0.040064 -0.000000 0.000000 0.000000 0.022952 0.000000 0.000000 0.000000 0.022026 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 24.96 43.57 45.40 C12 H18 F N2 O9 P 384.251 n 2'-O-FLUOROETHYL-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 F 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 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 O N 45 N P N 46 N O N 47 N O N 48 N O N 49 N C N 50 R C N 51 N O N 52 S C N 53 N O N 54 N C N 55 R C Y 56 N N Y 57 N C Y 58 N N Y 59 N C Y 60 N C N 61 N N Y 62 N N Y 63 N C Y 64 N N Y 65 N C N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N O N 81 N P N 82 N O N 83 N O N 84 N O N 85 N C N 86 R C N 87 N O N 88 S C N 89 N O N 90 N C N 91 R C N 92 N N N 93 N C N 94 N O N 95 N N N 96 N C N 97 N N N 98 N C N 99 N C N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 N C N 125 R C Y 126 N N Y 127 N C Y 128 N N Y 129 N C N 130 N C N 131 N O N 132 N N N 133 N C N 134 N N N 135 N N Y 136 N C N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N O N 152 N P N 153 N O N 154 N O N 155 N O N 156 N C N 157 R C N 158 N O N 159 S C N 160 N O N 161 N C N 162 R C N 163 N N N 164 N C N 165 N O N 166 N N N 167 N C N 168 N O N 169 N C N 170 N C N 171 N C N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N O N 188 N H N 189 N H N 190 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 doub 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 sing N 66 N sing N 67 N sing Y 68 N sing Y 69 N sing Y 70 N doub N 71 N sing Y 72 N sing Y 73 N sing Y 74 N doub N 75 N sing Y 76 N doub N 77 N sing N 78 N sing Y 79 N sing Y 80 N doub N 81 N sing Y 82 N sing N 83 N sing N 84 N sing N 85 N doub 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 sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub 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 doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub 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 N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing Y 141 N sing Y 142 N sing Y 143 N doub N 144 N sing Y 145 N sing N 146 N sing Y 147 N doub N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N doub N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N doub N 187 N sing N 188 N sing N 189 N doub N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 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/pdb1i0g/pdb pdb_00001i0g 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 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 3107.048 5'-D(*GP*CP*GP*TP*AP*(125)P*AP*CP*GP*C)-3' 2 syn polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 92 nat water no yes (DG)(DC)(DG)(DT)(DA)(125)(DA)(DC)(DG)(DC) GCGTAUACGC A,B polydeoxyribonucleotide n n n n n n n n n n 1 1.91 35.53 VAPOR DIFFUSION, HANGING DROP 6.0 Na, Mg salts, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298 K 298 3.005 1 19 A 1 B 20 -1.769 A_DG1:DC20_B 1 -9.902 -0.280 0.196 -0.232 6.503 1 19 A 2 B 19 1.803 A_DC2:DG19_B 2 -14.743 0.160 0.114 -0.086 -9.730 1 19 A 3 B 18 0.783 A_DG3:DC18_B 3 -18.698 -0.345 0.000 -0.140 -3.069 1 20 A 4 B 17 0.625 A_DT4:DA17_B 4 -17.144 -0.173 -0.121 -0.130 -2.838 1 20 A 5 B 16 -3.851 A_DA5:12516_B 5 -11.450 0.255 0.122 -0.042 5.184 1 20 A 6 B 15 4.196 A_1256:DA15_B 6 -13.212 -0.125 0.140 -0.060 4.464 1 20 A 7 B 14 3.094 A_DA7:DT14_B 7 -11.413 -0.065 -0.035 -0.144 6.331 1 19 A 8 B 13 2.140 A_DC8:DG13_B 8 -12.028 0.221 -0.146 -0.199 -5.611 1 19 A 9 B 12 2.686 A_DG9:DC12_B 9 -10.025 -0.025 0.158 -0.100 -2.302 1 19 A 10 B 11 0.137 A_DC10:DG11_B 10 2.684 0.300 0.211 -0.160 3.168 39.391 A A 1 2 0.752 B B 20 19 3.176 0.507 0.456 -1.373 AA_DG1DC2:DG19DC20_BB 1 0.893 -1.325 39.378 -2.095 -0.574 2.433 28.808 A A 2 3 23.341 B B 19 18 3.495 11.308 0.100 -2.053 AA_DC2DG3:DC18DG19_BB 2 1.438 -2.969 26.501 -6.518 0.103 2.792 37.219 A A 3 4 9.559 B B 18 17 3.000 6.073 -0.958 -1.359 AA_DG3DT4:DA17DC18_BB 3 -1.892 2.978 36.690 -2.849 1.277 1.653 33.912 A A 4 5 38.705 B B 17 16 3.186 21.007 0.653 -1.480 AA_DT4DA5:12516DA17_BB 4 1.482 -2.730 26.732 -5.352 -0.922 2.958 31.496 A A 5 6 6.889 B B 16 15 3.096 3.730 0.755 -1.271 AA_DA51256:DA1512516_BB 5 1.406 -2.597 31.249 -2.988 -1.146 2.279 34.678 A A 6 7 24.966 B B 15 14 3.110 14.451 -0.052 -1.379 AA_1256DA7:DT14DA15_BB 6 1.042 -1.800 31.591 -4.232 0.225 3.094 31.703 A A 7 8 7.138 B B 14 13 3.312 3.888 0.249 -1.691 AA_DA7DC8:DG13DT14_BB 7 1.524 -2.798 31.433 -3.799 -0.181 2.392 30.643 A A 8 9 23.859 B B 13 12 3.427 12.268 -0.249 -1.955 AA_DC8DG9:DC12DG13_BB 8 -1.228 2.388 28.108 -5.949 0.245 3.396 34.474 A A 9 10 -0.766 B B 12 11 3.372 -0.454 0.168 -1.659 AA_DG9DC10:DG11DC12_BB 9 0.890 -1.501 34.459 -2.726 -0.141 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.pdbx_leaving_atom_flag _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 REL NA SODIUM ION HOH water NA 22 2 NA NA 22 A HOH 23 3 HOH HOH 23 A HOH 100 3 HOH HOH 100 A HOH 101 3 HOH HOH 101 A HOH 104 3 HOH HOH 104 A HOH 105 3 HOH HOH 105 A HOH 109 3 HOH HOH 109 A HOH 110 3 HOH HOH 110 A HOH 112 3 HOH HOH 112 A HOH 113 3 HOH HOH 113 A HOH 114 3 HOH HOH 114 A HOH 115 3 HOH HOH 115 A HOH 116 3 HOH HOH 116 A HOH 117 3 HOH HOH 117 A HOH 118 3 HOH HOH 118 A HOH 120 3 HOH HOH 120 A HOH 122 3 HOH HOH 122 A HOH 126 3 HOH HOH 126 A HOH 127 3 HOH HOH 127 A HOH 128 3 HOH HOH 128 A HOH 130 3 HOH HOH 130 A HOH 133 3 HOH HOH 133 A HOH 137 3 HOH HOH 137 A HOH 140 3 HOH HOH 140 A HOH 141 3 HOH HOH 141 A HOH 144 3 HOH HOH 144 A HOH 146 3 HOH HOH 146 A HOH 147 3 HOH HOH 147 A HOH 148 3 HOH HOH 148 A HOH 150 3 HOH HOH 150 A HOH 152 3 HOH HOH 152 A HOH 153 3 HOH HOH 153 A HOH 155 3 HOH HOH 155 A HOH 158 3 HOH HOH 158 A HOH 160 3 HOH HOH 160 A HOH 161 3 HOH HOH 161 A HOH 162 3 HOH HOH 162 A HOH 163 3 HOH HOH 163 A HOH 164 3 HOH HOH 164 A HOH 166 3 HOH HOH 166 A HOH 167 3 HOH HOH 167 A HOH 173 3 HOH HOH 173 A HOH 175 3 HOH HOH 175 A HOH 179 3 HOH HOH 179 A HOH 182 3 HOH HOH 182 A HOH 184 3 HOH HOH 184 A HOH 185 3 HOH HOH 185 A HOH 186 3 HOH HOH 186 A HOH 190 3 HOH HOH 190 A HOH 24 3 HOH HOH 24 B HOH 102 3 HOH HOH 102 B HOH 106 3 HOH HOH 106 B HOH 107 3 HOH HOH 107 B HOH 108 3 HOH HOH 108 B HOH 111 3 HOH HOH 111 B HOH 121 3 HOH HOH 121 B HOH 123 3 HOH HOH 123 B HOH 124 3 HOH HOH 124 B HOH 125 3 HOH HOH 125 B HOH 129 3 HOH HOH 129 B HOH 131 3 HOH HOH 131 B HOH 132 3 HOH HOH 132 B HOH 134 3 HOH HOH 134 B HOH 135 3 HOH HOH 135 B HOH 136 3 HOH HOH 136 B HOH 138 3 HOH HOH 138 B HOH 139 3 HOH HOH 139 B HOH 142 3 HOH HOH 142 B HOH 143 3 HOH HOH 143 B HOH 149 3 HOH HOH 149 B HOH 151 3 HOH HOH 151 B HOH 154 3 HOH HOH 154 B HOH 156 3 HOH HOH 156 B HOH 157 3 HOH HOH 157 B HOH 159 3 HOH HOH 159 B HOH 165 3 HOH HOH 165 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 174 3 HOH HOH 174 B HOH 176 3 HOH HOH 176 B HOH 177 3 HOH HOH 177 B HOH 178 3 HOH HOH 178 B HOH 180 3 HOH HOH 180 B HOH 181 3 HOH HOH 181 B HOH 183 3 HOH HOH 183 B HOH 187 3 HOH HOH 187 B HOH 188 3 HOH HOH 188 B HOH 189 3 HOH HOH 189 B HOH 191 3 HOH HOH 191 B HOH 192 3 HOH HOH 192 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 125 6 n 6 125 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 125 16 n 6 125 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 DT 4 A O4 DT 4 1_555 A NA 22 C NA NA 1_555 B HOH 159 E O HOH 1_555 122.4 A 125 6 A 125 6 U B 125 16 B 125 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 B O O HOH HOH 167 187 1.36 1 B B O O HOH HOH 174 180 1.56 1 B B O O HOH HOH 156 171 1.74 1 B B O O HOH HOH 170 176 1.97 1 B B O O HOH HOH 180 181 2.02 1 A A O O HOH HOH 148 184 2.05 1 B B O O HOH HOH 138 168 2.06 1 A B O O HOH HOH 112 187 2.07 1 B B OP1 O DG HOH 13 178 2.19 1 B B O O HOH HOH 172 189 1.81 1_555 2_554 1 A B O O HOH HOH 152 156 1.87 1_555 3_555 1 A B O O HOH HOH 152 192 2.10 1_555 4_556 1 A B O O HOH HOH 160 188 2.19 1_555 3_555 0.19 0.159 0.159 1.45 20 8695 8695 random 1 THROUGHOUT 0 0 MOLECULAR REPLACEMENT 1.45 20 92 505 1 412 0 1.45 20 1I0G 8695 8695 0 0 0.058 1 99.7 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement SHELXL-97 1.45 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-FLUOROETHYL THYMINE IN PLACE OF T6, MEDIUM NA-SALT 1 N N 1 N N 2 N N 3 N N 3 N N covale 1.601 both A DA 5 A O3' DA 5 1_555 A 125 6 A P 125 6 1_555 covale 1.607 both A 125 6 A O3' 125 6 1_555 A DA 7 A P DA 7 1_555 covale 1.608 both B DA 15 B O3' DA 5 1_555 B 125 16 B P 125 6 1_555 covale 1.614 both B 125 16 B O3' 125 6 1_555 B DA 17 B P DA 7 1_555 metalc 2.726 A DT 4 A O4 DT 4 1_555 A NA 22 C NA NA 1_555 metalc 2.830 A NA 22 C NA NA 1_555 B HOH 159 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 125 16 B N3 125 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B 125 16 B O4 125 6 1_555 hydrog WATSON-CRICK A 125 6 A N3 125 6 1_555 B DA 15 B N1 DA 5 1_555 hydrog WATSON-CRICK A 125 6 A O4 125 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 1I0G PDB 1 1I0G 1 10 1I0G 1 10 1I0G A 1 1 10 11 20 1I0G 11 20 1I0G B 1 1 10 BINDING SITE FOR RESIDUE NA A 22 A NA 22 Software 3 A DT 4 A DT 4 3 1_555 A DA 5 A DA 5 3 1_555 B HOH 159 E HOH 3 1_555 19 orthorhombic P 21 21 21