0.039588 0.000000 0.000000 0.000000 0.022671 0.000000 0.000000 0.000000 0.021964 0.00000 0.00000 0.00000 Prhavc, M. Prakash, T.P. Minasov, G. Egli, M. Manoharan, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.260 44.110 45.530 C16 H28 N3 O10 P 453.381 n 2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate) 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 N 1 N P N 2 N O N 3 N O N 4 N O N 5 N C N 6 R C N 7 N O N 8 R C N 9 N N N 10 N C N 11 N C N 12 N O N 13 N N N 14 N C N 15 N O N 16 N C N 17 N C N 18 R C N 19 N O N 20 N C N 21 N C N 22 N O N 23 N C N 24 N C N 25 N N N 26 N C N 27 N C N 28 R C N 29 N O 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 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 O N 58 N H N 59 N O N 60 N P N 61 N O N 62 N O N 63 N O N 64 N C N 65 R C N 66 N O N 67 S C N 68 N O N 69 N C N 70 R C Y 71 N N Y 72 N C Y 73 N N Y 74 N C Y 75 N C N 76 N N Y 77 N N Y 78 N C Y 79 N N Y 80 N C N 81 N H N 82 N H N 83 N H 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 O N 96 N P N 97 N O N 98 N O N 99 N O N 100 N C N 101 R C N 102 N O N 103 S C N 104 N O N 105 N C N 106 R C N 107 N N N 108 N C N 109 N O N 110 N N N 111 N C N 112 N N N 113 N C N 114 N C N 115 N H N 116 N H N 117 N H 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 O N 130 N P N 131 N O N 132 N O N 133 N O N 134 N C N 135 R C N 136 N O N 137 S C N 138 N O N 139 N C N 140 R C Y 141 N N Y 142 N C Y 143 N N Y 144 N C N 145 N C N 146 N O N 147 N N N 148 N C N 149 N N N 150 N N Y 151 N C N 152 N H N 153 N H N 154 N H 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 O N 167 N P N 168 N O N 169 N O N 170 N O N 171 N C N 172 R C N 173 N O N 174 S C N 175 N O N 176 N C N 177 R C N 178 N N N 179 N C N 180 N O N 181 N N N 182 N C N 183 N O N 184 N C N 185 N C N 186 N C N 187 N H N 188 N H N 189 N H 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 O N 203 N H N 204 N H 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 doub N 19 N sing N 20 N doub N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing 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 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 doub N 63 N sing N 64 N sing N 65 N sing 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 Y 83 N sing Y 84 N sing Y 85 N doub N 86 N sing Y 87 N sing Y 88 N sing Y 89 N doub N 90 N sing Y 91 N doub N 92 N sing N 93 N sing Y 94 N sing Y 95 N doub N 96 N sing Y 97 N sing N 98 N sing 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 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 doub N 124 N sing N 125 N doub N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N doub N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing 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 Y 156 N sing Y 157 N sing Y 158 N doub N 159 N sing Y 160 N sing N 161 N sing Y 162 N doub N 163 N doub N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N doub N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N doub 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 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 doub N 198 N sing N 199 N sing N 200 N sing N 201 N doub N 202 N sing N 203 N sing N 204 N doub N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing US Org.Lett. 1523-7060 5 2017 2020 10.1021/ol0340991 12790517 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects 2003 10.2210/pdb1nzg/pdb pdb_00001nzg 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 Mirrors CCD 1999-06-08 MARRESEARCH Graphite SINGLE WAVELENGTH M x-ray 1 1.00000 1.0 5ID-B APS 1.00000 SYNCHROTRON APS BEAMLINE 5ID-B 3176.178 5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3' 2 syn polymer 18.015 water 101 nat water no yes (DG)(DC)(DG)(DT)(DA)(3ME)(DA)(DC)(DG)(DC) GCGTAUACGC A,B polydeoxyribonucleotide n n n n n n n n n n 1 1.71 27.47 VAPOR DIFFUSION, HANGING DROP 6.0 MPD, Sodium Cacodylate, Spermine, Sodium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K 295.0 MPD 1 Sodium Cacodylate 1 Spermine 1 Sodium Chloride 1 MPD 2 Sodium Chloride 2 0.799 1 19 A 1 B 20 -2.274 A_DG1:DC20_B 1 -7.020 -0.243 0.271 -0.168 7.658 1 19 A 2 B 19 0.675 A_DC2:DG19_B 2 -14.705 0.155 -0.009 -0.095 -8.232 1 19 A 3 B 18 1.268 A_DG3:DC18_B 3 -15.199 -0.373 0.001 -0.186 -3.162 1 20 A 4 B 17 0.288 A_DT4:DA17_B 4 -17.057 -0.157 -0.147 -0.136 -2.856 1 20 A 5 B 16 -5.065 A_DA5:3ME16_B 5 -12.201 0.257 0.114 0.007 5.327 1 20 A 6 B 15 6.126 A_3ME6:DA15_B 6 -13.532 -0.005 0.227 -0.112 5.597 1 20 A 7 B 14 2.212 A_DA7:DT14_B 7 -11.520 0.083 0.076 -0.159 10.890 1 19 A 8 B 13 2.842 A_DC8:DG13_B 8 -15.325 0.229 -0.318 -0.189 -5.636 1 19 A 9 B 12 2.209 A_DG9:DC12_B 9 -9.259 -0.014 -0.050 -0.171 -1.864 1 19 A 10 B 11 0.141 A_DC10:DG11_B 10 5.410 0.251 0.002 -0.085 3.104 39.254 A A 1 2 0.627 B B 20 19 3.102 0.421 0.351 -1.572 AA_DG1DC2:DG19DC20_BB 1 3.640 -5.426 39.090 -2.388 -0.110 2.556 27.174 A A 2 3 22.322 B B 19 18 3.566 10.238 0.258 -2.046 AA_DC2DG3:DC18DG19_BB 2 0.274 -0.598 25.204 -6.858 -0.482 2.848 37.822 A A 3 4 9.442 B B 18 17 3.059 6.094 -1.109 -1.356 AA_DG3DT4:DA17DC18_BB 3 -1.384 2.144 37.321 -2.805 1.549 1.621 32.713 A A 4 5 38.366 B B 17 16 3.193 20.125 0.590 -1.560 AA_DT4DA5:3ME16DA17_BB 4 1.461 -2.785 25.883 -5.649 -0.839 2.848 32.489 A A 5 6 9.834 B B 16 15 3.101 5.477 0.871 -1.327 AA_DA53ME6:DA153ME16_BB 5 0.246 -0.442 32.036 -3.250 -1.518 2.321 33.042 A A 6 7 23.142 B B 15 14 3.090 12.833 -0.327 -1.405 AA_3ME6DA7:DT14DA15_BB 6 0.546 -0.985 30.508 -4.344 0.655 2.994 32.072 A A 7 8 8.468 B B 14 13 3.245 4.655 0.250 -1.601 AA_DA7DC8:DG13DT14_BB 7 3.269 -5.947 31.577 -3.703 0.112 2.691 31.503 A A 8 9 22.572 B B 13 12 3.621 11.956 -0.308 -1.836 AA_DC8DG9:DC12DG13_BB 8 -1.628 3.073 29.154 -5.621 0.262 3.205 34.373 A A 9 10 3.954 B B 12 11 3.320 2.334 0.282 -1.753 AA_DG9DC10:DG11DC12_BB 9 1.360 -2.304 34.270 -3.330 -0.265 chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Non-polymer description Data collection Database references Derived calculations 1 0 2003-08-26 1 1 2008-04-29 1 2 2011-07-13 1 3 2011-11-02 1 4 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _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_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_comp_id _struct_conn.ptnr2_label_seq_id RCSB Y RCSB 2003-02-17 REL REL HOH water HOH 101 2 HOH HOH 101 A HOH 102 2 HOH HOH 102 A HOH 104 2 HOH HOH 104 A HOH 106 2 HOH HOH 106 A HOH 108 2 HOH HOH 108 A HOH 109 2 HOH HOH 109 A HOH 111 2 HOH HOH 111 A HOH 112 2 HOH HOH 112 A HOH 113 2 HOH HOH 113 A HOH 114 2 HOH HOH 114 A HOH 115 2 HOH HOH 115 A HOH 116 2 HOH HOH 116 A HOH 118 2 HOH HOH 118 A HOH 119 2 HOH HOH 119 A HOH 120 2 HOH HOH 120 A HOH 121 2 HOH HOH 121 A HOH 123 2 HOH HOH 123 A HOH 126 2 HOH HOH 126 A HOH 127 2 HOH HOH 127 A HOH 128 2 HOH HOH 128 A HOH 131 2 HOH HOH 131 A HOH 133 2 HOH HOH 133 A HOH 134 2 HOH HOH 134 A HOH 135 2 HOH HOH 135 A HOH 136 2 HOH HOH 136 A HOH 138 2 HOH HOH 138 A HOH 142 2 HOH HOH 142 A HOH 143 2 HOH HOH 143 A HOH 144 2 HOH HOH 144 A HOH 145 2 HOH HOH 145 A HOH 148 2 HOH HOH 148 A HOH 149 2 HOH HOH 149 A HOH 150 2 HOH HOH 150 A HOH 151 2 HOH HOH 151 A HOH 152 2 HOH HOH 152 A HOH 153 2 HOH HOH 153 A HOH 154 2 HOH HOH 154 A HOH 159 2 HOH HOH 159 A HOH 160 2 HOH HOH 160 A HOH 161 2 HOH HOH 161 A HOH 163 2 HOH HOH 163 A HOH 164 2 HOH HOH 164 A HOH 165 2 HOH HOH 165 A HOH 166 2 HOH HOH 166 A HOH 167 2 HOH HOH 167 A HOH 168 2 HOH HOH 168 A HOH 169 2 HOH HOH 169 A HOH 173 2 HOH HOH 173 A HOH 175 2 HOH HOH 175 A HOH 177 2 HOH HOH 177 A HOH 178 2 HOH HOH 178 A HOH 180 2 HOH HOH 180 A HOH 184 2 HOH HOH 184 A HOH 186 2 HOH HOH 186 A HOH 187 2 HOH HOH 187 A HOH 191 2 HOH HOH 191 A HOH 195 2 HOH HOH 195 A HOH 196 2 HOH HOH 196 A HOH 197 2 HOH HOH 197 A HOH 199 2 HOH HOH 199 A HOH 201 2 HOH HOH 201 A HOH 204 2 HOH HOH 204 A HOH 103 2 HOH HOH 103 B HOH 105 2 HOH HOH 105 B HOH 107 2 HOH HOH 107 B HOH 110 2 HOH HOH 110 B HOH 117 2 HOH HOH 117 B HOH 122 2 HOH HOH 122 B HOH 125 2 HOH HOH 125 B HOH 129 2 HOH HOH 129 B HOH 130 2 HOH HOH 130 B HOH 132 2 HOH HOH 132 B HOH 137 2 HOH HOH 137 B HOH 139 2 HOH HOH 139 B HOH 140 2 HOH HOH 140 B HOH 141 2 HOH HOH 141 B HOH 146 2 HOH HOH 146 B HOH 147 2 HOH HOH 147 B HOH 155 2 HOH HOH 155 B HOH 156 2 HOH HOH 156 B HOH 157 2 HOH HOH 157 B HOH 158 2 HOH HOH 158 B HOH 162 2 HOH HOH 162 B HOH 170 2 HOH HOH 170 B HOH 171 2 HOH HOH 171 B HOH 172 2 HOH HOH 172 B HOH 174 2 HOH HOH 174 B HOH 176 2 HOH HOH 176 B HOH 181 2 HOH HOH 181 B HOH 182 2 HOH HOH 182 B HOH 185 2 HOH HOH 185 B HOH 188 2 HOH HOH 188 B HOH 189 2 HOH HOH 189 B HOH 190 2 HOH HOH 190 B HOH 192 2 HOH HOH 192 B HOH 193 2 HOH HOH 193 B HOH 194 2 HOH HOH 194 B HOH 198 2 HOH HOH 198 B HOH 203 2 HOH HOH 203 B HOH 206 2 HOH HOH 206 B HOH 208 2 HOH HOH 208 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 3ME 6 n 6 3ME 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 3ME 16 n 6 3ME 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 3ME 6 A 3ME 6 U B 3ME 16 B 3ME 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 2.756 0.000 0.000 -10.058 0.000 7.302 0.224 0.192 1.60 20.0 687 7114 6676 93.8 Random 1 Isotropic THROUGHOUT 0.0 0.0 MOLECULAR REPLACEMENT PARKINSON ET AL. 1.60 20.0 101 523 0 422 0 0.009 1.30 0.353 0.312 1.64 35 80.1 1.60 20.0 1NZG 7031 7031 -3.0 0.063 1 22.9 8.2 97.6 0.182 1.60 1.66 6.5 575 1 4.9 82.9 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement CNS Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine 1 N N 1 N N 2 N N 2 N N covale 1.605 both A DA 5 A O3' DA 5 1_555 A 3ME 6 A P 3ME 6 1_555 covale 1.597 both A 3ME 6 A O3' 3ME 6 1_555 A DA 7 A P DA 7 1_555 covale 1.604 both B DA 15 B O3' DA 5 1_555 B 3ME 16 B P 3ME 6 1_555 covale 1.607 both B 3ME 16 B O3' 3ME 6 1_555 B DA 17 B P DA 7 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 3ME 16 B N3 3ME 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B 3ME 16 B O4 3ME 6 1_555 hydrog WATSON-CRICK A 3ME 6 A N3 3ME 6 1_555 B DA 15 B N1 DA 5 1_555 hydrog WATSON-CRICK A 3ME 6 A O4 3ME 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-DNA, 2'-modified oligonucleotides, DNA 1NZG PDB 1 1NZG 1 10 1NZG 1 10 1NZG A 1 1 10 11 20 1NZG 11 20 1NZG B 1 1 10 19 P 21 21 21