 19 C 11 D 2 -2.663 C_DC11:DG2_D 11 -13.807 0.238 0.207 -0.197 15.417 1 19 C 12 D 1 -1.580 C_DG12:DC1_D 12 6.986 -0.282 0.097 -0.263 3.920 A 8 B 6 -11.309 A_BRU8:A1AAZ6_B 13 -17.769 -1.678 0.400 -0.747 -2.793 1 19 A 9 B 4 -0.540 A_DC9:DG4_B 14 -19.014 0.284 0.365 -0.151 1.613 1 19 A 10 B 3 -0.203 A_DG10:DC3_B 15 -10.633 -0.354 0.351 -0.184 1.509 1 19 A 11 B 2 -0.873 A_DC11:DG2_B 16 5.792 0.334 0.019 -0.339 33.869 1 19 A 12 B 1 -2.820 A_DG12:DC1_B 17 2.036 -0.077 0.522 -0.019 3.386 30.522 B B 9 10 17.813 A A 4 3 3.268 9.237 0.626 0.899 BB_DC9DG10:DC3DG4_AA 1 -0.063 0.122 29.122 -0.207 -1.202 3.434 38.982 B B 10 11 -4.481 A A 3 2 3.455 -2.986 -0.319 0.308 BB_DG10DC11:DG2DC3_AA 2 -1.955 2.933 38.824 0.843 0.229 3.582 -70.205 B C 11 2 1.903 A D 2 11 3.549 -2.188 0.134 1.268 BC_DC11DG2:DC11DG2_DA 3 0.210 0.182 -70.175 -1.019 0.124 3.429 39.568 C C 2 3 -5.795 D D 11 10 3.476 -3.916 0.507 0.430 CC_DG2DC3:DG10DC11_DD 4 0.901 -1.333 39.371 1.121 -0.638 3.326 28.988 C C 3 4 18.958 D D 10 9 3.229 9.328 -0.615 0.848 CC_DC3DG4:DC9DG10_DD 5 0.235 -0.479 27.476 -0.426 1.282 3.414 35.812 C C 4 6 7.294 D D 9 8 3.485 4.473 -0.065 -0.386 CC_DG4A1AAZ6:BRU8DC9_DD 6 -1.198 1.954 35.521 -1.308 -0.076 4.578 73.084 C C 6 8 26.924 D D 8 6 6.162 31.282 -0.126 -2.982 CC_A1AAZ6BRU8:A1AAZ6BRU8_DD 7 0.294 -0.253 66.910 -4.273 0.123 3.370 36.071 C C 8 9 3.338 D D 6 4 3.391 2.064 0.155 -0.329 CC_BRU8DC9:DG4A1AAZ6_DD 8 2.455 -3.969 35.932 -0.834 0.110 3.530 33.072 C C 9 10 10.884 D D 4 3 3.260 6.149 1.302 1.119 CC_DC9DG10:DC3DG4_DD 9 3.691 -6.534 32.306 0.874 -1.632 3.244 40.402 C C 10 11 -3.937 D D 3 2 3.269 -2.717 -0.943 0.659 CC_DG10DC11:DG2DC3_DD 10 -1.148 1.663 40.299 1.259 1.236 3.207 33.734 C C 11 12 -6.029 D D 2 1 3.130 -3.481 1.720 1.174 CC_DC11DG12:DC1DG2_DD 11 4.871 -8.436 33.213 2.575 -2.193 3.333 35.915 A A 8 9 6.702 B B 6 4 3.422 4.124 -0.081 -0.592 AA_BRU8DC9:DG4A1AAZ6_BB 12 0.497 -0.808 35.681 -1.570 0.204 3.306 31.598 A A 9 10 16.540 B B 4 3 3.257 8.890 -0.466 0.675 AA_DC9DG10:DC3DG4_BB 13 0.750 -1.395 30.343 -0.448 0.999 3.474 39.926 A A 10 11 -3.520 B B 3 2 3.422 -2.399 1.319 0.807 AA_DG10DC11:DG2DC3_BB 14 3.716 -5.452 39.690 1.474 -1.480 2.697 30.032 A A 11 12 -5.424 B B 2 1 2.756 -2.807 -0.023 0.516 AA_DC11DG12:DC1DG2_BB 15 -0.484 0.936 29.900 1.477 -0.039 chem_comp_atom chem_comp_bond repository Initial release Data collection 1 0 2026-06-17 1 1 2026-07-01 _chem_comp_atom.atom_id _chem_comp_bond.atom_id_2 Japan Ministry of Education, Culture, Sports, Science and Technology (Japan) 17H03033 Japan Ministry of Education, Culture, Sports, Science and Technology (Japan) 21H01956 Japan Japan Agency for Medical Research and Development (AMED) JP23ama121014 j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ N PDBJ 2025-06-15 REL REL HG MERCURY (II) ION HOH water 32630 synthetic construct sample 1 12 Y N HG 1 2 HG HG 101 A HG 2 2 HG HG 102 A HG 3 2 HG HG 103 A HG 6 2 HG HG 101 C HG 4 2 HG HG 101 D HG 5 2 HG HG 102 D HOH 46 3 HOH HOH 201 A HOH 12 3 HOH HOH 202 A HOH 62 3 HOH HOH 203 A HOH 30 3 HOH HOH 204 A HOH 35 3 HOH HOH 205 A HOH 53 3 HOH HOH 206 A HOH 37 3 HOH HOH 207 A HOH 63 3 HOH HOH 208 A HOH 39 3 HOH HOH 209 A HOH 4 3 HOH HOH 210 A HOH 52 3 HOH HOH 211 A HOH 57 3 HOH HOH 212 A HOH 47 3 HOH HOH 213 A HOH 65 3 HOH HOH 214 A HOH 38 3 HOH HOH 215 A HOH 1 3 HOH HOH 101 B HOH 15 3 HOH HOH 102 B HOH 50 3 HOH HOH 103 B HOH 18 3 HOH HOH 104 B HOH 19 3 HOH HOH 105 B HOH 3 3 HOH HOH 106 B HOH 22 3 HOH HOH 107 B HOH 64 3 HOH HOH 108 B HOH 17 3 HOH HOH 109 B HOH 14 3 HOH HOH 110 B HOH 9 3 HOH HOH 111 B HOH 20 3 HOH HOH 112 B HOH 28 3 HOH HOH 113 B HOH 33 3 HOH HOH 114 B HOH 58 3 HOH HOH 115 B HOH 27 3 HOH HOH 116 B HOH 43 3 HOH HOH 201 C HOH 49 3 HOH HOH 202 C HOH 21 3 HOH HOH 203 C HOH 31 3 HOH HOH 204 C HOH 16 3 HOH HOH 205 C HOH 6 3 HOH HOH 206 C HOH 51 3 HOH HOH 207 C HOH 10 3 HOH HOH 208 C HOH 7 3 HOH HOH 209 C HOH 32 3 HOH HOH 210 C HOH 25 3 HOH HOH 211 C HOH 5 3 HOH HOH 212 C HOH 66 3 HOH HOH 213 C HOH 2 3 HOH HOH 201 D HOH 45 3 HOH HOH 202 D HOH 54 3 HOH HOH 203 D HOH 40 3 HOH HOH 204 D HOH 36 3 HOH HOH 205 D HOH 13 3 HOH HOH 206 D HOH 26 3 HOH HOH 207 D HOH 41 3 HOH HOH 208 D HOH 59 3 HOH HOH 209 D HOH 23 3 HOH HOH 210 D HOH 8 3 HOH HOH 211 D HOH 24 3 HOH HOH 212 D HOH 61 3 HOH HOH 213 D HOH 42 3 HOH HOH 214 D HOH 56 3 HOH HOH 215 D HOH 44 3 HOH HOH 216 D HOH 11 3 HOH HOH 217 D HOH 29 3 HOH HOH 218 D n 1 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 NDR 6 n 6 A1AAZ 6 A NDR 7 n 7 A1AAZ 7 A BRU 8 n 8 BRU 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 1 n 1 DC 1 B DG 2 n 2 DG 2 B DC 3 n 3 DC 3 B DG 4 n 4 DG 4 B DA 5 n 5 DA 5 B NDR 6 n 6 A1AAZ 6 B NDR 7 n 7 A1AAZ 7 B BRU 8 n 8 BRU 8 B DC 9 n 9 DC 9 B DG 10 n 10 DG 10 B DC 11 n 11 DC 11 B DG 12 n 12 DG 12 B n 1 1 C DG 2 n 2 DG 2 C DC 3 n 3 DC 3 C DG 4 n 4 DG 4 C DA 5 n 5 DA 5 C NDR 6 n 6 A1AAZ 6 C NDR 7 n 7 A1AAZ 7 C BRU 8 n 8 BRU 8 C DC 9 n 9 DC 9 C DG 10 n 10 DG 10 C DC 11 n 11 DC 11 C DG 12 n 12 DG 12 C DC 1 n 1 DC 1 D DG 2 n 2 DG 2 D DC 3 n 3 DC 3 D DG 4 n 4 DG 4 D DA 5 n 5 DA 5 D NDR 6 n 6 A1AAZ 6 D NDR 7 n 7 A1AAZ 7 D BRU 8 n 8 BRU 8 D DC 9 n 9 DC 9 D DG 10 n 10 DG 10 D DC 11 n 11 DC 11 D DG 12 n 12 DG 12 D author_defined_assembly 4 tetrameric none A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 A A1AAZ 6 A S1 A1AAZ 6 1_555 64.5 A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 A A1AAZ 7 A S1 A1AAZ 7 1_555 94.7 A A1AAZ 6 A S1 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 A A1AAZ 7 A S1 A1AAZ 7 1_555 106.7 A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B N3 BRU 8 1_555 128.1 A A1AAZ 6 A S1 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B N3 BRU 8 1_555 160.0 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 103 G HG HG 1_555 B BRU 8 B N3 BRU 8 1_555 88.8 A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O2 BRU 8 1_555 175.7 A A1AAZ 6 A S1 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O2 BRU 8 1_555 117.9 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O2 BRU 8 1_555 81.2 B BRU 8 B N3 BRU 8 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O2 BRU 8 1_555 50.8 A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 83.1 A A1AAZ 6 A S1 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 141.5 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 95.6 B BRU 8 B N3 BRU 8 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 45.1 B BRU 8 B O2 BRU 8 1_555 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 95.9 A A1AAZ 7 A N3 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 A A1AAZ 7 A S1 A1AAZ 7 1_555 60.1 A A1AAZ 7 A N3 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 B A1AAZ 7 B N3 A1AAZ 7 1_555 177.6 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 B A1AAZ 7 B N3 A1AAZ 7 1_555 120.5 A A1AAZ 7 A N3 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 120.6 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 73.2 B A1AAZ 7 B N3 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 58.3 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 A BRU 8 A O2 BRU 8 1_555 46.4 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 A BRU 8 A O4 BRU 8 1_555 50.0 A BRU 8 A O2 BRU 8 1_555 A HG 101 E HG HG 1_555 A BRU 8 A O4 BRU 8 1_555 96.4 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 128.9 A BRU 8 A O2 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 173.0 A BRU 8 A O4 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 79.1 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B S1 A1AAZ 6 1_555 160.7 A BRU 8 A O2 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B S1 A1AAZ 6 1_555 122.0 A BRU 8 A O4 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B S1 A1AAZ 6 1_555 137.7 B A1AAZ 6 B N3 A1AAZ 6 1_555 A HG 101 E HG HG 1_555 B A1AAZ 6 B S1 A1AAZ 6 1_555 64.0 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 87.1 A BRU 8 A O2 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 82.8 A BRU 8 A O4 BRU 8 1_555 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 92.5 B A1AAZ 6 B N3 A1AAZ 6 1_555 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 92.0 B A1AAZ 6 B S1 A1AAZ 6 1_555 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 108.1 C A1AAZ 6 C N3 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 C A1AAZ 6 C S1 A1AAZ 6 1_555 63.5 C A1AAZ 6 C N3 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 91.5 C A1AAZ 6 C S1 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 109.2 C A1AAZ 6 C N3 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O2 BRU 8 1_555 172.6 C A1AAZ 6 C S1 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O2 BRU 8 1_555 123.2 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O2 BRU 8 1_555 83.2 C A1AAZ 6 C N3 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O4 BRU 8 1_555 78.5 C A1AAZ 6 C S1 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O4 BRU 8 1_555 137.5 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O4 BRU 8 1_555 89.2 D BRU 8 D O2 BRU 8 1_555 D HG 101 I HG HG 1_555 D BRU 8 D O4 BRU 8 1_555 96.2 C A1AAZ 7 C N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 59.4 C A1AAZ 7 C N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 6 D O4 A1AAZ 6 1_555 102.7 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 6 D O4 A1AAZ 6 1_555 154.9 C A1AAZ 7 C N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D N3 A1AAZ 7 1_555 178.1 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D N3 A1AAZ 7 1_555 120.8 D A1AAZ 6 D O4 A1AAZ 6 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D N3 A1AAZ 7 1_555 76.5 C A1AAZ 7 C N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 120.3 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 74.6 D A1AAZ 6 D O4 A1AAZ 6 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 104.7 D A1AAZ 7 D N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 58.5 C BRU 8 C O2 BRU 8 1_555 C HG 101 H HG HG 1_555 C BRU 8 C O4 BRU 8 1_555 96.3 C BRU 8 C O2 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 6 D N3 A1AAZ 6 1_555 174.2 C BRU 8 C O4 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 6 D N3 A1AAZ 6 1_555 78.2 C BRU 8 C O2 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 6 D S1 A1AAZ 6 1_555 118.3 C BRU 8 C O4 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 6 D S1 A1AAZ 6 1_555 139.8 D A1AAZ 6 D N3 A1AAZ 6 1_555 C HG 101 H HG HG 1_555 D A1AAZ 6 D S1 A1AAZ 6 1_555 67.5 C BRU 8 C O2 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 84.0 C BRU 8 C O4 BRU 8 1_555 C HG 101 H HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 91.1 D A1AAZ 6 D N3 A1AAZ 6 1_555 C HG 101 H HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 94.0 D A1AAZ 6 D S1 A1AAZ 6 1_555 C HG 101 H HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 111.0 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 DC 1 A DC 1 1 Y 1 C DC 1 C DC 1 1 Y 1 -5.65 0.80 102.40 96.75 B B B C3' C2' C1' DG DG DG 10 10 10 N 1 2.20 0.30 108.30 110.50 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 1.84 0.30 108.30 110.14 C C C O4' C1' N9 DG DG DG 12 12 12 N 1 3.51 0.30 108.30 111.81 D D D O4' C1' N9 DG DG DG 10 10 10 N 1 B B O3' C3' DG DG 10 10 -0.037 0.006 1.419 1.382 N 0.204 0.169 0.173 1.91 38.55 1845 18409 10.020 99.9 0.150 1 FREE R-VALUE 1.420 SAD 18.790 0.90 1.10 ML FLAT BULK SOLVENT MODEL 1.91 38.55 62 1004 6 936 0 0.010 1044 1.692 1604 32.727 374 0.075 170 0.013 46 0.2446 0.1722 1.9600 135 1261 99.00 0.2071 0.1665 2.0200 137 1286 100.00 0.2171 0.1702 2.0800 137 1275 100.00 0.2012 0.1648 2.1600 142 1298 100.00 0.1840 0.1675 2.2400 147 1258 100.00 0.1995 0.1664 2.3400 143 1273 100.00 0.1891 0.1760 2.4700 141 1281 100.00 0.1977 0.1708 2.6200 144 1283 100.00 0.2589 0.1964 2.8200 141 1271 100.00 0.2337 0.2234 3.1100 146 1259 100.00 0.2211 0.1639 3.5600 146 1275 100.00 0.1946 0.1565 4.4800 141 1269 100.00 0.1695 0.1470 38.5500 145 1275 100.00 1.910 38.600 9VGY 18414 0.06200 1 19.7900 6.800 99.9 0.25200 1.91 1.96 1 refinement PHENIX (1.20.1_4487: ???) data scaling XSCALE phasing AutoSol data extraction PDB_EXTRACT N DNA duplex containing Mercury(II)-mediated base pairs with 2-Thiothymine and 5-bromouracyl 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N 3 N N 3 N N covale 1.607 both A DA 5 A O3' DA 5 1_555 A A1AAZ 6 A P A1AAZ 6 1_555 covale 1.597 one A A1AAZ 6 A O3' A1AAZ 6 1_555 A A1AAZ 7 A P A1AAZ 7 1_555 covale 1.601 one A A1AAZ 7 A O3' A1AAZ 7 1_555 A BRU 8 A P BRU 8 1_555 covale 1.609 both A BRU 8 A O3' BRU 8 1_555 A DC 9 A P DC 9 1_555 covale 1.605 both B DA 5 B O3' DA 5 1_555 B A1AAZ 6 B P A1AAZ 6 1_555 covale 1.623 one B A1AAZ 6 B O3' A1AAZ 6 1_555 B A1AAZ 7 B P A1AAZ 7 1_555 covale 1.608 one B A1AAZ 7 B O3' A1AAZ 7 1_555 B BRU 8 B P BRU 8 1_555 covale 1.607 both B BRU 8 B O3' BRU 8 1_555 B DC 9 B P DC 9 1_555 covale 1.614 both C DA 5 C O3' DA 5 1_555 C A1AAZ 6 C P A1AAZ 6 1_555 covale 1.605 one C A1AAZ 6 C O3' A1AAZ 6 1_555 C A1AAZ 7 C P A1AAZ 7 1_555 covale 1.616 one C A1AAZ 7 C O3' A1AAZ 7 1_555 C BRU 8 C P BRU 8 1_555 covale 1.608 both C BRU 8 C O3' BRU 8 1_555 C DC 9 C P DC 9 1_555 covale 1.612 both D DA 5 D O3' DA 5 1_555 D A1AAZ 6 D P A1AAZ 6 1_555 covale 1.613 one D A1AAZ 6 D O3' A1AAZ 6 1_555 D A1AAZ 7 D P A1AAZ 7 1_555 covale 1.615 one D A1AAZ 7 D O3' A1AAZ 7 1_555 D BRU 8 D P BRU 8 1_555 covale 1.606 both D BRU 8 D O3' BRU 8 1_555 D DC 9 D P DC 9 1_555 metalc 2.714 A A1AAZ 6 A N3 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 metalc 2.415 A A1AAZ 6 A S1 A1AAZ 6 1_555 A HG 103 G HG HG 1_555 metalc 2.169 A A1AAZ 7 A N3 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 metalc 3.057 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 102 F HG HG 1_555 metalc 2.788 A A1AAZ 7 A S1 A1AAZ 7 1_555 A HG 103 G HG HG 1_555 metalc 2.056 A BRU 8 A N3 BRU 8 1_555 A HG 101 E HG HG 1_555 metalc 3.192 A BRU 8 A O2 BRU 8 1_555 A HG 101 E HG HG 1_555 metalc 2.962 A BRU 8 A O4 BRU 8 1_555 A HG 101 E HG HG 1_555 metalc 2.761 A HG 101 E HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 metalc 2.458 A HG 101 E HG HG 1_555 B A1AAZ 6 B S1 A1AAZ 6 1_555 metalc 2.886 A HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 metalc 2.231 A HG 102 F HG HG 1_555 B A1AAZ 7 B N3 A1AAZ 7 1_555 metalc 3.046 A HG 102 F HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 metalc 2.015 A HG 103 G HG HG 1_555 B BRU 8 B N3 BRU 8 1_555 metalc 2.968 A HG 103 G HG HG 1_555 B BRU 8 B O2 BRU 8 1_555 metalc 3.187 A HG 103 G HG HG 1_555 B BRU 8 B O4 BRU 8 1_555 metalc 2.733 C A1AAZ 6 C N3 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 metalc 2.346 C A1AAZ 6 C S1 A1AAZ 6 1_555 D HG 101 I HG HG 1_555 metalc 2.807 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 101 I HG HG 1_555 metalc 2.168 C A1AAZ 7 C N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 metalc 2.972 C A1AAZ 7 C S1 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 metalc 3.054 C BRU 8 C O2 BRU 8 1_555 C HG 101 H HG HG 1_555 metalc 3.147 C BRU 8 C O4 BRU 8 1_555 C HG 101 H HG HG 1_555 metalc 2.550 C HG 101 H HG HG 1_555 D A1AAZ 6 D N3 A1AAZ 6 1_555 metalc 2.413 C HG 101 H HG HG 1_555 D A1AAZ 6 D S1 A1AAZ 6 1_555 metalc 2.803 C HG 101 H HG HG 1_555 D A1AAZ 7 D S1 A1AAZ 7 1_555 metalc 3.155 D A1AAZ 6 D O4 A1AAZ 6 1_555 D HG 102 J HG HG 1_555 metalc 2.188 D A1AAZ 7 D N3 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 metalc 3.034 D A1AAZ 7 D S1 A1AAZ 7 1_555 D HG 102 J HG HG 1_555 metalc 3.083 D BRU 8 D O2 BRU 8 1_555 D HG 101 I HG HG 1_555 metalc 3.086 D BRU 8 D O4 BRU 8 1_555 D HG 101 I HG HG 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 TYPE_4_PAIR A DG 2 A N2 DG 2 1_555 D DG 12 D N3 DG 12 1_555 hydrog TYPE_4_PAIR A DG 2 A N3 DG 2 1_555 D DG 12 D N2 DG 12 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 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 BRU-A1AAZ MISPAIR A BRU 8 A O4 BRU 8 1_555 B A1AAZ 6 B N3 A1AAZ 6 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 DG 10 A N1 DG 10 1_555 B DC 3 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 3 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 3 B N4 DC 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 DG 12 A N1 DG 12 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 1 B N4 DC 1 1_555 hydrog TYPE_4_PAIR B DG 12 B N2 DG 12 1_555 C DG 2 C N3 DG 2 1_555 hydrog TYPE_4_PAIR B DG 12 B N3 DG 12 1_555 C DG 2 C N2 DG 2 1_555 hydrog WATSON-CRICK C DG 2 C N1 DG 2 1_555 D DC 11 D N3 DC 11 1_555 hydrog WATSON-CRICK C DG 2 C N2 DG 2 1_555 D DC 11 D O2 DC 11 1_555 hydrog WATSON-CRICK C DG 2 C O6 DG 2 1_555 D DC 11 D N4 DC 11 1_555 hydrog WATSON-CRICK C DC 3 C N3 DC 3 1_555 D DG 10 D N1 DG 10 1_555 hydrog WATSON-CRICK C DC 3 C N4 DC 3 1_555 D DG 10 D O6 DG 10 1_555 hydrog WATSON-CRICK C DC 3 C O2 DC 3 1_555 D DG 10 D N2 DG 10 1_555 hydrog WATSON-CRICK C DG 4 C N1 DG 4 1_555 D DC 9 D N3 DC 9 1_555 hydrog WATSON-CRICK C DG 4 C N2 DG 4 1_555 D DC 9 D O2 DC 9 1_555 hydrog WATSON-CRICK C DG 4 C O6 DG 4 1_555 D DC 9 D N4 DC 9 1_555 hydrog A1AAZ-BRU MISPAIR C A1AAZ 6 C N3 A1AAZ 6 1_555 D BRU 8 D O4 BRU 8 1_555 hydrog BRU-A1AAZ MISPAIR C BRU 8 C O4 BRU 8 1_555 D A1AAZ 6 D N3 A1AAZ 6 1_555 hydrog WATSON-CRICK C DC 9 C N3 DC 9 1_555 D DG 4 D N1 DG 4 1_555 hydrog WATSON-CRICK C DC 9 C N4 DC 9 1_555 D DG 4 D O6 DG 4 1_555 hydrog WATSON-CRICK C DC 9 C O2 DC 9 1_555 D DG 4 D N2 DG 4 1_555 hydrog WATSON-CRICK C DG 10 C N1 DG 10 1_555 D DC 3 D N3 DC 3 1_555 hydrog WATSON-CRICK C DG 10 C N2 DG 10 1_555 D DC 3 D O2 DC 3 1_555 hydrog WATSON-CRICK C DG 10 C O6 DG 10 1_555 D DC 3 D N4 DC 3 1_555 hydrog WATSON-CRICK C DC 11 C N3 DC 11 1_555 D DG 2 D N1 DG 2 1_555 hydrog WATSON-CRICK C DC 11 C N4 DC 11 1_555 D DG 2 D O6 DG 2 1_555 hydrog WATSON-CRICK C DC 11 C O2 DC 11 1_555 D DG 2 D N2 DG 2 1_555 hydrog WATSON-CRICK C DG 12 C N1 DG 12 1_555 D DC 1 D N3 DC 1 1_555 hydrog WATSON-CRICK C DG 12 C N2 DG 12 1_555 D DC 1 D O2 DC 1 1_555 hydrog WATSON-CRICK C DG 12 C O6 DG 12 1_555 D DC 1 D N4 DC 1 1_555 DNA Mercury, metal-mediated base pair, DNA, X-ray analysis 9VGY PDB 1 1 9VGY 1 12 9VGY 1 12 9VGY A 1 1 12 1 12 9VGY 1 12 9VGY B 1 1 12 1 12 9VGY 1 12 9VGY C 1 1 12 1 12 9VGY 1 12 9VGY D 1 1 12 19 P 21 21 21