0.022181 0.012806 0.000000 0.000000 0.025612 0.000000 0.000000 0.000000 0.023969 0.00000 0.00000 0.00000 Kennard, O. Cruse, W.B.T. Nachman, J. Prange, T. Shakked, Z. Rabinovich, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 45.084 45.084 41.720 C9 H12 Br N2 O8 P 387.078 n 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA linking 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 H2 O 18.015 WATER non-polymer N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N BR N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N O N 35 N P N 36 N O N 37 N O N 38 N O N 39 N C N 40 R C N 41 N O N 42 S C N 43 N O N 44 N C N 45 R C Y 46 N N Y 47 N C Y 48 N N Y 49 N C Y 50 N C N 51 N N Y 52 N N Y 53 N C Y 54 N N Y 55 N C N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N O N 71 N P N 72 N O N 73 N O N 74 N O N 75 N C N 76 R C N 77 N O N 78 S C N 79 N O N 80 N C N 81 R C N 82 N N N 83 N C N 84 N O N 85 N N N 86 N C N 87 N N N 88 N C N 89 N C N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N O N 105 N P N 106 N O N 107 N O N 108 N O N 109 N C N 110 R C N 111 N O N 112 S C N 113 N O N 114 N C N 115 R C Y 116 N N Y 117 N C Y 118 N N Y 119 N C N 120 N C N 121 N O N 122 N N N 123 N C N 124 N N N 125 N N Y 126 N C N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N O N 142 N H N 143 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N doub N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N doub N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing Y 58 N sing Y 59 N sing Y 60 N doub N 61 N sing Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N doub N 67 N sing N 68 N sing Y 69 N sing Y 70 N doub N 71 N sing Y 72 N sing N 73 N sing N 74 N sing N 75 N doub N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N doub N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing Y 131 N sing Y 132 N sing Y 133 N doub N 134 N sing Y 135 N sing N 136 N sing Y 137 N doub N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 3 623 647 3271041 Ordered water structure in an A-DNA octamer at 1.7 A resolution. 1986 UK Nature NATUAS 0006 0028-0836 337 190 192 Coexistence of A-and B-Form DNA in a Single Crystal Lattice 1989 UK J.Mol.Biol. JMOBAK 0070 0022-2836 166 183 201 Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C) 1983 UK Proc.R.Soc.London,Ser.B PRLBA4 0338 0080-4649 213 479 487 Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C) 1981 10.2210/pdb115d/pdb pdb_0000115d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 1 DIFFRACTOMETER ENRAF-NONIUS CAD4 OSCILLATION CAMERA PHILLIPS M x-ray 1 M x-ray 2 1.0 1.0 SEALED TUBE LURE SYNCHROTRON LURE 2556.357 DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3') 2 syn polymer 18.015 water 85 nat water no yes (DG)(DG)(BRU)(DA)(BRU)(DA)(DC)(DC) GGUAUACC A,B polydeoxyribonucleotide n n n n n n n n 2.39 48.62 VAPOR DIFFUSION 7.00 pH 7.00, VAPOR DIFFUSION WATER 1 MPD 1 MG ACETATE 1 SPERMINE_HCL 1 WATER 2 MPD 2 -7.835 1 19 A 1 B 16 -1.602 A_DG1:DC16_B 1 -5.405 -0.362 -0.143 -0.169 -11.372 1 19 A 2 B 15 1.223 A_DG2:DC15_B 2 -9.608 -0.287 -0.154 -0.071 -6.810 1 20 A 3 B 14 -2.419 A_BRU3:DA14_B 3 -9.201 -0.051 -0.022 -0.088 0.193 1 20 A 4 B 13 1.580 A_DA4:BRU13_B 4 -7.217 0.096 0.245 -0.074 7.768 1 20 A 5 B 12 4.237 A_BRU5:DA12_B 5 -9.279 -0.099 0.054 -0.077 8.299 1 20 A 6 B 11 0.947 A_DA6:BRU11_B 6 -13.438 0.023 -0.060 -0.097 8.276 1 19 A 7 B 10 3.192 A_DC7:DG10_B 7 -13.947 0.385 -0.106 -0.059 6.726 1 19 A 8 B 9 -1.053 A_DC8:DG9_B 8 -1.093 0.266 -0.094 -0.099 3.000 34.367 A A 1 2 12.731 B B 16 15 3.465 7.466 0.149 -1.834 AA_DG1DG2:DC15DC16_BB 1 -0.138 0.235 33.570 -4.270 -0.273 3.270 33.153 A A 2 3 1.447 B B 15 14 3.302 0.826 -0.592 -1.237 AA_DG2BRU3:DA14DC15_BB 2 0.044 -0.076 33.143 -2.308 1.045 2.537 31.961 A A 3 4 19.007 B B 14 13 3.103 10.280 0.248 -1.220 AA_BRU3DA4:BRU13DA14_BB 3 -2.276 4.208 30.220 -3.868 -0.817 3.113 30.446 A A 4 5 6.487 B B 13 12 3.238 3.399 0.364 -1.087 AA_DA4BRU5:DA12BRU13_BB 4 1.376 -2.627 30.229 -2.732 -0.425 2.633 33.088 A A 5 6 20.653 B B 12 11 3.270 11.528 -0.506 -1.295 AA_BRU5DA6:BRU11DA12_BB 5 0.147 -0.263 31.067 -4.089 0.912 3.123 33.869 A A 6 7 8.088 B B 11 10 3.333 4.697 0.641 -1.403 AA_DA6DC7:DG10BRU11_BB 6 0.484 -0.834 33.548 -3.158 -1.023 2.685 31.796 A A 7 8 17.990 B B 10 9 3.398 9.706 -0.299 -1.887 AA_DC7DC8:DG9DG10_BB 7 -0.443 0.822 30.311 -5.138 0.468 diffrn_detector chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Data collection Database references Derived calculations 1 0 1993-07-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2018-04-18 1 4 2024-02-07 _diffrn_detector.detector _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag BNL Y NDB 1993-02-12 REL HOH water HOH 18 2 HOH HOH 18 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 24 2 HOH HOH 24 A HOH 27 2 HOH HOH 27 A HOH 29 2 HOH HOH 29 A HOH 30 2 HOH HOH 30 A HOH 31 2 HOH HOH 31 A HOH 33 2 HOH HOH 33 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 38 2 HOH HOH 38 A HOH 39 2 HOH HOH 39 A HOH 40 2 HOH HOH 40 A HOH 43 2 HOH HOH 43 A HOH 44 2 HOH HOH 44 A HOH 46 2 HOH HOH 46 A HOH 49 2 HOH HOH 49 A HOH 56 2 HOH HOH 56 A HOH 57 2 HOH HOH 57 A HOH 58 2 HOH HOH 58 A HOH 60 2 HOH HOH 60 A HOH 61 2 HOH HOH 61 A HOH 66 2 HOH HOH 66 A HOH 70 2 HOH HOH 70 A HOH 72 2 HOH HOH 72 A HOH 79 2 HOH HOH 79 A HOH 80 2 HOH HOH 80 A HOH 81 2 HOH HOH 81 A HOH 82 2 HOH HOH 82 A HOH 83 2 HOH HOH 83 A HOH 84 2 HOH HOH 84 A HOH 86 2 HOH HOH 86 A HOH 87 2 HOH HOH 87 A HOH 89 2 HOH HOH 89 A HOH 90 2 HOH HOH 90 A HOH 91 2 HOH HOH 91 A HOH 92 2 HOH HOH 92 A HOH 93 2 HOH HOH 93 A HOH 94 2 HOH HOH 94 A HOH 96 2 HOH HOH 96 A HOH 98 2 HOH HOH 98 A HOH 100 2 HOH HOH 100 A HOH 101 2 HOH HOH 101 A HOH 17 2 HOH HOH 17 B HOH 21 2 HOH HOH 21 B HOH 22 2 HOH HOH 22 B HOH 23 2 HOH HOH 23 B HOH 25 2 HOH HOH 25 B HOH 26 2 HOH HOH 26 B HOH 28 2 HOH HOH 28 B HOH 32 2 HOH HOH 32 B HOH 37 2 HOH HOH 37 B HOH 41 2 HOH HOH 41 B HOH 42 2 HOH HOH 42 B HOH 45 2 HOH HOH 45 B HOH 47 2 HOH HOH 47 B HOH 48 2 HOH HOH 48 B HOH 50 2 HOH HOH 50 B HOH 51 2 HOH HOH 51 B HOH 52 2 HOH HOH 52 B HOH 53 2 HOH HOH 53 B HOH 54 2 HOH HOH 54 B HOH 55 2 HOH HOH 55 B HOH 59 2 HOH HOH 59 B HOH 62 2 HOH HOH 62 B HOH 63 2 HOH HOH 63 B HOH 64 2 HOH HOH 64 B HOH 65 2 HOH HOH 65 B HOH 67 2 HOH HOH 67 B HOH 68 2 HOH HOH 68 B HOH 69 2 HOH HOH 69 B HOH 71 2 HOH HOH 71 B HOH 73 2 HOH HOH 73 B HOH 74 2 HOH HOH 74 B HOH 75 2 HOH HOH 75 B HOH 76 2 HOH HOH 76 B HOH 77 2 HOH HOH 77 B HOH 78 2 HOH HOH 78 B HOH 85 2 HOH HOH 85 B HOH 88 2 HOH HOH 88 B HOH 95 2 HOH HOH 95 B HOH 97 2 HOH HOH 97 B HOH 99 2 HOH HOH 99 B G 1 n 1 DG 1 A G 2 n 2 DG 2 A +U 3 n 3 BRU 3 A A 4 n 4 DA 4 A +U 5 n 5 BRU 5 A A 6 n 6 DA 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A G 9 n 1 DG 9 B G 10 n 2 DG 10 B +U 11 n 3 BRU 11 B A 12 n 4 DA 12 B +U 13 n 5 BRU 13 B A 14 n 6 DA 14 B C 15 n 7 DC 15 B C 16 n 8 DC 16 B author_defined_assembly 2 dimeric A BRU 3 A BRU 3 DU A BRU 5 A BRU 5 DU B BRU 11 B BRU 3 DU B BRU 13 B BRU 5 DU 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 A C5' O DG HOH 1 79 1.94 1 10.14 1.20 115.70 125.84 A A A C5' C4' C3' DG DG DG 1 1 1 N 1 9.69 1.50 119.60 129.29 A A A OP1 P OP2 DG DG DG 2 2 2 N 1 -7.57 0.90 105.70 98.13 A A A O5' P OP1 DG DG DG 2 2 2 N 1 -2.66 0.40 104.50 101.84 A A A O4' C4' C3' DA DA DA 4 4 4 N 1 -4.95 0.70 108.00 103.05 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 9.82 1.10 110.50 120.32 A A A O3' P OP2 BRU DA DA 5 6 6 Y 1 8.87 1.10 110.50 119.37 A A A O3' P OP2 DA DC DC 6 7 7 Y 1 1.91 0.30 108.30 110.21 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 -4.72 0.40 104.50 99.78 A A A O4' C4' C3' DC DC DC 8 8 8 N 1 7.21 1.10 109.80 117.01 B B B C5' C4' O4' DG DG DG 9 9 9 N 1 -4.47 0.70 102.20 97.73 B B B C4' C3' C2' DG DG DG 9 9 9 N 1 3.25 0.50 111.50 114.75 B B B C5 C6 N1 DG DG DG 9 9 9 N 1 6.83 1.10 110.50 117.33 B B B O3' P OP2 BRU DA DA 11 12 12 Y 1 -5.88 0.90 105.70 99.82 B B B O5' P OP2 DA DA DA 12 12 12 N 1 -2.88 0.40 104.50 101.62 B B B O4' C4' C3' DA DA DA 14 14 14 N 1 17.20 1.50 119.60 136.80 B B B OP1 P OP2 DC DC DC 16 16 16 N 1 A A P O5' DA DA 4 4 0.064 0.010 1.593 1.657 N 1 A A O3' P DA BRU 4 5 -0.083 0.012 1.607 1.524 Y 1 B B P OP2 DC DC 16 16 -0.110 0.017 1.485 1.375 N 1 B A OP1 O DC HOH 15 83 1.86 1_555 6_655 1 A B O O HOH HOH 35 88 1.94 1_555 3_664 1 A B O O HOH HOH 35 26 2.00 1_555 5_564 0.14 1.700 10.000 4428 1 2.000 TR isotropic TR isotropic 1.700 10.000 85 407 4 318 0 fix fix 1.700 115D 4669 2.000 1,2 refinement NUCLSQ ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION 1 N N 1 N N 2 N N 2 N N covale 1.602 both A DG 2 A O3' DG 2 1_555 A BRU 3 A P BRU 3 1_555 covale 1.586 both A BRU 3 A O3' BRU 3 1_555 A DA 4 A P DA 4 1_555 covale 1.524 both A DA 4 A O3' DA 4 1_555 A BRU 5 A P BRU 5 1_555 covale 1.536 both A BRU 5 A O3' BRU 5 1_555 A DA 6 A P DA 6 1_555 covale 1.540 both B DG 10 B O3' DG 2 1_555 B BRU 11 B P BRU 3 1_555 covale 1.567 both B BRU 11 B O3' BRU 3 1_555 B DA 12 B P DA 4 1_555 covale 1.625 both B DA 12 B O3' DA 4 1_555 B BRU 13 B P BRU 5 1_555 covale 1.658 both B BRU 13 B O3' BRU 5 1_555 B DA 14 B P DA 6 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 16 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 16 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 16 B N4 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 15 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 15 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 15 B N4 DC 7 1_555 hydrog WATSON-CRICK A BRU 3 A N3 BRU 3 1_555 B DA 14 B N1 DA 6 1_555 hydrog WATSON-CRICK A BRU 3 A O4 BRU 3 1_555 B DA 14 B N6 DA 6 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B BRU 13 B N3 BRU 5 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B BRU 13 B O4 BRU 5 1_555 hydrog WATSON-CRICK A BRU 5 A N3 BRU 5 1_555 B DA 12 B N1 DA 4 1_555 hydrog WATSON-CRICK A BRU 5 A O4 BRU 5 1_555 B DA 12 B N6 DA 4 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B BRU 11 B N3 BRU 3 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B BRU 11 B O4 BRU 3 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 10 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 10 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 10 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 9 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 9 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 9 B N2 DG 1 1_555 DNA A-DNA, DOUBLE HELIX, MODIFIED, DNA 115D PDB 1 115D 1 8 115D 1 8 115D A 1 1 8 9 16 115D 9 16 115D B 1 1 8 169 P 61