0.039793 -0.000000 0.000000 0.000000 0.022457 0.000000 0.000000 0.000000 0.022158 0.00000 0.00000 0.00000 Tereshko, V. Wilds, C.J. Minasov, G. Prakash, T.P. Maier, M.A. Howard, A. Wawrzak, Z. Manoharan, M. Egli, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90 90 90 25.13 44.53 45.13 C17 H29 N2 O12 P 484.392 n 2'-O-METHYL-[TRI(OXYETHYL)]-5-METHYL-URIDINE-5'-MONOPHOSPHATE RNA 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION non-polymer N 1 N P N 2 N O N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 R C N 10 N O N 11 R C N 12 N O N 13 R C N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N O N 20 N C N 21 N C N 22 N C N 23 N C N 24 N C N 25 N O N 26 N C N 27 N C N 28 N O N 29 N C N 30 N C N 31 N O N 32 N C N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H 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 O N 63 N P N 64 N O N 65 N O N 66 N O N 67 N C N 68 R C N 69 N O N 70 S C N 71 N O N 72 N C N 73 R C Y 74 N N Y 75 N C Y 76 N N Y 77 N C Y 78 N C N 79 N N Y 80 N N Y 81 N C Y 82 N N Y 83 N C N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H 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 O N 99 N P N 100 N O N 101 N O N 102 N O N 103 N C N 104 R C N 105 N O N 106 S C N 107 N O N 108 N C N 109 R C N 110 N N N 111 N C N 112 N O N 113 N N N 114 N C N 115 N N N 116 N C N 117 N C N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N O N 133 N P N 134 N O N 135 N O N 136 N O N 137 N C N 138 R C N 139 N O N 140 S C N 141 N O N 142 N C N 143 R C Y 144 N N Y 145 N C Y 146 N N Y 147 N C N 148 N C N 149 N O N 150 N N N 151 N C N 152 N N N 153 N N Y 154 N C N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N O N 170 N P N 171 N O N 172 N O N 173 N O N 174 N C N 175 R C N 176 N O N 177 S C N 178 N O N 179 N C N 180 R C N 181 N N N 182 N C N 183 N O N 184 N N N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N O N 206 N H N 207 N H N 208 N NA N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing 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 doub N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing 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 N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing 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 Y 86 N sing Y 87 N sing Y 88 N doub N 89 N sing Y 90 N sing Y 91 N sing Y 92 N doub N 93 N sing Y 94 N doub N 95 N sing N 96 N sing Y 97 N sing Y 98 N doub N 99 N sing Y 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing 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 doub N 127 N sing N 128 N doub N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N doub N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing Y 159 N sing Y 160 N sing Y 161 N doub N 162 N sing Y 163 N sing N 164 N sing Y 165 N doub N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N doub N 205 N sing N 206 N sing N 207 N doub N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 29 1208 1215 10.1093/nar/29.5.1208 11222771 Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. 2001 10.2210/pdb1i0q/pdb pdb_00001i0q 100 1 CCD 1999-11-01 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.8151 1.0 17-ID APS 0.8151 SYNCHROTRON APS BEAMLINE 17-ID 3207.189 5'-D(*GP*CP*GP*TP*AP*(126)P*AP*CP*GP*C)-3' 2 syn polymer 22.990 SODIUM ION 2 syn non-polymer 18.015 water 89 nat water no yes (DG)(DC)(DG)(DT)(DA)(126)(DA)(DC)(DG)(DC) GCGTAUACGC A,B polydeoxyribonucleotide n n n n n n n n n n 1 1.89 35.02 VAPOR DIFFUSION, HANGING DROP 6.0 Na salt, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298 K 298 3.748 1 19 A 1 B 20 -2.441 A_DG1:DC20_B 1 -8.741 -0.278 0.282 -0.184 4.351 1 19 A 2 B 19 1.361 A_DC2:DG19_B 2 -13.473 0.132 0.149 -0.084 -10.291 1 19 A 3 B 18 1.896 A_DG3:DC18_B 3 -13.487 -0.364 -0.061 -0.120 -4.814 1 20 A 4 B 17 1.584 A_DT4:DA17_B 4 -16.606 -0.161 -0.108 -0.144 -2.049 1 20 A 5 B 16 -4.815 A_DA5:12616_B 5 -12.939 0.234 0.207 -0.059 5.472 1 20 A 6 B 15 4.225 A_1266:DA15_B 6 -13.369 -0.069 0.241 -0.062 5.239 1 20 A 7 B 14 2.934 A_DA7:DT14_B 7 -11.935 -0.049 0.066 -0.106 6.871 1 19 A 8 B 13 0.862 A_DC8:DG13_B 8 -12.479 0.220 -0.100 -0.142 -4.398 1 19 A 9 B 12 0.795 A_DG9:DC12_B 9 -10.762 -0.014 0.229 -0.221 -1.648 1 19 A 10 B 11 -0.551 A_DC10:DG11_B 10 6.059 0.295 0.106 -0.120 3.182 39.454 A A 1 2 2.095 B B 20 19 3.224 1.414 0.450 -1.539 AA_DG1DC2:DG19DC20_BB 1 1.313 -1.946 39.409 -2.443 -0.515 2.550 27.115 A A 2 3 20.794 B B 19 18 3.495 9.534 0.308 -2.145 AA_DC2DG3:DC18DG19_BB 2 2.471 -5.390 25.295 -6.880 -0.060 2.821 36.922 A A 3 4 10.047 B B 18 17 3.057 6.331 -1.058 -1.429 AA_DG3DT4:DA17DC18_BB 3 -1.648 2.615 36.357 -3.031 1.469 1.542 33.278 A A 4 5 37.896 B B 17 16 3.090 20.259 0.602 -1.581 AA_DT4DA5:12616DA17_BB 4 0.621 -1.162 26.534 -5.445 -0.969 2.932 31.617 A A 5 6 7.734 B B 16 15 3.106 4.201 0.695 -1.356 AA_DA51266:DA1512616_BB 5 1.388 -2.555 31.314 -3.209 -1.038 2.319 33.875 A A 6 7 23.217 B B 15 14 3.091 13.188 -0.099 -1.413 AA_1266DA7:DT14DA15_BB 6 0.970 -1.708 31.257 -4.257 0.305 3.060 33.075 A A 7 8 7.020 B B 14 13 3.274 3.986 0.259 -1.689 AA_DA7DC8:DG13DT14_BB 7 1.137 -2.002 32.822 -3.622 -0.268 2.373 31.589 A A 8 9 22.709 B B 13 12 3.372 12.052 -0.255 -2.046 AA_DC8DG9:DC12DG13_BB 8 -2.381 4.487 29.158 -5.805 0.064 3.401 34.132 A A 9 10 -1.994 B B 12 11 3.345 -1.169 0.064 -1.842 AA_DG9DC10:DG11DC12_BB 9 2.467 -4.207 34.025 -2.947 0.294 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-04-04 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2001-01-29 REL NA SODIUM ION HOH water NA 22 2 NA NA 22 A NA 23 2 NA NA 23 A HOH 101 3 HOH HOH 101 A HOH 102 3 HOH HOH 102 A HOH 103 3 HOH HOH 103 A HOH 105 3 HOH HOH 105 A HOH 106 3 HOH HOH 106 A HOH 107 3 HOH HOH 107 A HOH 110 3 HOH HOH 110 A HOH 111 3 HOH HOH 111 A HOH 112 3 HOH HOH 112 A HOH 114 3 HOH HOH 114 A HOH 115 3 HOH HOH 115 A HOH 117 3 HOH HOH 117 A HOH 120 3 HOH HOH 120 A HOH 121 3 HOH HOH 121 A HOH 122 3 HOH HOH 122 A HOH 124 3 HOH HOH 124 A HOH 129 3 HOH HOH 129 A HOH 133 3 HOH HOH 133 A HOH 135 3 HOH HOH 135 A HOH 137 3 HOH HOH 137 A HOH 139 3 HOH HOH 139 A HOH 143 3 HOH HOH 143 A HOH 144 3 HOH HOH 144 A HOH 147 3 HOH HOH 147 A HOH 148 3 HOH HOH 148 A HOH 149 3 HOH HOH 149 A HOH 150 3 HOH HOH 150 A HOH 154 3 HOH HOH 154 A HOH 155 3 HOH HOH 155 A HOH 156 3 HOH HOH 156 A HOH 157 3 HOH HOH 157 A HOH 158 3 HOH HOH 158 A HOH 159 3 HOH HOH 159 A HOH 160 3 HOH HOH 160 A HOH 164 3 HOH HOH 164 A HOH 165 3 HOH HOH 165 A HOH 166 3 HOH HOH 166 A HOH 173 3 HOH HOH 173 A HOH 174 3 HOH HOH 174 A HOH 177 3 HOH HOH 177 A HOH 178 3 HOH HOH 178 A HOH 180 3 HOH HOH 180 A HOH 181 3 HOH HOH 181 A HOH 182 3 HOH HOH 182 A HOH 185 3 HOH HOH 185 A HOH 186 3 HOH HOH 186 A HOH 187 3 HOH HOH 187 A HOH 24 3 HOH HOH 24 B HOH 104 3 HOH HOH 104 B HOH 108 3 HOH HOH 108 B HOH 109 3 HOH HOH 109 B HOH 116 3 HOH HOH 116 B HOH 118 3 HOH HOH 118 B HOH 119 3 HOH HOH 119 B HOH 123 3 HOH HOH 123 B HOH 125 3 HOH HOH 125 B HOH 126 3 HOH HOH 126 B HOH 127 3 HOH HOH 127 B HOH 128 3 HOH HOH 128 B HOH 130 3 HOH HOH 130 B HOH 131 3 HOH HOH 131 B HOH 132 3 HOH HOH 132 B HOH 134 3 HOH HOH 134 B HOH 136 3 HOH HOH 136 B HOH 138 3 HOH HOH 138 B HOH 140 3 HOH HOH 140 B HOH 142 3 HOH HOH 142 B HOH 145 3 HOH HOH 145 B HOH 146 3 HOH HOH 146 B HOH 151 3 HOH HOH 151 B HOH 152 3 HOH HOH 152 B HOH 153 3 HOH HOH 153 B HOH 161 3 HOH HOH 161 B HOH 162 3 HOH HOH 162 B HOH 163 3 HOH HOH 163 B HOH 167 3 HOH HOH 167 B HOH 168 3 HOH HOH 168 B HOH 169 3 HOH HOH 169 B HOH 170 3 HOH HOH 170 B HOH 171 3 HOH HOH 171 B HOH 172 3 HOH HOH 172 B HOH 175 3 HOH HOH 175 B HOH 176 3 HOH HOH 176 B HOH 179 3 HOH HOH 179 B HOH 183 3 HOH HOH 183 B HOH 184 3 HOH HOH 184 B HOH 188 3 HOH HOH 188 B HOH 189 3 HOH HOH 189 B HOH 190 3 HOH HOH 190 B G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A 126 6 n 6 126 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A C 10 n 10 DC 10 A G 11 n 1 DG 11 B C 12 n 2 DC 12 B G 13 n 3 DG 13 B T 14 n 4 DT 14 B A 15 n 5 DA 15 B 126 16 n 6 126 16 B A 17 n 7 DA 17 B C 18 n 8 DC 18 B G 19 n 9 DG 19 B C 20 n 10 DC 20 B author_defined_assembly 2 dimeric A DC 10 A OP1 DC 10 1_555 A NA 23 D NA NA 1_555 A HOH 110 E O HOH 1_555 84.5 A 126 6 A 126 6 U B 126 16 B 126 6 U 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 N4 O DC HOH 8 187 1.95 1 B B O6 O DG HOH 11 171 1.96 1 B B O4' O DC HOH 18 189 1.97 1 B B O O HOH HOH 126 128 2.02 1 B B O O HOH HOH 183 188 2.05 1 A A O O HOH HOH 120 160 2.05 1 A A O O HOH HOH 155 157 2.13 1 A A O O HOH HOH 147 187 2.15 1 A A O O HOH HOH 150 160 2.18 1 A B O O HOH HOH 165 179 1.99 1_555 3_555 1 A B O O HOH HOH 186 161 2.02 1_555 3_545 1 B B O O HOH HOH 176 179 2.16 1_555 2_455 0.19 0.159 0.159 1.3 20 8695 8695 RANDOM 1 THROUGHOUT 0 0 MOLECULAR REPLACEMENT 1.3 20 89 517 2 426 0 1.3 20 1I0Q 8695 8695 0 0 0.058 1 99.7 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement SHELXL-97 1.3 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-METHYL-[TRI(OXYETHYL)] THYMINE IN PLACE OF T6, MEDIUM NA-SALT 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N covale 1.610 both A DA 5 A O3' DA 5 1_555 A 126 6 A P 126 6 1_555 covale 1.602 both A 126 6 A O3' 126 6 1_555 A DA 7 A P DA 7 1_555 covale 1.612 both B DA 15 B O3' DA 5 1_555 B 126 16 B P 126 6 1_555 covale 1.607 both B 126 16 B O3' 126 6 1_555 B DA 17 B P DA 7 1_555 metalc 2.580 A DT 4 A O4 DT 4 1_555 A NA 22 C NA NA 1_555 metalc 2.772 A DC 10 A OP1 DC 10 1_555 A NA 23 D NA NA 1_555 metalc 2.629 A NA 23 D NA NA 1_555 A HOH 110 E O HOH 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 20 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 20 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 20 B N4 DC 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 19 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 19 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 19 B N2 DG 9 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 18 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 18 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 18 B N4 DC 8 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 17 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 17 B N6 DA 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B 126 16 B N3 126 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B 126 16 B O4 126 6 1_555 hydrog WATSON-CRICK A 126 6 A N3 126 6 1_555 B DA 15 B N1 DA 5 1_555 hydrog WATSON-CRICK A 126 6 A O4 126 6 1_555 B DA 15 B N6 DA 5 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 13 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 13 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 12 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 12 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 12 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA A-form double helix, modified sugar, DNA 1I0Q PDB 1 1I0Q 1 10 1I0Q 1 10 1I0Q A 1 1 10 11 20 1I0Q 11 20 1I0Q B 1 1 10 BINDING SITE FOR RESIDUE NA A 22 A NA 22 Software 3 BINDING SITE FOR RESIDUE NA A 23 A NA 23 Software 4 A DG 3 A DG 3 3 1_555 A DT 4 A DT 4 3 1_555 A DA 5 A DA 5 3 1_555 A DC 10 A DC 10 4 1_555 A HOH 110 E HOH 4 1_555 B DT 14 B DT 4 4 4_556 B DC 20 B DC 10 4 2_555 19 orthorhombic P 21 21 21