1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schmidt, O.P. Jurt, S. Johannsen, S. Karimi, A. Sigel, R.K.O. Luedtke, N.W. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 UK Nat Commun 2041-1723 10 4818 4818 10.1038/s41467-019-12440-x 31645548 Concerted dynamics of metallo-base pairs in an A/B-form helical transition. 2019 0000-0001-7973-8996 4255.778 DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major 2 syn polymer 200.590 MERCURY (II) ION 2 syn non-polymer no no (DC)(DG)(DT)(DC)(DT)(DC)(DA)(DT)(DG)(DA)(DT)(DA)(DC)(DG) CGTCTCATGATACG A,B polydeoxyribonucleotide n n n n n n n n n n n n n n 0.955 1 19 A 1 B 28 3.081 A_DC1:DG28_B 1 -8.233 0.360 -0.165 -0.196 4.851 1 19 A 2 B 27 -1.494 A_DG2:DC27_B 2 -5.618 0.094 0.128 -0.212 -0.868 1 20 A 3 B 26 -0.285 A_DT3:DA26_B 3 -13.461 0.033 -0.043 -0.188 -4.534 1 20 A 5 B 24 0.212 A_DT5:DA24_B 4 -20.410 -0.072 0.139 -0.153 -3.347 1 19 A 6 B 23 -0.522 A_DC6:DG23_B 5 -11.118 0.211 0.135 -0.238 -1.111 1 20 A 7 B 22 -2.534 A_DA7:DT22_B 6 -11.301 0.165 0.055 -0.092 1.521 1 20 A 8 B 21 -2.528 A_DT8:DA21_B 7 -10.773 -0.176 0.042 -0.095 3.792 1 19 A 9 B 20 -0.591 A_DG9:DC20_B 8 -11.153 -0.219 0.155 -0.242 4.330 1 20 A 10 B 19 0.182 A_DA10:DT19_B 9 -20.640 0.059 0.125 -0.151 0.574 1 20 A 12 B 17 -0.164 A_DA12:DT17_B 10 -13.519 -0.027 -0.064 -0.180 -4.774 1 19 A 13 B 16 -1.391 A_DC13:DG16_B 11 -6.074 -0.066 0.106 -0.205 -0.607 1 19 A 14 B 15 3.275 A_DG14:DC15_B 12 -8.213 -0.358 -0.157 -0.190 3.423 36.114 A A 1 2 9.800 B B 28 27 3.392 6.047 -0.079 0.465 AA_DC1DG2:DC27DG28_BB 1 -1.545 2.503 35.588 -0.146 -0.102 3.250 32.317 A A 2 3 10.990 B B 27 26 3.425 6.080 0.019 -0.621 AA_DG2DT3:DA26DC27_BB 2 1.603 -2.897 31.716 -2.225 0.258 5.775 72.107 A A 3 5 11.224 B B 26 24 5.981 13.153 -0.082 -0.778 AA_DT3DT5:DA24DA26_BB 3 2.905 -2.479 71.006 -1.457 0.245 3.206 36.924 A A 5 6 1.530 B B 24 23 3.211 0.969 -0.053 -0.133 AA_DT5DC6:DG23DA24_BB 4 0.395 -0.623 36.910 -0.338 0.137 3.230 37.614 A A 6 7 9.427 B B 23 22 3.226 6.053 0.150 0.268 AA_DC6DA7:DT22DG23_BB 5 0.607 -0.945 37.136 -0.366 -0.155 3.121 31.752 A A 7 8 -5.771 B B 22 21 3.066 -3.152 0.000 -0.716 AA_DA7DT8:DA21DT22_BB 6 0.079 -0.144 31.600 -0.761 0.014 3.235 37.613 A A 8 9 9.117 B B 21 20 3.229 5.855 -0.148 0.269 AA_DT8DG9:DC20DA21_BB 7 -0.762 1.187 37.163 -0.341 0.131 3.232 36.894 A A 9 10 1.737 B B 20 19 3.237 1.099 0.058 -0.137 AA_DG9DA10:DT19DC20_BB 8 -0.118 0.187 36.878 -0.363 -0.107 5.774 72.121 A A 10 12 11.257 B B 19 17 5.980 13.194 0.091 -0.771 AA_DA10DA12:DT17DT19_BB 9 -2.875 2.453 71.014 -1.453 -0.251 3.236 32.447 A A 12 13 10.945 B B 17 16 3.409 6.079 -0.007 -0.617 AA_DA12DC13:DG16DT17_BB 10 -1.479 2.662 31.854 -2.200 -0.254 3.421 35.884 A A 13 14 10.043 B B 16 15 3.388 6.157 0.089 0.471 AA_DC13DG14:DC15DG16_BB 11 1.436 -2.342 35.340 -0.160 0.071 citation citation_author pdbx_database_related repository Initial release Database references 1 0 2019-10-09 1 1 2019-11-13 _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year Switzerland Swiss National Science Foundation 165949 Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species) N PDBE Y PDBE 2018-03-11 REL REL REL HG MERCURY (II) ION 32630 synthetic construct sample 1 14 structures with the lowest energy 200 20 isotropic 2 2D 1H-1H NOESY isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-1H COSY isotropic 1 2D 1H-1H TOCSY isotropic 1 2D 1H-13C HSQC aliphatic isotropic 1 2D 1H-13C HSQC aromatic isotropic 1 2D 1H-1H NOESY 0.4 mM none 1.2 mM none 0.4 mM none 1.2 mM none 50 mM conditions_2 7.75 pH ambient atm 277 K 50 mM conditions_3 7.35 pD ambient atm 298 K 2000 preliminary structures were calculated. The 20 lowest energy structures were selected and subsequently refined. Of the 200 refined conformers calculated the 20 lowest energy structures were chosen simulated annealing 1 fewest violations 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 90% H2O/10% D2O 1_H2O/D2O 90% H2O/10% D2O solution 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O 1_D2O 100% D2O solution Bruker Biospin collection TopSpin 4.0.0.b.16 G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra structure calculation Xplor-NIH 2.46 Goddard chemical shift assignment Sparky Goddard peak picking Sparky G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra refinement Xplor-NIH 2.46 600 Bruker AVANCE 700 Bruker AVANCE HG 30 2 HG HG 101 A HG 29 2 HG HG 102 A DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DT 3 n 3 DT 3 A DC 4 n 4 DC 4 A DT 5 n 5 DT 5 A DC 6 n 6 DC 6 A DA 7 n 7 DA 7 A DT 8 n 8 DT 8 A DG 9 n 9 DG 9 A DA 10 n 10 DA 10 A DT 11 n 11 DT 11 A DA 12 n 12 DA 12 A DC 13 n 13 DC 13 A DG 14 n 14 DG 14 A DC 15 n 1 DC 15 B DG 16 n 2 DG 16 B DT 17 n 3 DT 17 B DC 18 n 4 DC 18 B DT 19 n 5 DT 19 B DC 20 n 6 DC 20 B DA 21 n 7 DA 21 B DT 22 n 8 DT 22 B DG 23 n 9 DG 23 B DA 24 n 10 DA 24 B DT 25 n 11 DT 25 B DA 26 n 12 DA 26 B DC 27 n 13 DC 27 B DG 28 n 14 DG 28 B author_and_software_defined_assembly PISA 2 dimeric We performed CD spectroscopy and concentration dependant thermal melting temperature experiments to confirm formation of B-form duplex DNA. We used site-selective 15N-labeling and 199Hg-enriched Hg(ClO4)2 to determine the binding site. none 1660 -64 5140 A DC 4 A N3 DC 4 1_555 A HG 102 D HG HG 1_555 B DT 25 B N3 DT 11 1_555 178.8 A DT 11 A N3 DT 11 1_555 A HG 101 C HG HG 1_555 B DC 18 B N3 DC 4 1_555 178.8 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 N DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species) 1 N N 1 N N 2 N N 2 N N metalc 2.044 A DC 4 A N3 DC 4 1_555 A HG 102 D HG HG 1_555 metalc 2.047 A DT 11 A N3 DT 11 1_555 A HG 101 C HG HG 1_555 metalc 2.047 B DC 18 B N3 DC 4 1_555 A HG 101 C HG HG 1_555 metalc 2.045 B DT 25 B N3 DT 11 1_555 A HG 102 D HG HG 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 28 B N1 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 28 B O6 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 28 B N2 DG 14 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 27 B N3 DC 13 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 27 B O2 DC 13 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 27 B N4 DC 13 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 26 B N1 DA 12 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 26 B N6 DA 12 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 24 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 24 B N6 DA 10 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 23 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 23 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 23 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 22 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 22 B O4 DT 8 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 21 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 21 B N6 DA 7 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 20 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 20 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 20 B N4 DC 6 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 19 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 19 B O4 DT 5 1_555 hydrog WATSON-CRICK A DA 12 A N1 DA 12 1_555 B DT 17 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 12 A N6 DA 12 1_555 B DT 17 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 13 1_555 B DG 16 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 13 1_555 B DG 16 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 13 1_555 B DG 16 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 14 A N1 DG 14 1_555 B DC 15 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 14 A N2 DG 14 1_555 B DC 15 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 14 A O6 DG 14 1_555 B DC 15 B N4 DC 1 1_555 DNA metallated duplex DNA, B-form helix, A-form helix, mercury(II)-mediated base pair, DNA 6FY6 PDB 1 1 6FY6 1 14 6FY6 1 14 6FY6 A 1 1 14 15 28 6FY6 15 28 6FY6 B 1 1 14 binding site for residue HG A 101 A HG 101 Software 5 binding site for residue HG A 102 A HG 102 Software 5 A DA 10 A DA 10 5 1_555 A DT 11 A DT 11 5 1_555 A DA 12 A DA 12 5 1_555 B DC 18 B DC 4 5 1_555 B DT 19 B DT 5 5 1_555 A DC 4 A DC 4 5 1_555 A DT 5 A DT 5 5 1_555 B DA 24 B DA 10 5 1_555 B DT 25 B DT 11 5 1_555 B DA 26 B DA 12 5 1_555