1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Johannsen, S. Duepre, N. Boehme, D. Mueller, J. Sigel, R.K.O. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic Ag 1 107.868 SILVER ION non-polymer C8 H13 N2 O6 P 264.172 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking UK Nat.Chem. 1755-4330 2 229 234 10.1038/nchem.512 21124482 Solution structure of a DNA double helix with consecutive metal-mediated base pairs. 2010 5015.311 DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3') 2 syn polymer 107.868 SILVER ION 3 syn non-polymer no yes (DT)(DT)(DA)(DA)(DT)(DT)(DT)(D33)(D33)(D33)(DA)(DA)(DA)(DT)(DT)(DA)(DA) TTAATTTNNNAAATTAA A,B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n -2.527 1 20 A 1 B 34 2.110 A_DT1:DA34_B 1 -7.755 -0.389 0.088 -0.084 -1.107 1 20 A 2 B 33 4.022 A_DT2:DA33_B 2 -17.275 -0.125 -0.274 -0.212 -2.918 1 20 A 3 B 32 -1.153 A_DA3:DT32_B 3 -11.114 0.126 0.178 -0.209 -4.120 1 20 A 4 B 31 0.817 A_DA4:DT31_B 4 -11.599 0.138 -0.144 -0.140 -3.736 1 20 A 5 B 30 -2.846 A_DT5:DA30_B 5 -7.230 -0.545 -0.022 -0.169 -2.378 1 20 A 6 B 29 -2.585 A_DT6:DA29_B 6 -12.735 -0.428 -0.030 -0.221 -2.027 1 20 A 7 B 28 -1.476 A_DT7:DA28_B 7 -11.301 -0.376 -0.119 -0.085 1.545 1 20 A 11 B 24 -1.206 A_DA11:DT24_B 8 -11.046 0.342 -0.164 -0.087 1.063 1 20 A 12 B 23 -2.458 A_DA12:DT23_B 9 -11.729 0.447 -0.097 -0.207 3.836 1 20 A 13 B 22 -2.523 A_DA13:DT22_B 10 -7.247 0.546 -0.049 -0.147 3.978 1 20 A 14 B 21 0.791 A_DT14:DA21_B 11 -11.110 -0.169 -0.169 -0.126 2.172 1 20 A 15 B 20 -1.088 A_DT15:DA20_B 12 -10.524 -0.126 0.182 -0.208 1.382 1 20 A 16 B 19 3.709 A_DA16:DT19_B 13 -17.296 0.115 -0.263 -0.226 1.691 1 20 A 17 B 18 2.083 A_DA17:DT18_B 14 -6.810 0.411 0.108 -0.094 3.463 36.639 A A 1 2 -8.543 B B 34 33 3.500 -5.351 -0.126 -0.044 AA_DT1DT2:DA33DA34_BB 1 1.579 -2.520 36.226 0.716 0.432 3.420 36.727 A A 2 3 -4.850 B B 33 32 3.423 -3.038 -0.095 -0.519 AA_DT2DA3:DT32DA33_BB 2 -6.419 10.248 36.057 -0.386 -0.774 3.245 35.751 A A 3 4 -0.077 B B 32 31 3.261 -0.047 -0.072 -0.351 AA_DA3DA4:DT31DT32_BB 3 2.919 -4.759 35.636 -0.565 0.536 3.139 34.519 A A 4 5 6.147 B B 31 30 3.233 3.640 0.040 -0.698 AA_DA4DT5:DA30DT31_BB 4 -1.555 2.626 34.298 -1.727 -0.302 3.315 35.540 A A 5 6 5.785 B B 30 29 3.341 3.526 -0.155 -0.113 AA_DT5DT6:DA29DA30_BB 5 0.023 -0.037 35.371 -0.711 0.257 3.136 33.615 A A 6 7 13.961 B B 29 28 3.321 8.000 -0.271 -0.394 AA_DT6DT7:DA28DA29_BB 6 0.338 -0.591 32.674 -1.992 0.524 3.148 33.826 A A 11 12 14.536 B B 24 23 3.341 8.374 0.269 -0.377 AA_DA11DA12:DT23DT24_BB 7 -0.465 0.807 32.799 -2.012 -0.537 3.263 35.425 A A 12 13 5.408 B B 23 22 3.287 3.286 0.153 -0.104 AA_DA12DA13:DT22DT23_BB 8 -0.257 0.423 35.276 -0.655 -0.289 3.170 34.399 A A 13 14 5.949 B B 22 21 3.261 3.511 -0.049 -0.683 AA_DA13DT14:DA21DT22_BB 9 1.854 -3.142 34.176 -1.694 0.369 3.239 35.867 A A 14 15 1.097 B B 21 20 3.265 0.675 0.085 -0.351 AA_DT14DT15:DA20DA21_BB 10 -3.107 5.051 35.731 -0.665 -0.581 3.391 36.604 A A 15 16 -5.120 B B 20 19 3.395 -3.198 0.057 -0.524 AA_DT15DA16:DT19DA20_BB 11 6.145 -9.840 35.965 -0.374 0.794 3.481 36.866 A A 16 17 -8.382 B B 19 18 3.520 -5.281 0.136 -0.056 AA_DA16DA17:DT18DT19_BB 12 -2.031 3.223 36.444 0.681 -0.511 repository Initial release Version format compliance 1 0 2010-02-09 1 1 2011-07-13 NMR data related to NMR solutions structure of modified DNA containing imidazole nucleosides at acidic, neutral and basic pH NMR solutions structure of modified DNA containing imidazole nucleosides at acidic pH NMR solutions structure of modified DNA containing imidazole nucleosides at neutral pH NMR solutions structure of modified DNA containing imidazole nucleosides at basic pH BMRB Y RCSB 2009-01-27 REL REL AG SILVER ION 848 366 15 25 442 structures with the lowest energy 200 20 0.2 0.2 1.06 0.34 2D 1H-1H NOESY 2D 1H-1H TOCSY 2D 1H-13C HSQC 2D 1H-15N HSQC 1D 31P 2D 1H-1H NOESY 0.3-0.5 mM 120 mM 0.9-1.5 mM 0.3-0.5 mM 120 mM 0.9-1.5 mM 0.12 7.2 ambient 298 K 0.12 7.2 ambient 278 K torsion angle dynamics 1 lowest energy 0.3-0.5 mM DNA (34-MER)-1, 120 mM sodium perchlorate-2, 0.9-1.5 mM SILVER ION-3, 100% D2O 100% D2O 0.3-0.5 mM DNA (34-MER)-4, 120 mM sodium perchlorate-5, 0.9-1.5 mM SILVER ION-6, 90% H2O/10% D2O 90% H2O/10% D2O Bruker Biospin processing TOPSPIN 1.3, 2.0, 2.1 Goddard chemical shift assignment SPARKY 3.1 Goddard data analysis SPARKY 3.1 Goddard peak picking SPARKY 3.1 Guntert, Braun and Wuthrich structure solution DYANA 1.5 Schwieters, Kuszewski, Tjandra and Clore structure solution X-PLOR_NIH 2.15 Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR_NIH 2.15 700 Bruker Avance Bruker Avance 400 Bruker AV-2 Bruker AV-2 AG 35 2 AG AG 35 A AG 36 2 AG AG 36 A AG 37 2 AG AG 37 A DT 1 n 1 DT 1 A DT 2 n 2 DT 2 A DA 3 n 3 DA 3 A DA 4 n 4 DA 4 A DT 5 n 5 DT 5 A DT 6 n 6 DT 6 A DT 7 n 7 DT 7 A D33 8 n 8 D33 8 A D33 9 n 9 D33 9 A D33 10 n 10 D33 10 A DA 11 n 11 DA 11 A DA 12 n 12 DA 12 A DA 13 n 13 DA 13 A DT 14 n 14 DT 14 A DT 15 n 15 DT 15 A DA 16 n 16 DA 16 A DA 17 n 17 DA 17 A DT 18 n 1 DT 18 B DT 19 n 2 DT 19 B DA 20 n 3 DA 20 B DA 21 n 4 DA 21 B DT 22 n 5 DT 22 B DT 23 n 6 DT 23 B DT 24 n 7 DT 24 B D33 25 n 8 D33 25 B D33 26 n 9 D33 26 B D33 27 n 10 D33 27 B DA 28 n 11 DA 28 B DA 29 n 12 DA 29 B DA 30 n 13 DA 30 B DT 31 n 14 DT 31 B DT 32 n 15 DT 32 B DA 33 n 16 DA 33 B DA 34 n 17 DA 34 B author_defined_assembly 2 dimeric A D33 8 A N3 D33 8 1_555 A AG 35 C AG AG 1_555 B D33 27 B N3 D33 10 1_555 177.6 A D33 9 A N3 D33 9 1_555 A AG 36 D AG AG 1_555 B D33 26 B N3 D33 9 1_555 179.1 A D33 10 A N3 D33 10 1_555 A AG 37 E AG AG 1_555 B D33 25 B N3 D33 8 1_555 177.8 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 5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3' NMR solution structure of metal-modified DNA 1 N N 1 N N 2 N N 2 N N 2 N N covale 1.609 A DT 7 A O3' DT 7 1_555 A D33 8 A P D33 8 1_555 covale 1.613 A D33 8 A O3' D33 8 1_555 A D33 9 A P D33 9 1_555 covale 1.612 A D33 9 A O3' D33 9 1_555 A D33 10 A P D33 10 1_555 covale 1.618 A D33 10 A O3' D33 10 1_555 A DA 11 A P DA 11 1_555 covale 1.610 B DT 24 B O3' DT 7 1_555 B D33 25 B P D33 8 1_555 covale 1.611 B D33 25 B O3' D33 8 1_555 B D33 26 B P D33 9 1_555 covale 1.610 B D33 26 B O3' D33 9 1_555 B D33 27 B P D33 10 1_555 covale 1.616 B D33 27 B O3' D33 10 1_555 B DA 28 B P DA 11 1_555 metalc 2.127 A D33 8 A N3 D33 8 1_555 A AG 35 C AG AG 1_555 metalc 2.119 A D33 9 A N3 D33 9 1_555 A AG 36 D AG AG 1_555 metalc 2.128 A D33 10 A N3 D33 10 1_555 A AG 37 E AG AG 1_555 metalc 2.124 B D33 25 B N3 D33 8 1_555 A AG 37 E AG AG 1_555 metalc 2.117 B D33 26 B N3 D33 9 1_555 A AG 36 D AG AG 1_555 metalc 2.123 B D33 27 B N3 D33 10 1_555 A AG 35 C AG AG 1_555 hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 B DA 34 B N1 DA 17 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 B DA 34 B N6 DA 17 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 33 B N1 DA 16 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 33 B N6 DA 16 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 32 B N3 DT 15 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 32 B O4 DT 15 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 31 B N3 DT 14 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 31 B O4 DT 14 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 30 B N1 DA 13 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 30 B N6 DA 13 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 29 B N1 DA 12 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 29 B N6 DA 12 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 28 B N1 DA 11 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 28 B N6 DA 11 1_555 hydrog WATSON-CRICK A DA 11 A N1 DA 11 1_555 B DT 24 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 11 A N6 DA 11 1_555 B DT 24 B O4 DT 7 1_555 hydrog WATSON-CRICK A DA 12 A N1 DA 12 1_555 B DT 23 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 12 A N6 DA 12 1_555 B DT 23 B O4 DT 6 1_555 hydrog WATSON-CRICK A DA 13 A N1 DA 13 1_555 B DT 22 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 13 A N6 DA 13 1_555 B DT 22 B O4 DT 5 1_555 hydrog WATSON-CRICK A DT 14 A N3 DT 14 1_555 B DA 21 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 14 A O4 DT 14 1_555 B DA 21 B N6 DA 4 1_555 hydrog WATSON-CRICK A DT 15 A N3 DT 15 1_555 B DA 20 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 15 A O4 DT 15 1_555 B DA 20 B N6 DA 3 1_555 hydrog WATSON-CRICK A DA 16 A N1 DA 16 1_555 B DT 19 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 16 A N6 DA 16 1_555 B DT 19 B O4 DT 2 1_555 hydrog WATSON-CRICK A DA 17 A N1 DA 17 1_555 B DT 18 B N3 DT 1 1_555 hydrog WATSON-CRICK A DA 17 A N6 DA 17 1_555 B DT 18 B O4 DT 1 1_555 DNA DNA, artificial nucleobase, imidazole nucleoside, Ag+ 2KE8 PDB 1 2KE8 TTAATTTXXXAAATTAA 1 17 2KE8 1 17 2KE8 A 1 1 17 18 34 2KE8 18 34 2KE8 B 1 1 17 BINDING SITE FOR RESIDUE AG A 35 Software 2 BINDING SITE FOR RESIDUE AG A 36 Software 2 BINDING SITE FOR RESIDUE AG A 37 Software 2 A D33 8 A D33 8 2 1_555 B D33 27 B D33 10 2 1_555 A D33 9 A D33 9 2 1_555 B D33 26 B D33 9 2 1_555 A D33 10 A D33 10 2 1_555 B D33 25 B D33 8 2 1_555