0.039705 0.000000 0.000000 0.000000 0.024871 0.000000 0.000000 0.000000 0.015231 0.00000 0.00000 0.00000 Hu, L.D. Shui, X. McFail-Isom, L. Williams, G.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.186 40.208 65.656 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 H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C10 H26 N4 202.340 SPERMINE non-polymer US Biochemistry BICHAW 0033 0006-2960 37 8341 8355 10.1021/bi973073c 9622486 The B-DNA dodecamer at high resolution reveals a spine of water on sodium. 1998 10.2210/pdb355d/pdb pdb_0000355d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 136.00 1 CCD ADSC GRAPHITE M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 202.340 SPERMINE 1 syn non-polymer 18.015 water 166 nat water no no (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.27 45.78 VAPOR DIFFUSION, SITTING DROP 6.50 pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.00K 298.00 WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE_HCL 1 N,N'-BIS(4-AMINOBUTYL)-(2,7-ANTHROQUINONEDISULFONAMIDE DIHYDROCHLORIDE) 1 WATER 2 MPD 2 6.930 1 19 A 1 B 24 -0.606 A_DC1:DG24_B 1 -17.308 0.276 0.073 -0.140 9.341 1 19 A 2 B 23 -2.077 A_DG2:DC23_B 2 -14.302 -0.236 0.491 -0.182 -4.433 1 19 A 3 B 22 0.434 A_DC3:DG22_B 3 -5.405 0.244 0.159 -0.171 10.806 1 19 A 4 B 21 1.012 A_DG4:DC21_B 4 -9.449 -0.255 0.008 -0.115 4.724 1 20 A 5 B 20 1.601 A_DA5:DT20_B 5 -15.314 -0.037 0.011 -0.107 0.442 1 20 A 6 B 19 6.233 A_DA6:DT19_B 6 -15.001 0.051 0.065 -0.050 -0.264 1 20 A 7 B 18 3.928 A_DT7:DA18_B 7 -16.744 -0.037 0.173 -0.117 -1.561 1 20 A 8 B 17 5.120 A_DT8:DA17_B 8 -16.364 -0.108 -0.004 -0.120 -12.410 1 19 A 9 B 16 -1.223 A_DC9:DG16_B 9 -10.274 0.209 0.003 -0.127 4.205 1 19 A 10 B 15 3.206 A_DG10:DC15_B 10 -9.603 -0.106 0.239 -0.053 0.283 1 19 A 11 B 14 -1.755 A_DC11:DG14_B 11 -17.417 0.156 0.208 -0.130 4.671 1 19 A 12 B 13 -1.620 A_DG12:DC13_B 12 -4.954 -0.244 0.254 -0.069 3.090 33.940 A A 1 2 14.766 B B 24 23 3.200 8.520 0.087 0.039 AA_DC1DG2:DC23DG24_BB 1 -3.216 5.573 32.731 -1.273 -0.654 3.517 44.844 A A 2 3 -11.952 B B 23 22 3.691 -9.055 0.496 0.668 AA_DG2DC3:DG22DC23_BB 2 2.847 -3.757 43.879 1.792 -0.363 2.977 27.519 A A 3 4 24.457 B B 22 21 3.000 11.300 -0.138 0.593 AA_DC3DG4:DC21DG22_BB 3 0.967 -2.092 25.114 -1.405 0.518 3.396 37.556 A A 4 5 2.133 B B 21 20 3.388 1.373 -0.453 -0.139 AA_DG4DA5:DT20DC21_BB 4 -1.585 2.463 37.500 -0.402 0.489 3.293 37.524 A A 5 6 0.713 B B 20 19 3.298 0.459 0.171 -0.325 AA_DA5DA6:DT19DT20_BB 5 -0.330 0.514 37.520 -0.566 -0.310 3.256 32.512 A A 6 7 -4.783 B B 19 18 3.219 -2.675 -0.011 -0.601 AA_DA6DT7:DA18DT19_BB 6 -0.311 0.556 32.403 -0.610 -0.034 3.218 33.798 A A 7 8 -1.676 B B 18 17 3.216 -0.974 -0.082 -0.397 AA_DT7DT8:DA17DA18_BB 7 1.681 -2.893 33.744 -0.529 0.408 3.467 42.174 A A 8 9 -2.344 B B 17 16 3.465 -1.686 -0.267 -0.226 AA_DT8DC9:DG16DA17_BB 8 0.684 -0.951 42.136 -0.130 0.446 3.031 27.145 A A 9 10 8.967 B B 16 15 3.068 4.180 0.700 0.776 AA_DC9DG10:DC15DG16_BB 9 -3.656 7.844 26.581 0.660 -2.360 3.297 42.688 A A 10 11 -12.975 B B 15 14 3.371 -9.368 -1.311 0.360 AA_DG10DC11:DG14DC15_BB 10 -2.853 3.951 41.601 1.467 1.504 3.161 33.964 A A 11 12 11.528 B B 14 13 3.174 6.692 -0.309 0.211 AA_DC11DG12:DC13DG14_BB 11 -0.679 1.169 33.310 -0.686 0.423 database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Refinement description 1 0 1997-10-13 1 1 2008-05-22 1 2 2011-07-13 1 3 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id NDB Y NDB 1997-10-07 REL REL MG MAGNESIUM ION SPM SPERMINE HOH water 32630 synthetic construct sample 227D NDB ENTRY GDL036 (PDB ENTRY 227D) PDB experimental model MO6 25 2 MG MG 25 A SPM 26 3 SPM SPM 26 B HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 31 4 HOH HOH 31 A HOH 32 4 HOH HOH 32 A HOH 33 4 HOH HOH 33 A HOH 35 4 HOH HOH 35 A HOH 36 4 HOH HOH 36 A HOH 39 4 HOH HOH 39 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 42 4 HOH HOH 42 A HOH 47 4 HOH HOH 47 A HOH 49 4 HOH HOH 49 A HOH 51 4 HOH HOH 51 A HOH 52 4 HOH HOH 52 A HOH 53 4 HOH HOH 53 A HOH 54 4 HOH HOH 54 A HOH 55 4 HOH HOH 55 A HOH 57 4 HOH HOH 57 A HOH 58 4 HOH HOH 58 A HOH 59 4 HOH HOH 59 A HOH 60 4 HOH HOH 60 A HOH 62 4 HOH HOH 62 A HOH 64 4 HOH HOH 64 A HOH 65 4 HOH HOH 65 A HOH 66 4 HOH HOH 66 A HOH 67 4 HOH HOH 67 A HOH 68 4 HOH HOH 68 A HOH 69 4 HOH HOH 69 A HOH 71 4 HOH HOH 71 A HOH 72 4 HOH HOH 72 A HOH 76 4 HOH HOH 76 A HOH 78 4 HOH HOH 78 A HOH 80 4 HOH HOH 80 A HOH 84 4 HOH HOH 84 A HOH 86 4 HOH HOH 86 A HOH 87 4 HOH HOH 87 A HOH 91 4 HOH HOH 91 A HOH 92 4 HOH HOH 92 A HOH 95 4 HOH HOH 95 A HOH 96 4 HOH HOH 96 A HOH 97 4 HOH HOH 97 A HOH 98 4 HOH HOH 98 A HOH 99 4 HOH HOH 99 A HOH 100 4 HOH HOH 100 A HOH 101 4 HOH HOH 101 A HOH 102 4 HOH HOH 102 A HOH 104 4 HOH HOH 104 A HOH 106 4 HOH HOH 106 A HOH 110 4 HOH HOH 110 A HOH 111 4 HOH HOH 111 A HOH 113 4 HOH HOH 113 A HOH 115 4 HOH HOH 115 A HOH 118 4 HOH HOH 118 A HOH 119 4 HOH HOH 119 A HOH 120 4 HOH HOH 120 A HOH 122 4 HOH HOH 122 A HOH 123 4 HOH HOH 123 A HOH 124 4 HOH HOH 124 A HOH 125 4 HOH HOH 125 A HOH 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 130 4 HOH HOH 130 A HOH 131 4 HOH HOH 131 A HOH 135 4 HOH HOH 135 A HOH 137 4 HOH HOH 137 A HOH 142 4 HOH HOH 142 A HOH 150 4 HOH HOH 150 A HOH 155 4 HOH HOH 155 A HOH 158 4 HOH HOH 158 A HOH 159 4 HOH HOH 159 A HOH 160 4 HOH HOH 160 A HOH 161 4 HOH HOH 161 A HOH 162 4 HOH HOH 162 A HOH 166 4 HOH HOH 166 A HOH 168 4 HOH HOH 168 A HOH 170 4 HOH HOH 170 A HOH 172 4 HOH HOH 172 A HOH 173 4 HOH HOH 173 A HOH 174 4 HOH HOH 174 A HOH 175 4 HOH HOH 175 A HOH 182 4 HOH HOH 182 A HOH 183 4 HOH HOH 183 A HOH 185 4 HOH HOH 185 A HOH 186 4 HOH HOH 186 A MO6 25 4 HOH HOH 188 A MO6 25 4 HOH HOH 189 A MO6 25 4 HOH HOH 191 A HOH 27 4 HOH HOH 27 B HOH 30 4 HOH HOH 30 B HOH 34 4 HOH HOH 34 B HOH 37 4 HOH HOH 37 B HOH 38 4 HOH HOH 38 B HOH 43 4 HOH HOH 43 B HOH 44 4 HOH HOH 44 B HOH 45 4 HOH HOH 45 B HOH 46 4 HOH HOH 46 B HOH 48 4 HOH HOH 48 B HOH 50 4 HOH HOH 50 B HOH 56 4 HOH HOH 56 B HOH 61 4 HOH HOH 61 B HOH 63 4 HOH HOH 63 B HOH 70 4 HOH HOH 70 B HOH 73 4 HOH HOH 73 B HOH 74 4 HOH HOH 74 B HOH 75 4 HOH HOH 75 B HOH 77 4 HOH HOH 77 B HOH 79 4 HOH HOH 79 B HOH 81 4 HOH HOH 81 B HOH 82 4 HOH HOH 82 B HOH 83 4 HOH HOH 83 B HOH 85 4 HOH HOH 85 B HOH 88 4 HOH HOH 88 B HOH 89 4 HOH HOH 89 B HOH 90 4 HOH HOH 90 B HOH 93 4 HOH HOH 93 B HOH 94 4 HOH HOH 94 B HOH 103 4 HOH HOH 103 B HOH 105 4 HOH HOH 105 B HOH 107 4 HOH HOH 107 B HOH 108 4 HOH HOH 108 B HOH 109 4 HOH HOH 109 B HOH 112 4 HOH HOH 112 B HOH 114 4 HOH HOH 114 B HOH 116 4 HOH HOH 116 B HOH 117 4 HOH HOH 117 B HOH 121 4 HOH HOH 121 B HOH 128 4 HOH HOH 128 B HOH 129 4 HOH HOH 129 B HOH 132 4 HOH HOH 132 B HOH 133 4 HOH HOH 133 B HOH 134 4 HOH HOH 134 B HOH 136 4 HOH HOH 136 B HOH 138 4 HOH HOH 138 B HOH 139 4 HOH HOH 139 B HOH 140 4 HOH HOH 140 B HOH 141 4 HOH HOH 141 B HOH 143 4 HOH HOH 143 B HOH 144 4 HOH HOH 144 B HOH 145 4 HOH HOH 145 B HOH 146 4 HOH HOH 146 B HOH 147 4 HOH HOH 147 B HOH 148 4 HOH HOH 148 B HOH 149 4 HOH HOH 149 B HOH 151 4 HOH HOH 151 B HOH 152 4 HOH HOH 152 B HOH 153 4 HOH HOH 153 B HOH 154 4 HOH HOH 154 B HOH 156 4 HOH HOH 156 B HOH 157 4 HOH HOH 157 B HOH 163 4 HOH HOH 163 B HOH 164 4 HOH HOH 164 B HOH 165 4 HOH HOH 165 B HOH 167 4 HOH HOH 167 B HOH 169 4 HOH HOH 169 B HOH 171 4 HOH HOH 171 B HOH 176 4 HOH HOH 176 B HOH 177 4 HOH HOH 177 B HOH 178 4 HOH HOH 178 B HOH 179 4 HOH HOH 179 B HOH 180 4 HOH HOH 180 B HOH 181 4 HOH HOH 181 B HOH 184 4 HOH HOH 184 B MO6 25 4 HOH HOH 187 B MO6 25 4 HOH HOH 190 B MO6 25 4 HOH HOH 192 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B G 16 n 4 DG 16 B A 17 n 5 DA 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B T 20 n 8 DT 20 B C 21 n 9 DC 21 B G 22 n 10 DG 22 B C 23 n 11 DC 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric A HOH 188 E O HOH 1_555 A MG 25 C MG MG 1_555 A HOH 189 E O HOH 1_555 92.2 A HOH 188 E O HOH 1_555 A MG 25 C MG MG 1_555 A HOH 191 E O HOH 1_555 92.6 A HOH 189 E O HOH 1_555 A MG 25 C MG MG 1_555 A HOH 191 E O HOH 1_555 85.1 A HOH 188 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 187 F O HOH 1_555 86.0 A HOH 189 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 187 F O HOH 1_555 177.9 A HOH 191 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 187 F O HOH 1_555 96.3 A HOH 188 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 190 F O HOH 1_555 173.2 A HOH 189 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 190 F O HOH 1_555 93.9 A HOH 191 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 190 F O HOH 1_555 91.0 B HOH 187 F O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 190 F O HOH 1_555 87.8 A HOH 188 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 90.2 A HOH 189 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 89.7 A HOH 191 E O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 174.1 B HOH 187 F O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 89.1 B HOH 190 F O HOH 1_555 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 86.7 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 B C8 SPM 26 D C8 SPM 1 1 N 1 B C9 SPM 26 D C9 SPM 1 1 N 1 B N10 SPM 26 D N10 SPM 1 1 N 1 B C11 SPM 26 D C11 SPM 1 1 N 1 B C12 SPM 26 D C12 SPM 1 1 N 1 B C13 SPM 26 D C13 SPM 1 1 N 1 B N14 SPM 26 D N14 SPM 1 1 N 0.2160000 0.1970000 0.1970000 1.400 10.000 11438 1 0.000 NDB ENTRY GDL036 (PDB ENTRY 227D) TR isotropic TR isotropic 1.400 10.000 160 660 14 486 0 0.007 1.42 0.2410000 1.46 784 64.00 fix fix 1.380 355D 58307 11594 1 refinement X-PLOR data collection ADSC THE B-DNA DODECAMER AT HIGH RESOLUTION 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N metalc 2.043 A MG 25 C MG MG 1_555 A HOH 188 E O HOH 1_555 metalc 2.047 A MG 25 C MG MG 1_555 A HOH 189 E O HOH 1_555 metalc 2.063 A MG 25 C MG MG 1_555 A HOH 191 E O HOH 1_555 metalc 2.075 A MG 25 C MG MG 1_555 B HOH 187 F O HOH 1_555 metalc 2.074 A MG 25 C MG MG 1_555 B HOH 190 F O HOH 1_555 metalc 2.109 A MG 25 C MG MG 1_555 B HOH 192 F O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA B-DNA, DOUBLE HELIX, SODIUM FORM, DNA 355D PDB 1 355D 1 12 355D 1 12 355D A 1 1 12 13 24 355D 13 24 355D B 1 1 12 BINDING SITE FOR RESIDUE SPM B 26 B SPM 26 Software 4 BINDING SITE FOR RESIDUE MG A 25 A MG 25 Software 6 A DG 10 A DG 10 4 1_555 B DC 13 B DC 1 4 1_555 B DG 14 B DG 2 4 1_555 B HOH 152 F HOH 4 2_564 A HOH 188 E HOH 6 1_555 A HOH 189 E HOH 6 1_555 A HOH 191 E HOH 6 1_555 B HOH 187 F HOH 6 1_555 B HOH 190 F HOH 6 1_555 B HOH 192 F HOH 6 1_555 19 P 21 21 21