0.032755 -0.000000 0.000000 0.000000 0.022114 0.000000 0.000000 0.000000 0.006172 0.00000 0.00000 0.00000 Tereshko, V. Wallace, S. Usman, N. Wincott, F. Egli, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90 90 90 30.53 45.22 162.02 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C10 H26 N4 202.340 SPERMINE non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P 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 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C Y 85 N N Y 86 N C Y 87 N N Y 88 N C Y 89 N C N 90 N N Y 91 N N Y 92 N C Y 93 N N Y 94 N C 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 H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C N 121 N N N 122 N C N 123 N O N 124 N N N 125 N C N 126 N O N 127 N C N 128 N C N 129 N C 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 H N 142 N H N 143 N H N 144 N H N 145 N O N 146 N P N 147 N O N 148 N O N 149 N O N 150 N C N 151 R C N 152 N O N 153 S C N 154 N O N 155 R C N 156 N O N 157 R C Y 158 N N Y 159 N C Y 160 N N Y 161 N C N 162 N C N 163 N O N 164 N N N 165 N C N 166 N N N 167 N N Y 168 N C N 169 N H N 170 N H N 171 N H 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 O N 184 N H N 185 N H N 186 N N N 187 N C N 188 N C N 189 N C N 190 N N N 191 N C N 192 N C N 193 N C N 194 N C N 195 N N N 196 N C N 197 N C N 198 N C N 199 N N N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N O N 227 N P N 228 N O N 229 N O N 230 N O N 231 N C N 232 R C N 233 N O N 234 S C N 235 N O N 236 R C N 237 N O N 238 R C N 239 N N N 240 N C N 241 N O N 242 N N N 243 N C N 244 N O N 245 N C N 246 N C N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 1 N sing N 2 N sing N 3 N doub 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 Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub 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 sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 sing Y 99 N sing Y 100 N sing Y 101 N doub N 102 N sing Y 103 N sing Y 104 N sing Y 105 N doub N 106 N sing Y 107 N doub N 108 N sing N 109 N sing Y 110 N sing Y 111 N doub N 112 N sing Y 113 N sing N 114 N sing N 115 N sing N 116 N doub 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 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 doub 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 doub 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 doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing 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 Y 175 N sing Y 176 N sing Y 177 N doub N 178 N sing Y 179 N sing N 180 N sing Y 181 N doub N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub 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 sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N doub N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N doub N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N doub N 265 N sing N 266 N sing UK RNA RNARFU 2122 1355-8382 7 405 420 10.1017/S1355838201001935 11333021 X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid. 2001 10.2210/pdb1i2y/pdb pdb_00001i2y 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 1998-01-11 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.0 1.0 5ID-B APS 1.0 SYNCHROTRON APS BEAMLINE 5ID-B 3471.194 DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)-R(P*AP*CP*GP*U)-3') 6 syn polymer 202.340 SPERMINE 1 syn non-polymer 18.015 water 334 nat water no no GCG(DA)(DT)(DA)(DT)ACGU GCGATATACGU A,B,C,D,E,F polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n 1 2.66 53.77 VAPOR DIFFUSION, SITTING DROP 6.0 spermine, MPD. pH 6.0, VAPOR DIFFUSION, SITTING DROP at 298 298 spermine 1 MPD 1 MPD 2 3.947 28 D 121 C 111 -4.267 D_G121:U111_C 1 -9.161 -2.333 0.210 -0.640 9.718 1 19 D 122 C 110 0.818 D_C122:G110_C 2 -19.740 0.060 -0.039 -0.158 -10.405 1 19 D 123 C 109 -1.412 D_G123:C109_C 3 -19.384 -0.128 -0.057 -0.199 -12.983 1 20 D 124 C 107 2.125 D_DA124:DT107_C 4 -10.059 -0.099 -0.021 -0.093 -1.970 1 20 D 125 C 106 1.947 D_DT125:DA106_C 5 -1.983 0.119 0.033 -0.152 1.102 1 20 D 126 C 105 0.341 D_DA126:DT105_C 6 -1.981 0.153 -0.063 -0.115 13.631 1 20 D 127 C 104 2.729 D_DT127:DA104_C 7 -7.428 -0.067 -0.051 -0.065 12.407 1 19 D 129 C 103 2.922 D_C129:G103_C 8 -13.333 0.185 -0.525 -0.068 -7.533 1 19 D 130 C 102 0.672 D_G130:C102_C 9 -11.333 -0.297 -0.069 -0.133 -0.281 28 D 131 C 101 -4.642 D_U131:G101_C 10 -11.473 2.363 -0.012 -0.649 0.170 28 A 1 B 31 -0.794 A_G1:U31_B 11 -11.718 -2.429 0.046 -0.630 2.837 1 19 A 2 B 30 0.381 A_C2:G30_B 12 -14.158 0.178 0.141 -0.128 -9.414 1 19 A 3 B 29 -1.042 A_G3:C29_B 13 -13.609 -0.130 -0.035 -0.134 -7.563 1 20 A 4 B 27 6.875 A_DA4:DT27_B 14 -8.689 0.039 0.116 -0.130 0.216 1 20 A 5 B 26 0.203 A_DT5:DA26_B 15 -2.801 -0.105 -0.038 -0.168 2.316 1 20 A 6 B 25 -0.246 A_DA6:DT25_B 16 -4.914 -0.039 -0.035 -0.100 13.141 1 20 A 7 B 24 4.964 A_DT7:DA24_B 17 -15.090 -0.036 0.007 -0.107 5.449 1 19 A 9 B 23 3.257 A_C9:G23_B 18 -10.586 0.162 -0.187 -0.087 -3.959 1 19 A 10 B 22 2.302 A_G10:C22_B 19 -18.408 -0.315 -0.023 -0.234 -2.735 28 A 11 B 21 -1.685 A_U11:G21_B 20 -15.128 2.431 0.123 -0.717 0.267 28 E 201 F 231 -3.557 E_G201:U231_F 21 -13.239 -2.226 0.161 -0.609 7.566 1 19 E 202 F 230 0.999 E_C202:G230_F 22 -15.222 0.161 -0.024 -0.161 -6.771 1 19 E 203 F 229 -0.098 E_G203:C229_F 23 -16.090 -0.289 0.077 -0.119 -10.658 1 20 E 204 F 227 0.497 E_DA204:DT227_F 24 -7.755 0.273 0.047 -0.247 -2.473 1 20 E 205 F 226 1.801 E_DT205:DA226_F 25 -7.295 0.008 -0.006 -0.156 3.214 1 20 E 206 F 225 3.382 E_DA206:DT225_F 26 -2.577 0.157 -0.185 -0.288 15.844 1 20 E 207 F 224 5.124 E_DT207:DA224_F 27 -9.283 -0.097 0.033 0.035 10.180 1 19 E 209 F 223 0.590 E_C209:G223_F 28 -21.255 0.127 0.102 0.024 -0.190 1 19 E 210 F 222 3.926 E_G210:C222_F 29 -17.358 -0.171 0.089 -0.026 2.542 1 28 E 211 F 221 -0.825 E_U211:G221_F 30 -14.378 2.281 0.072 -0.583 2.978 40.997 D D 121 122 6.763 C C 111 110 3.125 4.727 -0.014 -1.152 DD_G121C122:G110U111_CC 1 -1.179 1.687 40.719 -2.127 -0.101 2.413 39.762 D D 122 123 26.863 C C 110 109 3.507 17.678 0.002 -1.751 DD_C122G123:C109G110_CC 2 -0.645 0.981 35.753 -4.542 -0.075 2.501 24.560 D D 123 124 19.916 C C 109 107 3.217 8.302 -0.963 -1.774 DD_G123DA124:DT107C109_CC 3 -1.759 4.220 23.068 -6.480 1.775 2.858 32.730 D D 124 125 13.948 C C 107 106 3.107 7.788 -0.295 -0.675 DD_DA124DT125:DA106DT107_CC 4 0.756 -1.354 31.806 -2.441 0.644 2.976 35.103 D D 125 126 11.431 C C 106 105 3.201 6.853 -0.097 -0.879 DD_DT125DA126:DT105DA106_CC 5 0.203 -0.339 34.448 -2.435 0.190 2.831 28.442 D D 126 127 9.550 C C 105 104 3.023 4.671 0.494 -0.877 DD_DA126DT127:DA104DT105_CC 6 -0.629 1.287 28.057 -2.750 -1.135 2.983 51.642 D D 127 129 11.633 C C 104 103 3.151 10.077 -2.200 -0.760 DD_DT127C129:G103DA104_CC 7 -0.573 0.662 50.713 -1.520 2.489 2.797 33.104 D D 129 130 22.185 C C 103 102 3.735 12.329 -0.933 -2.078 DD_C129G130:C102G103_CC 8 -3.383 6.088 30.599 -5.810 1.044 2.976 42.733 D D 130 131 3.157 C C 102 101 3.040 2.299 -0.032 -1.119 DD_G130U131:G101C102_CC 9 1.482 -2.034 42.650 -1.747 0.180 4.259 -37.956 D A 131 1 -16.814 C B 101 31 3.214 10.796 0.348 -4.266 DA_U131G1:U31G101_BC 10 0.408 0.635 -36.441 4.950 0.596 3.110 43.027 A A 1 2 1.450 B B 31 30 3.138 1.063 -0.051 -1.148 AA_G1C2:G30U31_BB 11 -1.532 2.090 42.989 -1.665 -0.075 2.790 32.616 A A 2 3 16.951 B B 30 29 3.476 9.384 0.394 -2.013 AA_C2G3:C29G30_BB 12 2.382 -4.304 31.184 -5.184 -0.295 2.543 21.130 A A 3 4 16.343 B B 29 27 3.102 5.899 -1.338 -2.104 AA_G3DA4:DT27C29_BB 13 -2.682 7.430 20.123 -7.915 2.659 2.931 31.558 A A 4 5 9.083 B B 27 26 3.152 4.918 -0.873 -0.859 AA_DA4DT5:DA26DT27_BB 14 1.817 -3.357 31.131 -2.436 1.921 3.070 33.727 A A 5 6 8.558 B B 26 25 3.206 4.948 -0.151 -0.743 AA_DT5DA6:DT25DA26_BB 15 -0.847 1.465 33.363 -2.056 0.127 2.673 30.149 A A 6 7 16.074 B B 25 24 3.063 8.250 0.674 -0.812 AA_DA6DT7:DA24DT25_BB 16 -2.368 4.614 28.928 -3.068 -1.729 3.135 52.622 A A 7 9 14.328 B B 24 23 3.331 12.591 -2.168 -0.871 AA_DT7C9:G23DA24_BB 17 -2.226 2.533 51.153 -1.807 2.300 2.277 32.039 A A 9 10 25.903 B B 23 22 3.405 13.845 -0.767 -1.975 AA_C9G10:C22G23_BB 18 -1.269 2.375 28.937 -5.864 1.180 3.113 42.682 A A 10 11 3.671 B B 22 21 3.201 2.670 -0.072 -1.401 AA_G10U11:G21C22_BB 19 -0.622 0.856 42.598 -2.183 0.039 4.424 -36.883 A E 11 201 -27.861 B F 21 231 2.922 17.000 0.035 -4.047 AE_U11G201:U231G21_FB 20 1.064 1.744 -32.836 3.649 0.228 3.064 40.413 E E 201 202 4.429 F F 231 230 3.123 3.056 0.304 -0.794 EE_G201C202:G230U231_FF 21 1.132 -1.640 40.287 -1.474 -0.319 2.752 36.614 E E 202 203 17.574 F F 230 229 3.447 10.884 0.601 -1.874 EE_C202G203:C229G230_FF 22 -0.571 0.922 35.007 -4.435 -1.032 2.932 29.093 E E 203 204 8.517 F F 229 227 3.236 4.264 -0.961 -1.808 EE_G203DA204:DT227C229_FF 23 0.328 -0.656 28.784 -4.486 1.981 2.895 29.592 E E 204 205 11.157 F F 227 226 3.127 5.664 -0.478 -0.880 EE_DA204DT205:DA226DT227_FF 24 0.671 -1.322 29.049 -2.837 1.069 2.916 35.374 E E 205 206 10.609 F F 226 225 3.100 6.413 -0.209 -0.749 EE_DT205DA206:DT225DA226_FF 25 0.646 -1.070 34.800 -2.110 0.433 2.775 29.081 E E 206 207 10.459 F F 225 224 3.022 5.214 0.636 -0.627 EE_DA206DT207:DA224DT225_FF 26 -3.303 6.625 28.432 -2.273 -1.916 1.913 23.433 E E 207 209 27.479 F F 224 223 3.193 10.735 1.433 -2.328 EE_DT207C209:G223DA224_FF 27 2.276 -5.827 20.737 -8.751 -2.889 1.728 31.836 E E 209 210 31.543 F F 223 222 3.257 16.478 -0.438 -2.167 EE_C209G210:C222G223_FF 28 -2.617 5.010 27.211 -6.434 0.404 2.889 43.947 E E 210 211 8.305 F F 222 221 3.072 6.196 -0.193 -1.129 EE_G210U211:G221C222_FF 29 0.761 -1.020 43.523 -2.046 0.323 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-04-21 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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2001-02-12 REL REL SPM SPERMINE HOH water SPM 300 2 SPM SPM 300 D HOH 303 3 HOH HOH 303 A HOH 304 3 HOH HOH 304 A HOH 308 3 HOH HOH 308 A HOH 326 3 HOH HOH 326 A HOH 327 3 HOH HOH 327 A HOH 330 3 HOH HOH 330 A HOH 331 3 HOH HOH 331 A HOH 332 3 HOH HOH 332 A HOH 335 3 HOH HOH 335 A HOH 337 3 HOH HOH 337 A HOH 341 3 HOH HOH 341 A HOH 342 3 HOH HOH 342 A HOH 346 3 HOH HOH 346 A HOH 351 3 HOH HOH 351 A HOH 359 3 HOH HOH 359 A HOH 361 3 HOH HOH 361 A HOH 365 3 HOH HOH 365 A HOH 374 3 HOH HOH 374 A HOH 378 3 HOH HOH 378 A HOH 383 3 HOH HOH 383 A HOH 387 3 HOH HOH 387 A HOH 388 3 HOH HOH 388 A HOH 398 3 HOH HOH 398 A HOH 400 3 HOH HOH 400 A HOH 420 3 HOH HOH 420 A HOH 422 3 HOH HOH 422 A HOH 426 3 HOH HOH 426 A HOH 438 3 HOH HOH 438 A HOH 440 3 HOH HOH 440 A HOH 442 3 HOH HOH 442 A HOH 462 3 HOH HOH 462 A HOH 464 3 HOH HOH 464 A HOH 470 3 HOH HOH 470 A HOH 476 3 HOH HOH 476 A HOH 478 3 HOH HOH 478 A HOH 480 3 HOH HOH 480 A HOH 484 3 HOH HOH 484 A HOH 485 3 HOH HOH 485 A HOH 486 3 HOH HOH 486 A HOH 507 3 HOH HOH 507 A HOH 509 3 HOH HOH 509 A HOH 517 3 HOH HOH 517 A HOH 518 3 HOH HOH 518 A HOH 519 3 HOH HOH 519 A HOH 520 3 HOH HOH 520 A HOH 528 3 HOH HOH 528 A HOH 534 3 HOH HOH 534 A HOH 537 3 HOH HOH 537 A HOH 548 3 HOH HOH 548 A HOH 557 3 HOH HOH 557 A HOH 559 3 HOH HOH 559 A HOH 575 3 HOH HOH 575 A HOH 578 3 HOH HOH 578 A HOH 588 3 HOH HOH 588 A HOH 594 3 HOH HOH 594 A HOH 599 3 HOH HOH 599 A HOH 606 3 HOH HOH 606 A HOH 609 3 HOH HOH 609 A HOH 620 3 HOH HOH 620 A HOH 621 3 HOH HOH 621 A HOH 630 3 HOH HOH 630 A HOH 631 3 HOH HOH 631 A HOH 301 3 HOH HOH 301 B HOH 309 3 HOH HOH 309 B HOH 313 3 HOH HOH 313 B HOH 321 3 HOH HOH 321 B HOH 323 3 HOH HOH 323 B HOH 324 3 HOH HOH 324 B HOH 328 3 HOH HOH 328 B HOH 334 3 HOH HOH 334 B HOH 343 3 HOH HOH 343 B HOH 348 3 HOH HOH 348 B HOH 349 3 HOH HOH 349 B HOH 356 3 HOH HOH 356 B HOH 360 3 HOH HOH 360 B HOH 363 3 HOH HOH 363 B HOH 364 3 HOH HOH 364 B HOH 366 3 HOH HOH 366 B HOH 370 3 HOH HOH 370 B HOH 372 3 HOH HOH 372 B HOH 375 3 HOH HOH 375 B HOH 376 3 HOH HOH 376 B HOH 377 3 HOH HOH 377 B HOH 380 3 HOH HOH 380 B HOH 393 3 HOH HOH 393 B HOH 399 3 HOH HOH 399 B HOH 401 3 HOH HOH 401 B HOH 402 3 HOH HOH 402 B HOH 405 3 HOH HOH 405 B HOH 407 3 HOH HOH 407 B HOH 408 3 HOH HOH 408 B HOH 415 3 HOH HOH 415 B HOH 417 3 HOH HOH 417 B HOH 418 3 HOH HOH 418 B HOH 421 3 HOH HOH 421 B HOH 431 3 HOH HOH 431 B HOH 432 3 HOH HOH 432 B HOH 436 3 HOH HOH 436 B HOH 446 3 HOH HOH 446 B HOH 450 3 HOH HOH 450 B HOH 457 3 HOH HOH 457 B HOH 465 3 HOH HOH 465 B HOH 466 3 HOH HOH 466 B HOH 474 3 HOH HOH 474 B HOH 482 3 HOH HOH 482 B HOH 483 3 HOH HOH 483 B HOH 488 3 HOH HOH 488 B HOH 495 3 HOH HOH 495 B HOH 504 3 HOH HOH 504 B HOH 505 3 HOH HOH 505 B HOH 529 3 HOH HOH 529 B HOH 531 3 HOH HOH 531 B HOH 541 3 HOH HOH 541 B HOH 544 3 HOH HOH 544 B HOH 554 3 HOH HOH 554 B HOH 555 3 HOH HOH 555 B HOH 556 3 HOH HOH 556 B HOH 563 3 HOH HOH 563 B HOH 568 3 HOH HOH 568 B HOH 574 3 HOH HOH 574 B HOH 580 3 HOH HOH 580 B HOH 604 3 HOH HOH 604 B HOH 608 3 HOH HOH 608 B HOH 611 3 HOH HOH 611 B HOH 615 3 HOH HOH 615 B HOH 310 3 HOH HOH 310 C HOH 314 3 HOH HOH 314 C HOH 318 3 HOH HOH 318 C HOH 333 3 HOH HOH 333 C HOH 340 3 HOH HOH 340 C HOH 347 3 HOH HOH 347 C HOH 353 3 HOH HOH 353 C HOH 357 3 HOH HOH 357 C HOH 368 3 HOH HOH 368 C HOH 369 3 HOH HOH 369 C HOH 384 3 HOH HOH 384 C HOH 391 3 HOH HOH 391 C HOH 394 3 HOH HOH 394 C HOH 406 3 HOH HOH 406 C HOH 412 3 HOH HOH 412 C HOH 413 3 HOH HOH 413 C HOH 416 3 HOH HOH 416 C HOH 424 3 HOH HOH 424 C HOH 430 3 HOH HOH 430 C HOH 439 3 HOH HOH 439 C HOH 460 3 HOH HOH 460 C HOH 471 3 HOH HOH 471 C HOH 473 3 HOH HOH 473 C HOH 477 3 HOH HOH 477 C HOH 479 3 HOH HOH 479 C HOH 481 3 HOH HOH 481 C HOH 487 3 HOH HOH 487 C HOH 492 3 HOH HOH 492 C HOH 506 3 HOH HOH 506 C HOH 511 3 HOH HOH 511 C HOH 513 3 HOH HOH 513 C HOH 521 3 HOH HOH 521 C HOH 522 3 HOH HOH 522 C HOH 527 3 HOH HOH 527 C HOH 530 3 HOH HOH 530 C HOH 538 3 HOH HOH 538 C HOH 540 3 HOH HOH 540 C HOH 553 3 HOH HOH 553 C HOH 562 3 HOH HOH 562 C HOH 566 3 HOH HOH 566 C HOH 572 3 HOH HOH 572 C HOH 584 3 HOH HOH 584 C HOH 586 3 HOH HOH 586 C HOH 587 3 HOH HOH 587 C HOH 589 3 HOH HOH 589 C HOH 591 3 HOH HOH 591 C HOH 597 3 HOH HOH 597 C HOH 603 3 HOH HOH 603 C HOH 607 3 HOH HOH 607 C HOH 610 3 HOH HOH 610 C HOH 612 3 HOH HOH 612 C HOH 613 3 HOH HOH 613 C HOH 616 3 HOH HOH 616 C HOH 618 3 HOH HOH 618 C HOH 622 3 HOH HOH 622 C HOH 624 3 HOH HOH 624 C HOH 626 3 HOH HOH 626 C HOH 632 3 HOH HOH 632 C HOH 305 3 HOH HOH 305 D HOH 311 3 HOH HOH 311 D HOH 312 3 HOH HOH 312 D HOH 316 3 HOH HOH 316 D HOH 317 3 HOH HOH 317 D HOH 320 3 HOH HOH 320 D HOH 322 3 HOH HOH 322 D HOH 325 3 HOH HOH 325 D HOH 338 3 HOH HOH 338 D HOH 339 3 HOH HOH 339 D HOH 345 3 HOH HOH 345 D HOH 350 3 HOH HOH 350 D HOH 352 3 HOH HOH 352 D HOH 354 3 HOH HOH 354 D HOH 358 3 HOH HOH 358 D HOH 362 3 HOH HOH 362 D HOH 367 3 HOH HOH 367 D HOH 371 3 HOH HOH 371 D HOH 373 3 HOH HOH 373 D HOH 379 3 HOH HOH 379 D HOH 381 3 HOH HOH 381 D HOH 385 3 HOH HOH 385 D HOH 389 3 HOH HOH 389 D HOH 390 3 HOH HOH 390 D HOH 392 3 HOH HOH 392 D HOH 395 3 HOH HOH 395 D HOH 396 3 HOH HOH 396 D HOH 397 3 HOH HOH 397 D HOH 403 3 HOH HOH 403 D HOH 404 3 HOH HOH 404 D HOH 409 3 HOH HOH 409 D HOH 410 3 HOH HOH 410 D HOH 423 3 HOH HOH 423 D HOH 425 3 HOH HOH 425 D HOH 427 3 HOH HOH 427 D HOH 429 3 HOH HOH 429 D HOH 433 3 HOH HOH 433 D HOH 443 3 HOH HOH 443 D HOH 444 3 HOH HOH 444 D HOH 448 3 HOH HOH 448 D HOH 451 3 HOH HOH 451 D HOH 455 3 HOH HOH 455 D HOH 456 3 HOH HOH 456 D HOH 458 3 HOH HOH 458 D HOH 459 3 HOH HOH 459 D HOH 472 3 HOH HOH 472 D HOH 498 3 HOH HOH 498 D HOH 499 3 HOH HOH 499 D HOH 501 3 HOH HOH 501 D HOH 503 3 HOH HOH 503 D HOH 512 3 HOH HOH 512 D HOH 516 3 HOH HOH 516 D HOH 524 3 HOH HOH 524 D HOH 525 3 HOH HOH 525 D HOH 533 3 HOH HOH 533 D HOH 539 3 HOH HOH 539 D HOH 543 3 HOH HOH 543 D HOH 545 3 HOH HOH 545 D HOH 560 3 HOH HOH 560 D HOH 561 3 HOH HOH 561 D HOH 569 3 HOH HOH 569 D HOH 570 3 HOH HOH 570 D HOH 576 3 HOH HOH 576 D HOH 581 3 HOH HOH 581 D HOH 582 3 HOH HOH 582 D HOH 593 3 HOH HOH 593 D HOH 595 3 HOH HOH 595 D HOH 302 3 HOH HOH 302 E HOH 319 3 HOH HOH 319 E HOH 336 3 HOH HOH 336 E HOH 386 3 HOH HOH 386 E HOH 411 3 HOH HOH 411 E HOH 414 3 HOH HOH 414 E HOH 449 3 HOH HOH 449 E HOH 452 3 HOH HOH 452 E HOH 454 3 HOH HOH 454 E HOH 461 3 HOH HOH 461 E HOH 468 3 HOH HOH 468 E HOH 475 3 HOH HOH 475 E HOH 489 3 HOH HOH 489 E HOH 494 3 HOH HOH 494 E HOH 496 3 HOH HOH 496 E HOH 497 3 HOH HOH 497 E HOH 515 3 HOH HOH 515 E HOH 523 3 HOH HOH 523 E HOH 526 3 HOH HOH 526 E HOH 546 3 HOH HOH 546 E HOH 547 3 HOH HOH 547 E HOH 549 3 HOH HOH 549 E HOH 551 3 HOH HOH 551 E HOH 558 3 HOH HOH 558 E HOH 571 3 HOH HOH 571 E HOH 577 3 HOH HOH 577 E HOH 579 3 HOH HOH 579 E HOH 583 3 HOH HOH 583 E HOH 585 3 HOH HOH 585 E HOH 590 3 HOH HOH 590 E HOH 592 3 HOH HOH 592 E HOH 596 3 HOH HOH 596 E HOH 598 3 HOH HOH 598 E HOH 602 3 HOH HOH 602 E HOH 617 3 HOH HOH 617 E HOH 625 3 HOH HOH 625 E HOH 627 3 HOH HOH 627 E HOH 628 3 HOH HOH 628 E HOH 629 3 HOH HOH 629 E HOH 306 3 HOH HOH 306 F HOH 307 3 HOH HOH 307 F HOH 315 3 HOH HOH 315 F HOH 329 3 HOH HOH 329 F HOH 344 3 HOH HOH 344 F HOH 355 3 HOH HOH 355 F HOH 382 3 HOH HOH 382 F HOH 419 3 HOH HOH 419 F HOH 428 3 HOH HOH 428 F HOH 434 3 HOH HOH 434 F HOH 435 3 HOH HOH 435 F HOH 437 3 HOH HOH 437 F HOH 441 3 HOH HOH 441 F HOH 445 3 HOH HOH 445 F HOH 447 3 HOH HOH 447 F HOH 453 3 HOH HOH 453 F HOH 463 3 HOH HOH 463 F HOH 467 3 HOH HOH 467 F HOH 469 3 HOH HOH 469 F HOH 490 3 HOH HOH 490 F HOH 491 3 HOH HOH 491 F HOH 493 3 HOH HOH 493 F HOH 500 3 HOH HOH 500 F HOH 502 3 HOH HOH 502 F HOH 508 3 HOH HOH 508 F HOH 510 3 HOH HOH 510 F HOH 514 3 HOH HOH 514 F HOH 532 3 HOH HOH 532 F HOH 535 3 HOH HOH 535 F HOH 536 3 HOH HOH 536 F HOH 542 3 HOH HOH 542 F HOH 550 3 HOH HOH 550 F HOH 552 3 HOH HOH 552 F HOH 564 3 HOH HOH 564 F HOH 565 3 HOH HOH 565 F HOH 567 3 HOH HOH 567 F HOH 573 3 HOH HOH 573 F HOH 600 3 HOH HOH 600 F HOH 601 3 HOH HOH 601 F HOH 605 3 HOH HOH 605 F HOH 614 3 HOH HOH 614 F HOH 619 3 HOH HOH 619 F HOH 623 3 HOH HOH 623 F HOH 633 3 HOH HOH 633 F HOH 634 3 HOH HOH 634 F G 1 n 1 G 1 A C 2 n 2 C 2 A G 3 n 3 G 3 A A 4 n 4 DA 4 A T 5 n 5 DT 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A A 8 n 8 A 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A G 21 n 1 G 21 B C 22 n 2 C 22 B G 23 n 3 G 23 B A 24 n 4 DA 24 B T 25 n 5 DT 25 B A 26 n 6 DA 26 B T 27 n 7 DT 27 B A 28 n 8 A 28 B C 29 n 9 C 29 B G 30 n 10 G 30 B U 31 n 11 U 31 B G 101 n 1 G 101 C C 102 n 2 C 102 C G 103 n 3 G 103 C A 104 n 4 DA 104 C T 105 n 5 DT 105 C A 106 n 6 DA 106 C T 107 n 7 DT 107 C A 108 n 8 A 108 C C 109 n 9 C 109 C G 110 n 10 G 110 C U 111 n 11 U 111 C G 121 n 1 G 121 D C 122 n 2 C 122 D G 123 n 3 G 123 D A 124 n 4 DA 124 D T 125 n 5 DT 125 D A 126 n 6 DA 126 D T 127 n 7 DT 127 D A 128 n 8 A 128 D C 129 n 9 C 129 D G 130 n 10 G 130 D U 131 n 11 U 131 D G 201 n 1 G 201 E C 202 n 2 C 202 E G 203 n 3 G 203 E A 204 n 4 DA 204 E T 205 n 5 DT 205 E A 206 n 6 DA 206 E T 207 n 7 DT 207 E A 208 n 8 A 208 E C 209 n 9 C 209 E G 210 n 10 G 210 E U 211 n 11 U 211 E G 221 n 1 G 221 F C 222 n 2 C 222 F G 223 n 3 G 223 F A 224 n 4 DA 224 F T 225 n 5 DT 225 F A 226 n 6 DA 226 F T 227 n 7 DT 227 F A 228 n 8 A 228 F C 229 n 9 C 229 F G 230 n 10 G 230 F U 231 n 11 U 231 F author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric 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 DA 4 0.060 SIDE CHAIN 1 B G 30 0.054 SIDE CHAIN 1 D G 130 0.055 SIDE CHAIN 1 F G 230 0.065 SIDE CHAIN 1 9.06 1.30 114.00 123.06 F F F N9 C1' C2' A A A 228 228 228 N 0.248 0.217 1.66 10 2335 26418 26418 8.8 random 1 througout 0 0 MOLECULAR REPLACEMENT 1.66 10 334 1728 14 1380 0 1.66 20 1I2Y 26418 26418 0 0 1 100 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement CNS 1.0 1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM 1 N N 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N hydrog TYPE_28_PAIR A G 1 A N1 G 1 1_555 B U 31 B O2 U 11 1_555 hydrog TYPE_28_PAIR A G 1 A O6 G 1 1_555 B U 31 B N3 U 11 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 30 B N1 G 10 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 30 B O6 G 10 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 30 B N2 G 10 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 B C 29 B N3 C 9 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 B C 29 B O2 C 9 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 B C 29 B N4 C 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 27 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 27 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 26 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 26 B N6 DA 6 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 25 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 25 B O4 DT 5 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 24 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 24 B N6 DA 4 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 23 B N1 G 3 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 23 B O6 G 3 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 23 B N2 G 3 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 B C 22 B N3 C 2 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 B C 22 B O2 C 2 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 B C 22 B N4 C 2 1_555 hydrog TYPE_28_PAIR A U 11 A N3 U 11 1_555 B G 21 B O6 G 1 1_555 hydrog TYPE_28_PAIR A U 11 A O2 U 11 1_555 B G 21 B N1 G 1 1_555 hydrog TYPE_28_PAIR C G 101 C N1 G 1 1_555 D U 131 D O2 U 11 1_555 hydrog TYPE_28_PAIR C G 101 C O6 G 1 1_555 D U 131 D N3 U 11 1_555 hydrog WATSON-CRICK C C 102 C N3 C 2 1_555 D G 130 D N1 G 10 1_555 hydrog WATSON-CRICK C C 102 C N4 C 2 1_555 D G 130 D O6 G 10 1_555 hydrog WATSON-CRICK C C 102 C O2 C 2 1_555 D G 130 D N2 G 10 1_555 hydrog WATSON-CRICK C G 103 C N1 G 3 1_555 D C 129 D N3 C 9 1_555 hydrog WATSON-CRICK C G 103 C N2 G 3 1_555 D C 129 D O2 C 9 1_555 hydrog WATSON-CRICK C G 103 C O6 G 3 1_555 D C 129 D N4 C 9 1_555 hydrog WATSON-CRICK C DA 104 C N1 DA 4 1_555 D DT 127 D N3 DT 7 1_555 hydrog WATSON-CRICK C DA 104 C N6 DA 4 1_555 D DT 127 D O4 DT 7 1_555 hydrog WATSON-CRICK C DT 105 C N3 DT 5 1_555 D DA 126 D N1 DA 6 1_555 hydrog WATSON-CRICK C DT 105 C O4 DT 5 1_555 D DA 126 D N6 DA 6 1_555 hydrog WATSON-CRICK C DA 106 C N1 DA 6 1_555 D DT 125 D N3 DT 5 1_555 hydrog WATSON-CRICK C DA 106 C N6 DA 6 1_555 D DT 125 D O4 DT 5 1_555 hydrog WATSON-CRICK C DT 107 C N3 DT 7 1_555 D DA 124 D N1 DA 4 1_555 hydrog WATSON-CRICK C DT 107 C O4 DT 7 1_555 D DA 124 D N6 DA 4 1_555 hydrog WATSON-CRICK C C 109 C N3 C 9 1_555 D G 123 D N1 G 3 1_555 hydrog WATSON-CRICK C C 109 C N4 C 9 1_555 D G 123 D O6 G 3 1_555 hydrog WATSON-CRICK C C 109 C O2 C 9 1_555 D G 123 D N2 G 3 1_555 hydrog WATSON-CRICK C G 110 C N1 G 10 1_555 D C 122 D N3 C 2 1_555 hydrog WATSON-CRICK C G 110 C N2 G 10 1_555 D C 122 D O2 C 2 1_555 hydrog WATSON-CRICK C G 110 C O6 G 10 1_555 D C 122 D N4 C 2 1_555 hydrog TYPE_28_PAIR C U 111 C N3 U 11 1_555 D G 121 D O6 G 1 1_555 hydrog TYPE_28_PAIR C U 111 C O2 U 11 1_555 D G 121 D N1 G 1 1_555 hydrog TYPE_28_PAIR E G 201 E N1 G 1 1_555 F U 231 F O2 U 11 1_555 hydrog TYPE_28_PAIR E G 201 E O6 G 1 1_555 F U 231 F N3 U 11 1_555 hydrog WATSON-CRICK E C 202 E N3 C 2 1_555 F G 230 F N1 G 10 1_555 hydrog WATSON-CRICK E C 202 E N4 C 2 1_555 F G 230 F O6 G 10 1_555 hydrog WATSON-CRICK E C 202 E O2 C 2 1_555 F G 230 F N2 G 10 1_555 hydrog WATSON-CRICK E G 203 E N1 G 3 1_555 F C 229 F N3 C 9 1_555 hydrog WATSON-CRICK E G 203 E N2 G 3 1_555 F C 229 F O2 C 9 1_555 hydrog WATSON-CRICK E G 203 E O6 G 3 1_555 F C 229 F N4 C 9 1_555 hydrog WATSON-CRICK E DA 204 E N1 DA 4 1_555 F DT 227 F N3 DT 7 1_555 hydrog WATSON-CRICK E DA 204 E N6 DA 4 1_555 F DT 227 F O4 DT 7 1_555 hydrog WATSON-CRICK E DT 205 E N3 DT 5 1_555 F DA 226 F N1 DA 6 1_555 hydrog WATSON-CRICK E DT 205 E O4 DT 5 1_555 F DA 226 F N6 DA 6 1_555 hydrog WATSON-CRICK E DA 206 E N1 DA 6 1_555 F DT 225 F N3 DT 5 1_555 hydrog WATSON-CRICK E DA 206 E N6 DA 6 1_555 F DT 225 F O4 DT 5 1_555 hydrog WATSON-CRICK E DT 207 E N3 DT 7 1_555 F DA 224 F N1 DA 4 1_555 hydrog WATSON-CRICK E DT 207 E O4 DT 7 1_555 F DA 224 F N6 DA 4 1_555 hydrog WATSON-CRICK E C 209 E N3 C 9 1_555 F G 223 F N1 G 3 1_555 hydrog WATSON-CRICK E C 209 E N4 C 9 1_555 F G 223 F O6 G 3 1_555 hydrog WATSON-CRICK E C 209 E O2 C 9 1_555 F G 223 F N2 G 3 1_555 hydrog WATSON-CRICK E G 210 E N1 G 10 1_555 F C 222 F N3 C 2 1_555 hydrog WATSON-CRICK E G 210 E N2 G 10 1_555 F C 222 F O2 C 2 1_555 hydrog WATSON-CRICK E G 210 E O6 G 10 1_555 F C 222 F N4 C 2 1_555 hydrog TYPE_28_PAIR E U 211 E N3 U 11 1_555 F G 221 F O6 G 1 1_555 hydrog TYPE_28_PAIR E U 211 E O2 U 11 1_555 F G 221 F N1 G 1 1_555 DNA-RNA HYBRID adenine bulge, A-type NA, DNA/RNA hybrid, DNA-RNA HYBRID 1I2Y PDB 1 1I2Y 1 11 1I2Y 1 11 1I2Y A 1 1 11 21 31 1I2Y 21 31 1I2Y B 1 1 11 101 111 1I2Y 101 111 1I2Y C 1 1 11 121 131 1I2Y 121 131 1I2Y D 1 1 11 201 211 1I2Y 201 211 1I2Y E 1 1 11 221 231 1I2Y 221 231 1I2Y F 1 1 11 BINDING SITE FOR RESIDUE SPM D 300 D SPM 300 Software 11 A G 1 A G 1 11 1_555 A C 2 A C 2 11 1_555 B G 30 B G 10 11 1_555 B U 31 B U 11 11 1_555 B U 31 B U 11 11 3_655 B HOH 399 I HOH 11 1_555 C G 101 C G 1 11 1_555 C HOH 310 J HOH 11 3_655 D C 129 D C 9 11 1_555 D G 130 D G 10 11 1_555 D U 131 D U 11 11 1_555 19 orthorhombic P 21 21 21