0.038912 0.000000 0.000000 0.000000 0.024350 0.000000 0.000000 0.000000 0.021686 0.000000 0.000000 0.000000 Han, G.W. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 25.699 41.067 46.113 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 Ca 2 40.078 CALCIUM ION non-polymer 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 C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C6 H14 O2 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL non-polymer 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 CA N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 N C N 85 R C N 86 N N N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N C N 93 N C N 94 N H 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 O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C Y 120 N N Y 121 N C Y 122 N N Y 123 N C N 124 N C N 125 N O N 126 N N N 127 N C N 128 N N N 129 N N Y 130 N C 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 N C N 156 R C N 157 N N N 158 N C N 159 N O N 160 N N N 161 N C N 162 N O N 163 N C N 164 N C N 165 N C N 166 N H N 167 N H N 168 N H 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 O N 182 N P N 183 N O N 184 N O N 185 N O N 186 N C N 187 R C N 188 N O N 189 S C N 190 N O N 191 R C N 192 N O N 193 R C Y 194 N N Y 195 N C Y 196 N N Y 197 N C N 198 N C N 199 N O N 200 N N N 201 N C N 202 N N N 203 N N Y 204 N C 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 O N 220 N H N 221 N H N 222 N C N 223 N C N 224 N O N 225 N C N 226 N C N 227 S C N 228 N O N 229 N C N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 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 N 99 N sing N 100 N sing N 101 N doub 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 doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub 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 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 Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing N 139 N sing Y 140 N doub N 141 N doub N 142 N sing N 143 N sing 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 doub N 153 N sing 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 N 175 N doub N 176 N sing N 177 N sing N 178 N sing N 179 N doub 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 sing 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 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 Y 211 N sing Y 212 N sing Y 213 N doub N 214 N sing Y 215 N sing N 216 N sing Y 217 N doub N 218 N doub N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N doub 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 sing 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 57 213 218 10.1107/S0907444900017595 11173466 Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution. 2001 UK J.Mol.Biol. JMOBAK 0070 0022-2836 334 653 665 10.1016/j.jmb.2003.09.057 14636594 An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. 2003 10.2210/pdb1g4q/pdb pdb_00001g4q 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 123 1 mirrors CCD ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 1.07200 1.0 X8C NSLS 1.07200 SYNCHROTRON NSLS BEAMLINE X8C 3255.076 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3' POLYPURINE TRACT OF HIV-1 1 syn polymer 2991.961 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3' 1 syn polymer 40.078 CALCIUM ION 3 syn non-polymer 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL 1 syn non-polymer 18.015 water 137 nat water no no CAAAGAAAAG CAAAGAAAAG A polyribonucleotide no no (DC)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DT)(DG) CTTTTCTTTG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 1 1.93 36.36 VAPOR DIFFUSION, SITTING DROP 6.8 calcium acetate, spermidine, beta-octaglucoside, MPD, sodium cacodylate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 calcium acetate 1 spermidine 1 beta-octaglucoside 1 MPD 1 sodium cacodylate 1 MPD 2 -28.092 1 19 A 1 B 20 -1.574 A_C1:DG20_B 1 -11.024 0.112 0.591 -0.086 2.486 1 20 A 2 B 19 -4.172 A_A2:DT19_B 2 -8.284 0.102 -0.049 -0.080 7.174 1 20 A 3 B 18 0.062 A_A3:DT18_B 3 -20.833 -0.003 0.233 -0.135 0.853 1 20 A 4 B 17 11.748 A_A4:DT17_B 4 -24.298 0.044 0.079 -0.065 -18.043 1 19 A 5 B 16 -1.525 A_G5:DC16_B 5 -4.301 -0.271 -0.194 -0.146 -15.926 1 20 A 6 B 15 -2.910 A_A6:DT15_B 6 -4.856 0.079 -0.316 -0.129 -5.355 1 20 A 7 B 14 0.398 A_A7:DT14_B 7 -6.343 0.058 -0.134 -0.074 -1.749 1 20 A 8 B 13 2.956 A_A8:DT13_B 8 -12.382 -0.021 -0.130 -0.169 -5.219 1 20 A 9 B 12 1.368 A_A9:DT12_B 9 -3.683 -0.071 -0.124 -0.174 7.344 1 19 A 10 B 11 3.362 A_G10:DC11_B 10 -6.757 -0.090 0.159 -0.032 2.762 28.770 A A 1 2 16.090 B B 20 19 2.782 7.886 -0.268 0.433 AA_C1A2:DT19DG20_BB 1 2.575 -5.254 27.573 -0.659 1.039 3.118 33.908 A A 2 3 -0.491 B B 19 18 3.190 -0.286 0.348 -0.947 AA_A2A3:DT18DT19_BB 2 -4.875 8.386 33.565 -1.579 -1.355 3.194 33.514 A A 3 4 12.294 B B 18 17 3.495 7.038 0.589 -1.020 AA_A3A4:DT17DT18_BB 3 -1.020 1.781 32.772 -2.967 -1.195 2.998 42.445 A A 4 5 26.126 B B 17 16 3.551 18.234 -1.817 -1.207 AA_A4G5:DC16DT17_BB 4 -8.031 11.507 37.670 -3.646 1.638 2.710 33.712 A A 5 6 18.579 B B 16 15 3.387 10.576 0.214 -1.687 AA_G5A6:DT15DC16_BB 5 4.103 -7.209 31.798 -4.562 0.272 2.676 28.048 A A 6 7 16.588 B B 15 14 3.200 7.928 0.734 -1.579 AA_A6A7:DT14DT15_BB 6 1.782 -3.729 26.867 -4.975 -1.129 2.776 26.256 A A 7 8 12.303 B B 14 13 3.251 5.547 0.960 -2.103 AA_A7A8:DT13DT14_BB 7 0.974 -2.160 25.655 -6.024 -1.868 3.102 37.457 A A 8 9 9.003 B B 13 12 3.260 5.749 -1.253 -1.613 AA_A8A9:DT12DT13_BB 8 -4.253 6.661 36.792 -3.252 1.403 2.815 28.132 A A 9 10 5.506 B B 12 11 2.991 2.672 0.753 -1.763 AA_A9G10:DC11DT12_BB 9 0.045 -0.093 28.008 -4.184 -1.540 software chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations 1 0 2003-07-08 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id NDB Y NDB 2000-10-27 REL REL CA CALCIUM ION MPD (4S)-2-METHYL-2,4-PENTANEDIOL HOH water CA 31 3 CA CA 31 A CA 33 3 CA CA 33 A CA 34 3 CA CA 34 A MPD 25 4 MPD MPD 25 A HOH 101 5 HOH HOH 101 A HOH 102 5 HOH HOH 102 A HOH 103 5 HOH HOH 103 A HOH 104 5 HOH HOH 104 A HOH 105 5 HOH HOH 105 A HOH 106 5 HOH HOH 106 A HOH 107 5 HOH HOH 107 A HOH 108 5 HOH HOH 108 A HOH 109 5 HOH HOH 109 A HOH 110 5 HOH HOH 110 A HOH 111 5 HOH HOH 111 A HOH 112 5 HOH HOH 112 A HOH 113 5 HOH HOH 113 A HOH 115 5 HOH HOH 115 A HOH 118 5 HOH HOH 118 A HOH 132 5 HOH HOH 132 A HOH 135 5 HOH HOH 135 A HOH 136 5 HOH HOH 136 A HOH 137 5 HOH HOH 137 A HOH 138 5 HOH HOH 138 A HOH 139 5 HOH HOH 139 A HOH 140 5 HOH HOH 140 A HOH 141 5 HOH HOH 141 A HOH 142 5 HOH HOH 142 A HOH 143 5 HOH HOH 143 A HOH 144 5 HOH HOH 144 A HOH 145 5 HOH HOH 145 A HOH 146 5 HOH HOH 146 A HOH 147 5 HOH HOH 147 A HOH 151 5 HOH HOH 151 A HOH 152 5 HOH HOH 152 A HOH 153 5 HOH HOH 153 A HOH 154 5 HOH HOH 154 A HOH 155 5 HOH HOH 155 A HOH 156 5 HOH HOH 156 A HOH 157 5 HOH HOH 157 A HOH 158 5 HOH HOH 158 A HOH 159 5 HOH HOH 159 A HOH 160 5 HOH HOH 160 A HOH 162 5 HOH HOH 162 A HOH 163 5 HOH HOH 163 A HOH 164 5 HOH HOH 164 A HOH 166 5 HOH HOH 166 A HOH 167 5 HOH HOH 167 A HOH 168 5 HOH HOH 168 A HOH 170 5 HOH HOH 170 A HOH 171 5 HOH HOH 171 A HOH 172 5 HOH HOH 172 A HOH 176 5 HOH HOH 176 A HOH 177 5 HOH HOH 177 A HOH 178 5 HOH HOH 178 A HOH 179 5 HOH HOH 179 A HOH 182 5 HOH HOH 182 A HOH 183 5 HOH HOH 183 A HOH 185 5 HOH HOH 185 A HOH 188 5 HOH HOH 188 A HOH 192 5 HOH HOH 192 A HOH 195 5 HOH HOH 195 A HOH 196 5 HOH HOH 196 A HOH 199 5 HOH HOH 199 A HOH 201 5 HOH HOH 201 A HOH 206 5 HOH HOH 206 A HOH 208 5 HOH HOH 208 A HOH 210 5 HOH HOH 210 A HOH 211 5 HOH HOH 211 A HOH 213 5 HOH HOH 213 A HOH 217 5 HOH HOH 217 A HOH 218 5 HOH HOH 218 A HOH 223 5 HOH HOH 223 A HOH 225 5 HOH HOH 225 A HOH 226 5 HOH HOH 226 A HOH 228 5 HOH HOH 228 A HOH 229 5 HOH HOH 229 A HOH 230 5 HOH HOH 230 A HOH 231 5 HOH HOH 231 A HOH 237 5 HOH HOH 237 A HOH 238 5 HOH HOH 238 A HOH 241 5 HOH HOH 241 A HOH 243 5 HOH HOH 243 A HOH 244 5 HOH HOH 244 A HOH 245 5 HOH HOH 245 A HOH 246 5 HOH HOH 246 A HOH 249 5 HOH HOH 249 A HOH 251 5 HOH HOH 251 A HOH 100 5 HOH HOH 100 B HOH 119 5 HOH HOH 119 B HOH 120 5 HOH HOH 120 B HOH 121 5 HOH HOH 121 B HOH 122 5 HOH HOH 122 B HOH 124 5 HOH HOH 124 B HOH 125 5 HOH HOH 125 B HOH 126 5 HOH HOH 126 B HOH 127 5 HOH HOH 127 B HOH 128 5 HOH HOH 128 B HOH 129 5 HOH HOH 129 B HOH 130 5 HOH HOH 130 B HOH 131 5 HOH HOH 131 B HOH 133 5 HOH HOH 133 B HOH 134 5 HOH HOH 134 B HOH 173 5 HOH HOH 173 B HOH 174 5 HOH HOH 174 B HOH 181 5 HOH HOH 181 B HOH 186 5 HOH HOH 186 B HOH 187 5 HOH HOH 187 B HOH 189 5 HOH HOH 189 B HOH 190 5 HOH HOH 190 B HOH 193 5 HOH HOH 193 B HOH 194 5 HOH HOH 194 B HOH 197 5 HOH HOH 197 B HOH 200 5 HOH HOH 200 B HOH 202 5 HOH HOH 202 B HOH 203 5 HOH HOH 203 B HOH 204 5 HOH HOH 204 B HOH 205 5 HOH HOH 205 B HOH 207 5 HOH HOH 207 B HOH 209 5 HOH HOH 209 B HOH 212 5 HOH HOH 212 B HOH 214 5 HOH HOH 214 B HOH 215 5 HOH HOH 215 B HOH 216 5 HOH HOH 216 B HOH 219 5 HOH HOH 219 B HOH 220 5 HOH HOH 220 B HOH 221 5 HOH HOH 221 B HOH 222 5 HOH HOH 222 B HOH 224 5 HOH HOH 224 B HOH 227 5 HOH HOH 227 B HOH 232 5 HOH HOH 232 B HOH 233 5 HOH HOH 233 B HOH 234 5 HOH HOH 234 B HOH 235 5 HOH HOH 235 B HOH 236 5 HOH HOH 236 B HOH 239 5 HOH HOH 239 B HOH 240 5 HOH HOH 240 B HOH 247 5 HOH HOH 247 B HOH 250 5 HOH HOH 250 B HOH 252 5 HOH HOH 252 B HOH 253 5 HOH HOH 253 B C 1 n 1 C 1 A A 2 n 2 A 2 A A 3 n 3 A 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A A 6 n 6 A 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A A 9 n 9 A 9 A G 10 n 10 G 10 A C 11 n 1 DC 11 B T 12 n 2 DT 12 B T 13 n 3 DT 13 B T 14 n 4 DT 14 B T 15 n 5 DT 15 B C 16 n 6 DC 16 B T 17 n 7 DT 17 B T 18 n 8 DT 18 B T 19 n 9 DT 19 B G 20 n 10 DG 20 B 0.14 0.143 0.182 805 5 5 15321 author_defined_assembly 2 dimeric A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 A HOH 111 G O HOH 1_555 84.1 A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 A HOH 113 G O HOH 1_555 99.0 A HOH 111 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 113 G O HOH 1_555 83.0 A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 A HOH 115 G O HOH 1_555 83.9 A HOH 111 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 115 G O HOH 1_555 93.1 A HOH 113 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 115 G O HOH 1_555 174.8 A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 A HOH 118 G O HOH 1_555 171.2 A HOH 111 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 118 G O HOH 1_555 87.7 A HOH 113 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 118 G O HOH 1_555 83.1 A HOH 115 G O HOH 1_555 A CA 31 C CA CA 1_555 A HOH 118 G O HOH 1_555 93.3 A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 90.9 A HOH 111 G O HOH 1_555 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 172.3 A HOH 113 G O HOH 1_555 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 91.9 A HOH 115 G O HOH 1_555 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 92.4 A HOH 118 G O HOH 1_555 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 97.5 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 163 G O HOH 1_555 87.3 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 164 G O HOH 1_555 85.3 A HOH 163 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 164 G O HOH 1_555 93.1 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 166 G O HOH 1_555 172.3 A HOH 163 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 166 G O HOH 1_555 94.7 A HOH 164 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 166 G O HOH 1_555 87.2 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 167 G O HOH 1_555 89.3 A HOH 163 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 167 G O HOH 1_555 176.6 A HOH 164 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 167 G O HOH 1_555 87.0 A HOH 166 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 167 G O HOH 1_555 88.7 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 93.9 A HOH 163 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 90.4 A HOH 164 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 176.3 A HOH 166 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 93.5 A HOH 167 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 89.4 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 A HOH 105 G O HOH 2_555 88.4 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 A HOH 112 G O HOH 1_555 81.1 A HOH 105 G O HOH 2_555 A CA 34 E CA CA 1_555 A HOH 112 G O HOH 1_555 109.6 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 A HOH 176 G O HOH 1_555 159.9 A HOH 105 G O HOH 2_555 A CA 34 E CA CA 1_555 A HOH 176 G O HOH 1_555 93.2 A HOH 112 G O HOH 1_555 A CA 34 E CA CA 1_555 A HOH 176 G O HOH 1_555 79.5 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 B DT 18 B OP1 DT 8 3_646 91.4 A HOH 105 G O HOH 2_555 A CA 34 E CA CA 1_555 B DT 18 B OP1 DT 8 3_646 161.5 A HOH 112 G O HOH 1_555 A CA 34 E CA CA 1_555 B DT 18 B OP1 DT 8 3_646 88.6 A HOH 176 G O HOH 1_555 A CA 34 E CA CA 1_555 B DT 18 B OP1 DT 8 3_646 93.4 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 72.0 A HOH 105 G O HOH 2_555 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 87.5 A HOH 112 G O HOH 1_555 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 147.7 A HOH 176 G O HOH 1_555 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 128.1 B DT 18 B OP1 DT 8 3_646 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 74.9 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 10.22 1.30 114.00 124.22 A A A N1 C1' C2' C C C 1 1 1 N 1 -3.13 0.50 117.40 114.27 A A A C4 C5 C6 C C C 1 1 1 N 1 -4.33 0.70 120.20 115.87 A A A C5 C4 N4 C C C 1 1 1 N 1 -5.44 0.70 101.30 95.86 A A A C3' C2' C1' A A A 2 2 2 N 1 5.95 0.70 108.50 114.45 A A A O4' C1' N9 A A A 2 2 2 N 1 10.25 1.20 119.70 129.95 A A A C3' O3' P A A A 2 2 3 Y 1 5.17 0.70 108.50 113.67 A A A O4' C1' N9 A A A 6 6 6 N 1 3.63 0.60 118.60 122.23 A A A C6 N1 C2 A A A 8 8 8 N 1 -3.10 0.50 117.70 114.60 A A A C5 C6 N1 A A A 8 8 8 N 1 -9.09 1.10 112.00 102.91 A A A N9 C1' C2' G G G 10 10 10 N 1 5.21 0.70 108.50 113.71 A A A O4' C1' N9 G G G 10 10 10 N 1 2.03 0.30 108.30 110.33 B B B O4' C1' N1 DT DT DT 12 12 12 N 1 3.10 0.30 108.30 111.40 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 2.49 0.30 108.30 110.79 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 3.01 0.30 108.30 111.31 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 A A C2' C1' A A 2 2 0.070 0.011 1.529 1.599 N 1 A A C2' C1' G G 10 10 0.069 0.011 1.529 1.598 N Konnert-Hendrickson conjugate-gradient algorithm 0.186 0.143 1.15 9.59 4330 864 16408 16408 11665 96.1 RANDOM 1 0.0 0.0 AB INITIO PHASING 1.15 9.59 145 562 3 414 0 0.017 0.019 1.10 9.59 1G4Q 19181 0.081 1 93.5 0.081 1.10 1.13 19181 0.424 65.7 data reduction DENZO refinement SHELXL-97 RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG 1 N N 2 N N 3 N N 3 N N 3 N N 4 N N 5 N N 5 N N metalc 2.198 A A 9 A OP1 A 9 1_555 A CA 31 C CA CA 1_555 metalc 2.023 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 metalc 2.184 A G 10 A OP1 G 10 1_555 A CA 34 E CA CA 1_555 metalc 2.280 A CA 31 C CA CA 1_555 A HOH 111 G O HOH 1_555 metalc 2.260 A CA 31 C CA CA 1_555 A HOH 113 G O HOH 1_555 metalc 2.293 A CA 31 C CA CA 1_555 A HOH 115 G O HOH 1_555 metalc 2.321 A CA 31 C CA CA 1_555 A HOH 118 G O HOH 1_555 metalc 2.245 A CA 31 C CA CA 1_555 B DT 18 B OP2 DT 8 3_646 metalc 2.038 A CA 33 D CA CA 1_555 A HOH 163 G O HOH 1_555 metalc 2.128 A CA 33 D CA CA 1_555 A HOH 164 G O HOH 1_555 metalc 1.993 A CA 33 D CA CA 1_555 A HOH 166 G O HOH 1_555 metalc 2.158 A CA 33 D CA CA 1_555 A HOH 167 G O HOH 1_555 metalc 2.071 A CA 33 D CA CA 1_555 A HOH 168 G O HOH 1_555 metalc 2.425 A CA 34 E CA CA 1_555 A HOH 105 G O HOH 2_555 metalc 2.457 A CA 34 E CA CA 1_555 A HOH 112 G O HOH 1_555 metalc 2.310 A CA 34 E CA CA 1_555 A HOH 176 G O HOH 1_555 metalc 2.225 A CA 34 E CA CA 1_555 B DT 18 B OP1 DT 8 3_646 metalc 2.898 A CA 34 E CA CA 1_555 B DG 20 B OP1 DG 10 2_555 hydrog WATSON-CRICK A C 1 A N3 C 1 1_555 B DG 20 B N1 DG 10 1_555 hydrog WATSON-CRICK A C 1 A N4 C 1 1_555 B DG 20 B O6 DG 10 1_555 hydrog WATSON-CRICK A C 1 A O2 C 1 1_555 B DG 20 B N2 DG 10 1_555 hydrog WATSON-CRICK A A 2 A N1 A 2 1_555 B DT 19 B N3 DT 9 1_555 hydrog WATSON-CRICK A A 2 A N6 A 2 1_555 B DT 19 B O4 DT 9 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 B DT 17 B N3 DT 7 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 B DT 17 B O4 DT 7 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 B DC 16 B N3 DC 6 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 B DC 16 B O2 DC 6 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 B DC 16 B N4 DC 6 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 B DT 15 B N3 DT 5 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 B DT 15 B O4 DT 5 1_555 hydrog WATSON-CRICK A A 7 A N1 A 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A A 7 A N6 A 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B DT 13 B N3 DT 3 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B DT 13 B O4 DT 3 1_555 hydrog WATSON-CRICK A A 9 A N1 A 9 1_555 B DT 12 B N3 DT 2 1_555 hydrog WATSON-CRICK A A 9 A N6 A 9 1_555 B DT 12 B O4 DT 2 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 B DC 11 B N3 DC 1 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 B DC 11 B O2 DC 1 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 B DC 11 B N4 DC 1 1_555 DNA-RNA HYBRID RNA/DNA HYBRID, POLYPURINE TRACT OF HIV-1, DIRECT METHODS, DNA-RNA COMPLEX, DNA-RNA HYBRID 1G4Q PDB 1 1G4Q 1G4Q PDB 2 1G4Q 1 10 1G4Q 1 10 1G4Q A 1 1 10 11 20 1G4Q 11 20 1G4Q B 2 1 10 BINDING SITE FOR RESIDUE CA A 31 A CA 31 Software 6 BINDING SITE FOR RESIDUE CA A 33 A CA 33 Software 6 BINDING SITE FOR RESIDUE CA A 34 A CA 34 Software 6 BINDING SITE FOR RESIDUE MPD A 25 A MPD 25 Software 8 A A 9 A A 9 6 1_555 A HOH 111 G HOH 6 1_555 A HOH 113 G HOH 6 1_555 A HOH 115 G HOH 6 1_555 A HOH 118 G HOH 6 1_555 B DT 18 B DT 8 6 3_646 A A 9 A A 9 6 1_555 A HOH 163 G HOH 6 1_555 A HOH 164 G HOH 6 1_555 A HOH 166 G HOH 6 1_555 A HOH 167 G HOH 6 1_555 A HOH 168 G HOH 6 1_555 A G 10 A G 10 6 1_555 A HOH 105 G HOH 6 2_555 A HOH 112 G HOH 6 1_555 A HOH 176 G HOH 6 1_555 B DT 18 B DT 8 6 3_646 B DG 20 B DG 10 6 2_555 A A 4 A A 4 8 1_555 A G 5 A G 5 8 1_555 A A 6 A A 6 8 1_555 A HOH 107 G HOH 8 1_555 A HOH 208 G HOH 8 1_555 A HOH 211 G HOH 8 1_555 A HOH 238 G HOH 8 1_555 B HOH 133 H HOH 8 1_555 19 P 21 21 21