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')_minor 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 -2.420 1 19 A 1 B 28 4.543 A_DC1:DG28_B 1 -15.325 0.747 0.191 -0.232 -0.611 1 19 A 2 B 27 0.453 A_DG2:DC27_B 2 -11.942 -0.008 0.003 -0.188 0.941 1 20 A 3 B 26 -2.049 A_DT3:DA26_B 3 -14.997 -0.200 -0.099 -0.245 -0.564 1 20 A 5 B 24 -4.975 A_DT5:DA24_B 4 -17.221 -0.025 -0.038 -0.181 -6.587 1 19 A 6 B 23 2.054 A_DC6:DG23_B 5 -10.686 0.195 -0.171 -0.192 -1.796 1 20 A 7 B 22 -3.147 A_DA7:DT22_B 6 -8.923 0.502 -0.077 -0.131 1.840 1 20 A 8 B 21 -3.280 A_DT8:DA21_B 7 -8.451 -0.533 -0.060 -0.105 6.444 1 19 A 9 B 20 2.123 A_DG9:DC20_B 8 -10.757 -0.203 -0.150 -0.182 -0.089 1 20 A 10 B 19 -4.563 A_DA10:DT19_B 9 -16.769 0.039 -0.063 -0.171 -0.747 1 20 A 12 B 17 -1.686 A_DA12:DT17_B 10 -15.097 0.204 -0.100 -0.249 0.745 1 19 A 13 B 16 0.473 A_DC13:DG16_B 11 -11.637 0.016 -0.025 -0.213 2.739 1 19 A 14 B 15 4.511 A_DG14:DC15_B 12 -15.041 -0.761 0.190 -0.261 3.368 35.353 A A 1 2 7.734 B B 28 27 3.346 4.682 -0.106 0.380 AA_DC1DG2:DC27DG28_BB 1 -1.737 2.869 35.010 -0.087 -0.089 3.099 31.825 A A 2 3 5.299 B B 27 26 3.173 2.902 -0.406 -0.744 AA_DG2DT3:DA26DC27_BB 2 -0.409 0.747 31.694 -1.866 0.669 6.112 71.121 A A 3 5 5.299 B B 26 24 6.244 6.155 -0.340 -1.634 AA_DT3DT5:DA24DA26_BB 3 -4.081 3.514 70.786 -1.806 0.027 3.367 36.994 A A 5 6 9.174 B B 24 23 3.426 5.798 0.176 -0.125 AA_DT5DC6:DG23DA24_BB 4 -0.166 0.262 36.552 -1.012 -0.301 3.394 39.162 A A 6 7 15.034 B B 23 22 3.285 9.974 -0.319 0.845 AA_DC6DA7:DT22DG23_BB 5 -0.302 0.454 37.917 0.019 0.438 3.075 32.195 A A 7 8 4.128 B B 22 21 3.118 2.287 -0.005 -0.510 AA_DA7DT8:DA21DT22_BB 6 -0.203 0.367 32.115 -1.306 -0.025 3.397 39.267 A A 8 9 14.682 B B 21 20 3.289 9.770 0.320 0.839 AA_DT8DG9:DC20DA21_BB 7 0.367 -0.552 38.077 0.038 -0.431 3.389 37.002 A A 9 10 9.028 B B 20 19 3.447 5.708 -0.162 -0.115 AA_DG9DA10:DT19DC20_BB 8 0.439 -0.694 36.572 -0.989 0.317 6.082 71.003 A A 10 12 5.538 B B 19 17 6.218 6.423 0.352 -1.612 AA_DA10DA12:DT17DT19_BB 9 4.032 -3.477 70.650 -1.806 -0.041 3.111 31.970 A A 12 13 5.199 B B 17 16 3.180 2.860 0.395 -0.727 AA_DA12DC13:DG16DT17_BB 10 0.640 -1.163 31.839 -1.818 -0.606 3.361 35.422 A A 13 14 8.038 B B 16 15 3.340 4.874 0.101 0.371 AA_DC13DG14:DC15DG16_BB 11 1.482 -2.443 35.065 -0.127 0.058 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 (minor 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 COSY isotropic 1 2D 1H-1H TOCSY isotropic 1 2D 1H-13C HSQC aliphatic isotropic 1 2D 1H-13C HSQC aromatic 0.4 mM none 1.2 mM none 50 mM conditions_3 7.35 pD ambient atm 298 K 2000 preliminary structures were calculated. The 20 lowest energy structures were subsequently refined. From the 200 calculated refined conformers the 20 lowest energy structures were chosen simulated annealing 1 fewest violations 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O 1_D2O 100% D2O solution Goddard peak picking Sparky G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandra refinement Xplor-NIH 2.46 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 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 binding site. none 1680 -62 5220 A DC 4 A N4 DC 4 1_555 A HG 102 D HG HG 1_555 B DT 25 B N3 DT 11 1_555 178.4 A DT 11 A N3 DT 11 1_555 A HG 101 C HG HG 1_555 B DC 18 B N4 DC 4 1_555 178.3 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')_minor Concerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species) 1 N N 1 N N 2 N N 2 N N metalc 2.135 A DC 4 A N4 DC 4 1_555 A HG 102 D HG HG 1_555 metalc 2.132 A DT 11 A N3 DT 11 1_555 A HG 101 C HG HG 1_555 metalc 2.135 B DC 18 B N4 DC 4 1_555 A HG 101 C HG HG 1_555 metalc 2.135 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 6FY7 PDB 1 1 6FY7 1 14 6FY7 1 14 6FY7 A 1 1 14 15 28 6FY7 15 28 6FY7 B 1 1 14 binding site for residue HG A 101 A HG 101 Software 4 binding site for residue HG A 102 A HG 102 Software 4 A DA 10 A DA 10 4 1_555 A DT 11 A DT 11 4 1_555 A DA 12 A DA 12 4 1_555 B DC 18 B DC 4 4 1_555 A DC 4 A DC 4 4 1_555 B DA 24 B DA 10 4 1_555 B DT 25 B DT 11 4 1_555 B DA 26 B DA 12 4 1_555