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 C9 H13 N2 O8 P 308.182 1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5'-PHOSPHATE 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/pdb1dk6/pdb pdb_00001dk6 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 2716.784 5'-D(GP*TP*AP*CP*(NP3)P*CP*AP*TP*GP*)-3' 1 syn polymer no no (DC)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC) CATGAGTAC A polydeoxyribonucleotide no yes (DG)(DT)(DA)(DC)(NP3)(DC)(DA)(DT)(DG) GTACNCATG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n -7.626 1 19 A 1 B 18 -3.915 A_DC1:DG18_B 1 15.615 0.246 0.324 -0.441 9.979 1 20 A 2 B 17 -2.394 A_DA2:DT17_B 2 -1.206 -0.308 0.505 -0.228 6.059 1 20 A 3 B 16 -0.612 A_DT3:DA16_B 3 -6.086 -0.058 0.104 -0.388 -5.286 1 19 A 4 B 15 1.715 A_DG4:DC15_B 4 -15.324 -0.389 -0.356 -0.520 7.519 1 19 A 6 B 13 6.230 A_DG6:DC13_B 5 -4.396 -0.934 0.548 -0.337 5.839 1 20 A 7 B 12 2.046 A_DT7:DA12_B 6 -13.062 -0.201 0.078 -0.341 -10.103 1 20 A 8 B 11 7.281 A_DA8:DT11_B 7 -13.704 -0.018 0.065 -0.271 -28.912 1 19 A 9 B 10 5.372 A_DC9:DG10_B 8 9.510 0.418 1.243 -0.459 1.887 30.441 A A 1 2 37.542 B B 18 17 2.648 18.400 0.304 -0.368 AA_DC1DA2:DT17DG18_BB 1 -1.692 3.452 24.298 -3.556 -0.842 3.254 37.567 A A 2 3 -0.460 B B 17 16 3.252 -0.296 0.122 -0.695 AA_DA2DT3:DA16DT17_BB 2 3.792 -5.898 37.381 -1.040 0.303 2.887 35.633 A A 3 4 15.482 B B 16 15 3.224 9.356 -0.203 -0.778 AA_DT3DG4:DC15DA16_BB 3 3.375 -5.585 34.260 -2.568 0.799 5.188 71.733 A A 4 6 10.190 B B 15 13 5.428 11.896 0.517 -1.083 AA_DG4DG6:DC13DC15_BB 4 -3.590 3.075 70.792 -1.581 -0.640 2.898 31.746 A A 6 7 1.127 B B 13 12 3.028 0.615 -1.029 -0.995 AA_DG6DT7:DA12DC13_BB 5 3.076 -5.633 31.594 -1.921 2.394 2.996 40.512 A A 7 8 12.746 B B 12 11 3.228 8.757 0.270 -0.831 AA_DT7DA8:DT11DA12_BB 6 2.485 -3.617 39.518 -2.144 -0.122 3.685 34.557 A A 8 9 -4.710 B B 11 10 3.813 -2.768 0.282 -0.813 AA_DA8DC9:DG10DT11_BB 7 -8.563 14.574 33.399 -0.869 -2.020 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-01-11 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag 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 285 K THE STRUCTURE IS BASED ON A TOTAL OF 624 RESTRAINTS, 198 ARE DERIVED FROM ASSIGNED NOES, 394 ARE LOWER BOUND NOE-DERIVED RESTRAINTS TO UNASSIGN 1H5*/2H5* PROTONS, AND 32 ARE DIHEDRAL ANGLE RESTRAINTS SIMULATED ANNEALING MOLECULAR DYNAMICS 4.5MM DUPLEX; 100MM NACL, 10MM NAOP, 1MM EDTA, PH 7 LIU structure solution CORMA 5.2 BORGIAS, JAMES iterative matrix relaxation MARDIGRAS 5.2 DELAGLIO processing NMRPipe 1.7 BRUNGER refinement X-PLOR V3.840 VARIAN collection VNMR 6.1B DAY, KNELLER data analysis Sparky 3.74 600 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 NP3 14 n 5 NP3 14 B CYT 15 n 6 DC 15 B ADE 16 n 7 DA 16 B THY 17 n 8 DT 17 B G 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 H41 O6 DC DG 1 18 1.47 1 A B H21 O2 DG DC 4 15 1.50 1 A B O2 H21 DC DG 9 10 1.52 1 A B O6 H41 DG DC 4 15 1.52 1 A B H21 O2 DG DC 6 13 1.54 1 A B H1 N3 DG DC 4 15 1.58 1 A B H3 N1 DT DA 7 12 1.59 1 A B H3 N1 DT DA 3 16 1.59 1 A DG 4 0.088 SIDE CHAIN 1 A DG 6 0.080 SIDE CHAIN 1 B DG 10 0.104 SIDE CHAIN 1 B DC 13 0.111 SIDE CHAIN 1 B DA 16 0.119 SIDE CHAIN 1 B DT 17 0.079 SIDE CHAIN 1 B DG 18 0.080 SIDE CHAIN 1 -4.85 0.80 105.90 101.05 A A A O4' C1' C2' DA DA DA 2 2 2 N 1 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DA DA DA 2 2 2 N 1 3.06 0.50 113.80 116.86 A A A N7 C8 N9 DA DA DA 2 2 2 N 1 3.51 0.30 108.30 111.81 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 3.57 0.50 113.10 116.67 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 2.68 0.30 108.30 110.98 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 3.08 0.50 113.80 116.88 A A A N7 C8 N9 DA DA DA 5 5 5 N 1 3.60 0.50 113.10 116.70 A A A N7 C8 N9 DG DG DG 6 6 6 N 1 3.38 0.50 113.80 117.18 A A A N7 C8 N9 DA DA DA 8 8 8 N 1 7.13 0.30 108.30 115.43 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.40 0.50 113.10 116.50 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 -2.42 0.40 106.40 103.98 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 7.21 1.10 109.80 117.01 B B B C5' C4' O4' DA DA DA 12 12 12 N 1 5.04 0.30 108.30 113.34 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 6.65 1.10 109.80 116.45 B B B C5' C4' O4' DC DC DC 15 15 15 N 1 4.44 0.30 108.30 112.74 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 -4.89 0.80 105.90 101.01 B B B O4' C1' C2' DA DA DA 16 16 16 N 1 3.40 0.50 113.80 117.20 B B B N7 C8 N9 DA DA DA 16 16 16 N 1 4.14 0.60 119.00 123.14 B B B C4 C5 C7 DT DT DT 17 17 17 N 1 -6.35 0.60 122.90 116.55 B B B C6 C5 C7 DT DT DT 17 17 17 N 1 2.15 0.30 108.30 110.45 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 3.72 0.50 113.10 116.82 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 A A C5 C7 DT DT 3 3 0.037 0.006 1.496 1.533 N 1 B B C5 C7 DT DT 11 11 0.036 0.006 1.496 1.532 N NMR structure analysis of the DNA nine base pair duplex D(CATGAGTAC) D(GTAC(NP3)CATG) 1 N N 2 N N covale 1.624 both B DC 13 B O3' DC 4 1_555 B NP3 14 B P NP3 5 1_555 covale 1.621 both B NP3 14 B O3' NP3 5 1_555 B DC 15 B P DC 6 1_555 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 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 DOUBLE HELIX, 3-NITROPYRROLE, DNA 1DK6 PDB 1 1DK6 1DK6 PDB 2 1DK6 1 9 1DK6 1 9 1DK6 A 1 1 9 10 18 1DK6 10 18 1DK6 B 2 1 9 1 P 1