0.015877 0.009166 0.000000 0.000000 0.018333 0.000000 0.000000 0.000000 0.022767 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 18 90.00 90.00 120.00 62.985 62.985 43.924 C10 H15 N2 O7 P S 338.274 n 2-thio-thymidine 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-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 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 Y 49 N N Y 50 N C Y 51 N N Y 52 N C Y 53 N C N 54 N N Y 55 N N Y 56 N C Y 57 N N Y 58 N C 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 H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 92 N C 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 H N 107 N O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 N C N 118 R C Y 119 N N Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N N Y 129 N C 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 P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C N 156 N N N 157 N C N 158 N O N 159 N N N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C 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 H N 178 N H N 179 N H N 180 N HG N 181 N O N 182 N H N 183 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 doub N 41 N sing 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 Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing Y 66 N sing Y 67 N doub N 68 N sing Y 69 N doub N 70 N sing N 71 N sing Y 72 N sing Y 73 N doub N 74 N sing Y 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub 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 Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing N 139 N sing Y 140 N doub N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N doub 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 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 doub N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing To Be Published 0353 DNA-Stabilized Triangular Mercury(II) Nanocluster 0000-0002-5682-3685 0000-0002-2150-7084 10.2210/pdb9vgx/pdb pdb_00009vgx 100 1 N PIXEL 2017-11-17 DECTRIS PILATUS 2M-F SINGLE WAVELENGTH M x-ray 1 1.0 1.0 AR-NE3A Photon Factory 1.0 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 3686.510 DNA (5'-D(*CP*GP*CP*GP*AP*XP*XP*TP*CP*GP*CP*G)-3') 3 syn polymer 200.590 MERCURY (II) ION 3 syn non-polymer 18.015 water 1 nat water no yes (DC)(DG)(DC)(DG)(DA)(A1AAZ)(A1AAZ)(DT)(DC)(DG)(DC)(DG) CGCGAXXTCGCG A,B,C polydeoxyribonucleotide n n n n n n n n n n n n 1 2.02 39.01 VAPOR DIFFUSION, HANGING DROP MOPS, Spermine, MPD, NaNO3 293 10.972 1 20 A 8 B 5 2.945 A_DT8:DA5_B 1 -20.569 -0.148 -0.357 -0.266 -13.796 1 19 A 9 B 4 1.778 A_DC9:DG4_B 2 -12.086 0.575 0.582 -0.339 2.924 1 19 A 10 B 3 3.626 A_DG10:DC3_B 3 -10.294 -0.383 0.390 -0.132 -2.419 1 19 A 11 B 2 -4.326 A_DC11:DG2_B 4 -5.157 -0.678 -0.383 -0.086 -14.058 1 20 B 8 C 5 12.390 B_DT8:DA5_C 5 -19.381 -0.675 -0.005 -0.103 -16.971 1 19 B 9 C 4 4.278 B_DC9:DG4_C 6 1.518 -0.070 0.033 0.206 8.704 1 19 B 10 C 3 -3.901 B_DG10:DC3_C 7 -1.033 0.741 0.544 -0.140 12.084 1 19 B 11 C 2 2.642 B_DC11:DG2_C 8 -7.097 0.722 0.349 -0.059 3.667 41.578 A A 8 9 7.738 B B 5 4 3.810 5.467 0.260 -0.474 AA_DT8DC9:DG4DA5_BB 1 -4.862 6.882 40.957 -1.335 -0.959 3.027 27.757 A A 9 10 11.269 B B 4 3 3.082 5.373 -0.266 0.039 AA_DC9DG10:DC3DG4_BB 2 0.548 -1.150 27.237 -1.139 0.680 3.283 38.170 A A 10 11 5.084 B B 3 2 3.383 3.314 -0.459 -0.151 AA_DG10DC11:DG2DC3_BB 3 4.536 -6.959 37.770 -0.659 1.288 3.367 32.372 B B 8 9 21.748 C C 5 4 3.379 11.847 -0.631 0.492 BB_DT8DC9:DG4DA5_CC 4 -2.309 4.238 30.093 -1.357 0.695 3.058 37.881 B B 9 10 13.019 C C 4 3 2.834 8.370 0.300 1.588 BB_DC9DG10:DC3DG4_CC 5 -4.248 6.607 36.742 1.463 -0.961 3.308 37.520 B B 10 11 -4.832 C C 3 2 3.352 -3.105 -0.254 0.480 BB_DG10DC11:DG2DC3_CC 6 -0.799 1.243 37.388 1.161 0.289 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 3 2 HG HG 101 B HG 1 2 HG HG 101 C HG 2 2 HG HG 102 C HOH 1 3 HOH HOH 201 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 NDR 6 n 6 A1AAZ 6 A NDR 7 n 7 A1AAZ 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 n 12 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 DT 8 n 8 DT 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 DT 8 n 8 DT 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 author_and_software_defined_assembly PISA 3 trimeric none 4930 -72 5740 A A1AAZ 6 A O4 A1AAZ 6 1_555 B HG 101 D HG HG 1_555 A DT 8 A O2 DT 8 1_555 81.8 A A1AAZ 6 A O4 A1AAZ 6 1_555 B HG 101 D HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 71.9 A DT 8 A O2 DT 8 1_555 B HG 101 D HG HG 1_555 B A1AAZ 6 B N3 A1AAZ 6 1_555 123.3 A A1AAZ 6 A N3 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 A A1AAZ 6 A S1 A1AAZ 6 1_555 67.7 A A1AAZ 6 A N3 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 C A1AAZ 7 C N3 A1AAZ 7 1_555 150.3 A A1AAZ 6 A S1 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 C A1AAZ 7 C N3 A1AAZ 7 1_555 105.0 A A1AAZ 6 A N3 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 139.5 A A1AAZ 6 A S1 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 118.8 C A1AAZ 7 C N3 A1AAZ 7 1_555 C HG 102 F HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 69.8 B A1AAZ 7 B N3 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 B A1AAZ 7 B S1 A1AAZ 7 1_555 66.8 B A1AAZ 7 B N3 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 130.4 B A1AAZ 7 B S1 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 C A1AAZ 7 C S1 A1AAZ 7 1_555 68.7 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 DG 12 A DG 12 1 Y 1 C DC 1 C DC 1 1 Y 1 1.94 0.30 108.30 110.24 B B B O4' C1' N1 DC DC DC 1 1 1 N 1 1.83 0.30 108.30 110.13 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 -5.15 0.80 102.40 97.25 C C C C3' C2' C1' DG DG DG 10 10 10 N 1 A A O3' C3' DA DA 5 5 -0.036 0.006 1.419 1.383 N 0.182 0.164 0.166 3.10 34.20 371 3551 10.450 99.9 0.300 1 FREE R-VALUE 1.380 SAD 19.540 0.90 1.10 ML FLAT BULK SOLVENT MODEL 3.10 34.20 1 692 3 688 0 0.009 767 1.360 1178 36.291 293 0.050 128 0.005 34 0.2450 0.2139 3.5400 122 1054 100.00 0.2332 0.1954 4.4600 122 1064 100.00 0.1286 0.1248 34.2000 127 1062 100.00 3.100 34.200 9VGX 3551 0.08000 1 14.3800 5.300 100.0 0.32700 3.10 3.18 1 refinement PHENIX (1.20.1_4487: ???) data scaling XSCALE data reduction XDS phasing AutoSol data extraction PDB_EXTRACT N DNA-Stabilized Triangular Mercury(II) Nanocluster 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 3 N N covale 1.597 both A DA 5 A O3' DA 5 1_555 A A1AAZ 6 A P A1AAZ 6 1_555 covale 1.611 one A A1AAZ 6 A O3' A1AAZ 6 1_555 A A1AAZ 7 A P A1AAZ 7 1_555 covale 1.598 one A A1AAZ 7 A O3' A1AAZ 7 1_555 A DT 8 A P DT 8 1_555 covale 1.606 both B DA 5 B O3' DA 5 1_555 B A1AAZ 6 B P A1AAZ 6 1_555 covale 1.615 one B A1AAZ 6 B O3' A1AAZ 6 1_555 B A1AAZ 7 B P A1AAZ 7 1_555 covale 1.612 one B A1AAZ 7 B O3' A1AAZ 7 1_555 B DT 8 B P DT 8 1_555 covale 1.600 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 1.598 one C A1AAZ 7 C O3' A1AAZ 7 1_555 C DT 8 C P DT 8 1_555 metalc 2.474 A A1AAZ 6 A O4 A1AAZ 6 1_555 B HG 101 D HG HG 1_555 metalc 2.540 A A1AAZ 6 A N3 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 metalc 2.303 A A1AAZ 6 A S1 A1AAZ 6 1_555 C HG 102 F HG HG 1_555 metalc 3.184 A DT 8 A O2 DT 8 1_555 B HG 101 D HG HG 1_555 metalc 2.466 B A1AAZ 6 B N3 A1AAZ 6 1_555 B HG 101 D HG HG 1_555 metalc 2.452 B A1AAZ 7 B N3 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 metalc 2.465 B A1AAZ 7 B S1 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 metalc 3.251 C A1AAZ 7 C S1 A1AAZ 7 1_555 C HG 101 E HG HG 1_555 metalc 2.274 C A1AAZ 7 C N3 A1AAZ 7 1_555 C HG 102 F HG HG 1_555 metalc 2.413 C A1AAZ 7 C S1 A1AAZ 7 1_555 C HG 102 F HG HG 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 5 B N6 DA 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 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 B DT 8 B N3 DT 8 1_555 C DA 5 C N1 DA 5 1_555 hydrog WATSON-CRICK B DT 8 B O4 DT 8 1_555 C DA 5 C N6 DA 5 1_555 hydrog WATSON-CRICK B DC 9 B N3 DC 9 1_555 C DG 4 C N1 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B N4 DC 9 1_555 C DG 4 C O6 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B O2 DC 9 1_555 C DG 4 C N2 DG 4 1_555 hydrog WATSON-CRICK B DG 10 B N1 DG 10 1_555 C DC 3 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B N2 DG 10 1_555 C DC 3 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B O6 DG 10 1_555 C DC 3 C N4 DC 3 1_555 hydrog WATSON-CRICK B DC 11 B N3 DC 11 1_555 C DG 2 C N1 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B N4 DC 11 1_555 C DG 2 C O6 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B O2 DC 11 1_555 C DG 2 C N2 DG 2 1_555 DNA Mercury, Nanocluster, DNA, X-ray analysis 9VGX PDB 1 1 9VGX 1 12 9VGX 1 12 9VGX A 1 1 12 1 12 9VGX 1 12 9VGX B 1 1 12 1 12 9VGX 1 12 9VGX C 1 1 12 152 P 31 2 1