1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Klewer, D.A. Hoskins, A. Davisson, V.J. Bergstrom, D.E. LiWang, A.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 28 4514 4522 10.1093/nar/28.22.4514 11071940 NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control. 2000 10.2210/pdb1dk9/pdb pdb_00001dk9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2739.824 5'-D(CP*AP*TP*GP*AP*GP*TP*AP*CP*)-3' 1 syn polymer 2730.810 5'-D(GP*TP*AP*CP*TP*CP*AP*TP*GP*)-3' 1 syn polymer no no (DC)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC) CATGAGTAC A polydeoxyribonucleotide no no (DG)(DT)(DA)(DC)(DT)(DC)(DA)(DT)(DG) GTACTCATG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n 11.032 1 19 A 1 B 18 0.988 A_DC1:DG18_B 1 -20.539 0.299 0.156 -0.468 3.758 1 20 A 2 B 17 4.559 A_DA2:DT17_B 2 -9.696 0.108 0.360 -0.357 1.353 1 20 A 3 B 16 10.682 A_DT3:DA16_B 3 -12.621 0.124 0.573 -0.326 3.994 1 19 A 4 B 15 -0.372 A_DG4:DC15_B 4 -1.764 -0.157 0.084 -0.485 -1.271 1 20 A 5 B 14 3.075 A_DA5:DT14_B 5 -7.882 0.296 -0.111 -0.370 -5.926 1 19 A 6 B 13 2.040 A_DG6:DC13_B 6 -10.084 -0.273 0.136 -0.508 -15.253 1 20 A 7 B 12 -1.035 A_DT7:DA12_B 7 -0.937 -0.083 0.069 -0.359 -15.567 1 20 A 8 B 11 1.908 A_DA8:DT11_B 8 -3.001 0.043 -0.264 -0.377 -11.700 1 19 A 9 B 10 -0.778 A_DC9:DG10_B 9 2.336 0.324 0.302 -0.466 2.288 32.392 A A 1 2 21.018 B B 18 17 2.928 11.459 -0.296 -1.368 AA_DC1DA2:DT17DG18_BB 1 -3.550 6.512 30.144 -4.125 0.012 3.201 37.445 A A 2 3 -8.652 B B 17 16 3.109 -5.535 0.290 -0.913 AA_DA2DT3:DA16DT17_BB 2 -0.842 1.316 37.038 -0.717 -0.559 2.747 37.904 A A 3 4 2.044 B B 16 15 2.799 1.327 -0.248 -0.825 AA_DT3DG4:DC15DA16_BB 3 2.620 -4.038 37.794 -1.414 0.667 3.023 40.752 A A 4 5 5.086 B B 15 14 3.104 3.535 0.103 -0.842 AA_DG4DA5:DT14DC15_BB 4 2.900 -4.172 40.506 -1.576 0.153 2.952 34.973 A A 5 6 5.928 B B 14 13 3.075 3.553 -0.182 -1.149 AA_DA5DG6:DC13DT14_BB 5 -2.708 4.518 34.696 -2.408 -0.075 3.390 42.940 A A 6 7 -7.579 B B 13 12 3.308 -5.527 -0.119 -1.051 AA_DG6DT7:DA12DC13_BB 6 3.786 -5.191 42.438 -0.871 0.550 2.850 40.176 A A 7 8 11.101 B B 12 11 2.988 7.570 0.385 -0.621 AA_DT7DA8:DT11DA12_BB 7 4.238 -6.214 39.265 -1.682 -0.125 3.009 30.090 A A 8 9 -4.014 B B 11 10 3.047 -2.074 0.252 -0.624 AA_DA8DC9:DG10DT11_BB 8 -4.660 9.018 29.665 -0.807 -1.374 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 1999-12-16 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession Residue 14 is replaced by 3-nitropyrrole RCSB Y RCSB 1999-12-06 REL THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED sample THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED sample 1 2D NOESY DQF-COSY 7 ambient 278 K 4.5mM duplex, 100mM NaCl, 10mM NaOP, 1mM EDTA 95% H2O/5% D2O Liu iterative matrix relaxation CORMA 5.2 Borgias, James iterative matrix relaxation MARDIGRAS 5.2 Delaglio processing NMRPipe 7.1 Varian collection VNMR 6.1B Brunger refinement X-PLOR V3.840 Garrett data analysis PIPP 4.2.7 600 Varian INOVA CYT 1 n 1 DC 1 A ADE 2 n 2 DA 2 A THY 3 n 3 DT 3 A GUA 4 n 4 DG 4 A ADE 5 n 5 DA 5 A GUA 6 n 6 DG 6 A THY 7 n 7 DT 7 A ADE 8 n 8 DA 8 A CYT 9 n 9 DC 9 A GUA 10 n 1 DG 10 B THY 11 n 2 DT 11 B ADE 12 n 3 DA 12 B CYT 13 n 4 DC 13 B THY 14 n 5 DT 14 B CYT 15 n 6 DC 15 B ADE 16 n 7 DA 16 B THY 17 n 8 DT 17 B GUA 18 n 9 DG 18 B author_defined_assembly 2 dimeric 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 B H21 O2 DG DC 6 13 1.40 1 A B H21 O2 DG DC 4 15 1.47 1 A B O2 H21 DC DG 1 18 1.48 1 A B O2 H21 DC DG 9 10 1.50 1 A B O6 H41 DG DC 4 15 1.50 1 A B H41 O6 DC DG 9 10 1.54 1 A B H1 N3 DG DC 6 13 1.54 1 A B H1 N3 DG DC 4 15 1.55 1 A B N1 H3 DA DT 8 11 1.56 1 A B N1 H3 DA DT 5 14 1.56 1 A B N1 H3 DA DT 2 17 1.58 1 A B O6 H41 DG DC 6 13 1.58 1 A B N3 H1 DC DG 1 18 1.58 1 A B O4 H61 DT DA 7 12 1.59 1 A B H3 N1 DT DA 7 12 1.59 1 3.62 0.30 108.30 111.92 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 3.31 0.50 113.10 116.41 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 4.61 0.30 108.30 112.91 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 3.80 0.30 108.30 112.10 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 3.63 0.50 113.10 116.73 A A A N7 C8 N9 DG DG DG 6 6 6 N 1 -4.77 0.70 108.00 103.23 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 -5.46 0.80 105.90 100.44 A A A O4' C1' C2' DC DC DC 9 9 9 N 1 5.93 0.30 108.30 114.23 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.49 0.50 113.10 116.59 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 7.72 0.30 108.30 116.02 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 -6.21 0.60 122.90 116.69 B B B C6 C5 C7 DT DT DT 11 11 11 N 1 1.90 0.30 108.30 110.20 B B B O4' C1' N9 DA DA DA 12 12 12 N 1 3.52 0.30 108.30 111.82 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 3.33 0.50 113.80 117.13 B B B N7 C8 N9 DA DA DA 16 16 16 N 1 -3.63 0.60 122.90 119.27 B B B C6 C5 C7 DT DT DT 17 17 17 N 1 -6.03 1.00 110.10 104.07 B B B C1' O4' C4' DG DG DG 18 18 18 N 1 2.55 0.30 108.30 110.85 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 3.08 0.50 113.10 116.18 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 A A C5 C7 DT DT 7 7 0.046 0.006 1.496 1.542 N 1 B B C5 C7 DT DT 17 17 0.038 0.006 1.496 1.534 N SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG) 1 N N 2 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 18 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 18 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 18 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 17 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 17 B O4 DT 8 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 16 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 16 B N6 DA 7 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 15 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 15 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 15 B N4 DC 6 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 14 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 14 B O4 DT 5 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 13 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 13 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 13 B N4 DC 4 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 12 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 12 B N6 DA 3 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 11 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 11 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 10 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 10 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 10 B N2 DG 1 1_555 DNA DNA, DUPLEX 1DK9 PDB 1 1DK9 1DK9 PDB 2 1DK9 1 9 1DK9 1 9 1DK9 A 1 1 9 10 18 1DK9 10 18 1DK9 B 2 1 9 1 P 1