0.038909 0.000000 0.000000 0.000000 0.024347 0.000000 0.000000 0.000000 0.021684 0.00000 0.00000 0.00000 Kopka, M.L. Lavelle, L. Han, G.W. Ng, H.-L. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 25.701 41.073 46.116 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 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 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 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 57 213 218 10.1107/S0907444900017595 Direct Methods Determination of an RNA/DNA Hybrid Decamer at 1.15A Resolution 2001 To be Published 0353 Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation: Dimer Formation by Base-pair Swapping 2003 10.2210/pdb1pjg/pdb pdb_00001pjg 123 1 mirrors CCD 1999-10-27 ADSC QUANTUM 4 mirrors 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 4 syn non-polymer 18.015 water 124 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 36.38 VAPOR DIFFUSION, HANGING DROP 6.8 calcium acetate, cacodylate, beta-octylglucoside, spermidine hydrochloride, 2-methyl,2,4-pentanediol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K 278 calcium acetate 1 cacodylate 1 beta-octylglucoside 1 spermidine HCl 1 2-methyl,2,4-pentanediol 1 calcium acetate 2 2-methyl,2,4-pentanediol 2 -27.603 1 19 A 1 B 20 -2.053 A_C1:DG20_B 1 -11.591 0.062 0.595 -0.059 4.117 1 20 A 2 B 19 -4.074 A_A2:DT19_B 2 -7.661 0.073 -0.044 -0.105 6.983 1 20 A 3 B 18 0.111 A_A3:DT18_B 3 -21.085 -0.018 0.251 -0.153 0.592 1 20 A 4 B 17 11.907 A_A4:DT17_B 4 -24.926 0.030 0.088 -0.063 -18.398 1 19 A 5 B 16 -1.300 A_G5:DC16_B 5 -5.100 -0.267 -0.261 -0.156 -16.435 1 20 A 6 B 15 -2.781 A_A6:DT15_B 6 -4.501 0.107 -0.319 -0.119 -4.640 1 20 A 7 B 14 0.170 A_A7:DT14_B 7 -5.931 0.055 -0.101 -0.112 -1.369 1 20 A 8 B 13 3.333 A_A8:DT13_B 8 -12.642 -0.045 -0.089 -0.171 -4.920 1 20 A 9 B 12 1.540 A_A9:DT12_B 9 -4.145 -0.103 -0.108 -0.166 6.679 1 19 A 10 B 11 2.862 A_G10:DC11_B 10 -6.456 -0.064 0.097 -0.049 2.735 28.884 A A 1 2 17.375 B B 20 19 2.757 8.532 -0.231 0.436 AA_C1A2:DT19DG20_BB 1 2.481 -5.052 27.511 -0.758 0.939 3.175 34.352 A A 2 3 -0.830 B B 19 18 3.241 -0.489 0.328 -0.953 AA_A2A3:DT18DT19_BB 2 -5.007 8.506 33.993 -1.538 -1.328 3.216 33.328 A A 3 4 11.819 B B 18 17 3.506 6.733 0.598 -1.027 AA_A3A4:DT17DT18_BB 3 -1.002 1.758 32.645 -2.955 -1.216 2.974 42.753 A A 4 5 26.552 B B 17 16 3.553 18.662 -1.821 -1.181 AA_A4G5:DC16DT17_BB 4 -7.328 10.427 37.957 -3.609 1.718 2.709 33.641 A A 5 6 18.916 B B 16 15 3.393 10.747 0.217 -1.669 AA_G5A6:DT15DC16_BB 5 3.408 -5.999 31.747 -4.571 0.160 2.667 27.646 A A 6 7 15.829 B B 15 14 3.167 7.468 0.707 -1.595 AA_A6A7:DT14DT15_BB 6 1.731 -3.670 26.581 -4.989 -1.096 2.796 25.995 A A 7 8 11.924 B B 14 13 3.253 5.326 1.011 -2.110 AA_A7A8:DT13DT14_BB 7 0.975 -2.184 25.434 -6.060 -1.996 3.068 37.599 A A 8 9 9.365 B B 13 12 3.248 6.001 -1.258 -1.634 AA_A8A9:DT12DT13_BB 8 -3.942 6.151 36.931 -3.297 1.452 2.884 28.450 A A 9 10 5.271 B B 12 11 3.037 2.587 0.743 -1.751 AA_A9G10:DC11DT12_BB 9 0.627 -1.277 28.328 -4.101 -1.382 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2003-12-09 1 1 2008-04-29 1 2 2011-07-13 1 3 2024-02-14 1 4 2024-04-03 _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_alt_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.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _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_alt_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.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _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.ptnr1_symmetry _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 Same sequence and crystal, solved by Direct Methods Same sequence crystallized in different space group with different packing Same sequence, MgOAc in the crystallization batch RCSB Y RCSB 2003-06-02 REL REL CA CALCIUM ION HOH water 404D NDB ID AH0001 PDB experimental model OC6 32 3 CA CA 32 A OC5 33 3 CA CA 33 A OC4 31 3 CA CA 31 B OC4 34 3 CA CA 34 B HOH 27 4 HOH HOH 27 A HOH 28 4 HOH HOH 28 A HOH 37 4 HOH HOH 37 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 44 4 HOH HOH 44 A HOH 45 4 HOH HOH 45 A HOH 46 4 HOH HOH 46 A HOH 49 4 HOH HOH 49 A HOH 51 4 HOH HOH 51 A HOH 52 4 HOH HOH 52 A HOH 53 4 HOH HOH 53 A HOH 54 4 HOH HOH 54 A HOH 56 4 HOH HOH 56 A HOH 57 4 HOH HOH 57 A HOH 58 4 HOH HOH 58 A HOH 60 4 HOH HOH 60 A HOH 62 4 HOH HOH 62 A HOH 63 4 HOH HOH 63 A HOH 65 4 HOH HOH 65 A HOH 66 4 HOH HOH 66 A HOH 68 4 HOH HOH 68 A HOH 70 4 HOH HOH 70 A HOH 71 4 HOH HOH 71 A HOH 72 4 HOH HOH 72 A HOH 73 4 HOH HOH 73 A HOH 76 4 HOH HOH 76 A HOH 77 4 HOH HOH 77 A HOH 78 4 HOH HOH 78 A HOH 83 4 HOH HOH 83 A HOH 84 4 HOH HOH 84 A HOH 85 4 HOH HOH 85 A HOH 86 4 HOH HOH 86 A HOH 88 4 HOH HOH 88 A HOH 94 4 HOH HOH 94 A HOH 98 4 HOH HOH 98 A HOH 103 4 HOH HOH 103 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 A HOH 109 4 HOH HOH 109 A HOH 111 4 HOH HOH 111 A HOH 114 4 HOH HOH 114 A HOH 116 4 HOH HOH 116 A HOH 117 4 HOH HOH 117 A HOH 118 4 HOH HOH 118 A HOH 120 4 HOH HOH 120 A HOH 121 4 HOH HOH 121 A HOH 122 4 HOH HOH 122 A HOH 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 128 4 HOH HOH 128 A HOH 130 4 HOH HOH 130 A HOH 131 4 HOH HOH 131 A HOH 132 4 HOH HOH 132 A HOH 133 4 HOH HOH 133 A OC6 32 4 HOH HOH 138 A OC6 32 4 HOH HOH 139 A OC6 32 4 HOH HOH 140 A OC6 32 4 HOH HOH 141 A OC6 32 4 HOH HOH 142 A OC6 32 4 HOH HOH 143 A OC5 33 4 HOH HOH 144 A OC5 33 4 HOH HOH 145 A OC5 33 4 HOH HOH 146 A OC5 33 4 HOH HOH 147 A OC5 33 4 HOH HOH 148 A HOH 25 4 HOH HOH 25 B HOH 26 4 HOH HOH 26 B HOH 29 4 HOH HOH 29 B HOH 30 4 HOH HOH 30 B HOH 35 4 HOH HOH 35 B HOH 36 4 HOH HOH 36 B HOH 38 4 HOH HOH 38 B HOH 39 4 HOH HOH 39 B HOH 42 4 HOH HOH 42 B HOH 43 4 HOH HOH 43 B HOH 47 4 HOH HOH 47 B HOH 48 4 HOH HOH 48 B HOH 50 4 HOH HOH 50 B HOH 55 4 HOH HOH 55 B HOH 59 4 HOH HOH 59 B HOH 61 4 HOH HOH 61 B HOH 64 4 HOH HOH 64 B HOH 67 4 HOH HOH 67 B HOH 69 4 HOH HOH 69 B HOH 74 4 HOH HOH 74 B HOH 75 4 HOH HOH 75 B HOH 79 4 HOH HOH 79 B HOH 80 4 HOH HOH 80 B HOH 81 4 HOH HOH 81 B HOH 82 4 HOH HOH 82 B HOH 87 4 HOH HOH 87 B HOH 89 4 HOH HOH 89 B HOH 90 4 HOH HOH 90 B HOH 91 4 HOH HOH 91 B HOH 92 4 HOH HOH 92 B HOH 93 4 HOH HOH 93 B HOH 95 4 HOH HOH 95 B HOH 96 4 HOH HOH 96 B HOH 97 4 HOH HOH 97 B HOH 99 4 HOH HOH 99 B HOH 100 4 HOH HOH 100 B HOH 101 4 HOH HOH 101 B HOH 102 4 HOH HOH 102 B HOH 104 4 HOH HOH 104 B HOH 105 4 HOH HOH 105 B HOH 108 4 HOH HOH 108 B HOH 110 4 HOH HOH 110 B HOH 112 4 HOH HOH 112 B HOH 113 4 HOH HOH 113 B HOH 115 4 HOH HOH 115 B HOH 119 4 HOH HOH 119 B HOH 123 4 HOH HOH 123 B HOH 124 4 HOH HOH 124 B HOH 125 4 HOH HOH 125 B HOH 129 4 HOH HOH 129 B OC4 31 4 HOH HOH 134 B OC4 31 4 HOH HOH 135 B OC4 31 4 HOH HOH 136 B OC4 31 4 HOH HOH 137 B OC4 34 4 HOH HOH 149 B OC4 34 4 HOH HOH 150 B OC4 34 4 HOH HOH 151 B OC4 34 4 HOH HOH 152 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 0.129 0.132 0.158 820 5.000 15369 author_defined_assembly 2 dimeric A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 84 G O HOH 1_555 56.2 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 138 A G O HOH 1_555 84.4 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 138 A G O HOH 1_555 78.2 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 139 G O HOH 1_555 158.9 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 139 G O HOH 1_555 137.5 A HOH 138 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 139 G O HOH 1_555 84.1 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 140 G O HOH 1_555 90.3 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 140 G O HOH 1_555 112.0 A HOH 138 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 140 G O HOH 1_555 163.1 A HOH 139 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 140 G O HOH 1_555 95.6 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 141 A G O HOH 1_555 94.2 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 141 A G O HOH 1_555 137.5 A HOH 138 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 141 A G O HOH 1_555 68.2 A HOH 139 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 141 A G O HOH 1_555 65.0 A HOH 140 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 141 A G O HOH 1_555 96.3 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 85.0 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 45.8 A HOH 138 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 117.2 A HOH 139 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 116.0 A HOH 140 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 78.2 A HOH 141 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 142 A G O HOH 1_555 174.4 A G 5 A OP2 G 5 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 120.7 A HOH 84 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 67.0 A HOH 138 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 68.2 A HOH 139 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 70.6 A HOH 140 G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 127.7 A HOH 141 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 119.4 A HOH 142 A G O HOH 1_555 A CA 32 A C CA CA 1_555 A HOH 143 G O HOH 1_555 65.5 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 144 G O HOH 1_555 173.5 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 145 G O HOH 1_555 91.5 A HOH 144 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 145 G O HOH 1_555 88.2 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 146 G O HOH 1_555 93.1 A HOH 144 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 146 G O HOH 1_555 93.3 A HOH 145 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 146 G O HOH 1_555 90.2 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 147 G O HOH 1_555 87.3 A HOH 144 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 147 G O HOH 1_555 93.0 A HOH 145 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 147 G O HOH 1_555 178.7 A HOH 146 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 147 G O HOH 1_555 90.4 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 86.2 A HOH 144 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 87.4 A HOH 145 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 89.0 A HOH 146 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 178.9 A HOH 147 G O HOH 1_555 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 90.4 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 B DT 18 B OP2 DT 8 1_555 90.8 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 B HOH 134 H O HOH 1_555 83.0 B DT 18 B OP2 DT 8 1_555 B CA 31 E CA CA 1_555 B HOH 134 H O HOH 1_555 92.4 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 B HOH 135 H O HOH 1_555 83.9 B DT 18 B OP2 DT 8 1_555 B CA 31 E CA CA 1_555 B HOH 135 H O HOH 1_555 171.8 B HOH 134 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 135 H O HOH 1_555 93.1 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 B HOH 136 H O HOH 1_555 99.4 B DT 18 B OP2 DT 8 1_555 B CA 31 E CA CA 1_555 B HOH 136 H O HOH 1_555 92.0 B HOH 134 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 136 H O HOH 1_555 174.9 B HOH 135 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 136 H O HOH 1_555 82.7 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 172.4 B DT 18 B OP2 DT 8 1_555 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 96.6 B HOH 134 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 94.8 B HOH 135 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 89.0 B HOH 136 H O HOH 1_555 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 82.2 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B DT 18 B OP1 DT 8 1_555 91.2 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B DG 20 B B OP1 DG 10 4_567 69.5 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 B DG 20 B B OP1 DG 10 4_567 78.4 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B HOH 149 H O HOH 1_555 87.4 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 B HOH 149 H O HOH 1_555 164.0 B DG 20 B B OP1 DG 10 4_567 B CA 34 F CA CA 1_555 B HOH 149 H O HOH 1_555 86.2 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B HOH 150 H O HOH 1_555 122.7 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 B HOH 150 H O HOH 1_555 90.4 B DG 20 B B OP1 DG 10 4_567 B CA 34 F CA CA 1_555 B HOH 150 H O HOH 1_555 54.9 B HOH 149 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 150 H O HOH 1_555 77.1 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 157.9 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 94.3 B DG 20 B B OP1 DG 10 4_567 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 132.6 B HOH 149 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 93.0 B HOH 150 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 78.7 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 80.5 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 87.0 B DG 20 B B OP1 DG 10 4_567 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 146.0 B HOH 149 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 108.4 B HOH 150 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 156.7 B HOH 151 H O HOH 1_555 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_555 78.4 A HOH 138 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 139 G O HOH 1_555 83.9 A HOH 138 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 140 G O HOH 1_555 71.7 A HOH 139 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 140 G O HOH 1_555 83.8 A HOH 138 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 141 B G O HOH 1_555 89.0 A HOH 139 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 141 B G O HOH 1_555 72.1 A HOH 140 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 141 B G O HOH 1_555 150.7 A HOH 138 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 142 B G O HOH 1_555 82.6 A HOH 139 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 142 B G O HOH 1_555 166.0 A HOH 140 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 142 B G O HOH 1_555 95.3 A HOH 141 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 142 B G O HOH 1_555 104.0 A HOH 138 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 143 G O HOH 1_555 147.8 A HOH 139 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 143 G O HOH 1_555 64.4 A HOH 140 G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 143 G O HOH 1_555 108.3 A HOH 141 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 143 G O HOH 1_555 76.5 A HOH 142 B G O HOH 1_555 A CA 32 B C CA CA 1_555 A HOH 143 G O HOH 1_555 128.5 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 9.42 1.30 114.00 123.42 A A A N1 C1' C2' C C C 1 1 1 N 1 5.14 0.70 108.50 113.64 A A A O4' C1' N9 A A A 2 2 2 N 1 -8.91 1.10 112.00 103.09 A A A N9 C1' C2' G G G 10 10 10 N 1 5.37 0.70 108.50 113.87 A A A O4' C1' N9 G G G 10 10 10 N 1 1.93 0.30 108.30 110.23 B B B O4' C1' N1 DC DC DC 11 11 11 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 17 17 17 N 1 -5.89 0.80 109.40 103.51 B B B O5' C5' C4' DG DG DG 20 20 20 B B B N 1 5.45 0.90 103.10 108.55 B B B C4' C3' C2' DG DG DG 20 20 20 B B N 1 4.02 0.30 108.30 112.32 B B B O4' C1' N9 DG DG DG 20 20 20 A N 1 3.08 0.30 108.30 111.38 B B B O4' C1' N9 DG DG DG 20 20 20 B N 1 A A C2' C1' G G 10 10 0.077 0.011 1.529 1.606 N 1 B B C2' C1' DG DG 20 20 0.061 0.010 1.519 1.580 N 10.71 0.163 0.132 1.15 8.0 871 16497 16497 5. 95.1 random 1 0.0 MOLECULAR REPLACEMENT NDB ID AH0001 1.00 1.00 1.15 8.0 124 542 4 414 0 0.027 0.009 0.132 1.18 93.9 8.170 1.15 50.00 1PJG 17368 4.7 0.081 1 29.6 96.2 0.261 1.15 1.18 11.09 882 93.9 data collection ADSC Quantum 4 data scaling SCALEPACK phasing EPMR refinement SHELXL-97 data reduction DENZO RNA/DNA Hybrid Decamer of CAAAGAAAAG/CTTTTCTTTG 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 4 N N 4 N N metalc 2.283 A A G 5 A OP2 G 5 1_555 A CA 32 C CA CA 1_555 metalc 2.011 A A 9 A OP2 A 9 1_555 A CA 33 D CA CA 1_555 metalc 2.195 A A 9 A OP1 A 9 3_646 B CA 31 E CA CA 1_555 metalc 2.213 A G 10 A OP1 G 10 3_646 B CA 34 F CA CA 1_555 metalc 3.263 A A CA 32 C CA CA 1_555 A HOH 84 G O HOH 1_555 metalc 2.227 A A A CA 32 C CA CA 1_555 A HOH 138 G O HOH 1_555 metalc 2.510 B B A CA 32 C CA CA 1_555 A HOH 138 G O HOH 1_555 metalc 2.100 A A CA 32 C CA CA 1_555 A HOH 139 G O HOH 1_555 metalc 2.279 B A CA 32 C CA CA 1_555 A HOH 139 G O HOH 1_555 metalc 2.009 A A CA 32 C CA CA 1_555 A HOH 140 G O HOH 1_555 metalc 2.277 B A CA 32 C CA CA 1_555 A HOH 140 G O HOH 1_555 metalc 2.122 A A A CA 32 C CA CA 1_555 A HOH 141 G O HOH 1_555 metalc 2.573 B B A CA 32 C CA CA 1_555 A HOH 141 G O HOH 1_555 metalc 2.524 A A A CA 32 C CA CA 1_555 A HOH 142 G O HOH 1_555 metalc 1.922 B B A CA 32 C CA CA 1_555 A HOH 142 G O HOH 1_555 metalc 2.216 A A CA 32 C CA CA 1_555 A HOH 143 G O HOH 1_555 metalc 2.401 B A CA 32 C CA CA 1_555 A HOH 143 G O HOH 1_555 metalc 2.038 A CA 33 D CA CA 1_555 A HOH 144 G O HOH 1_555 metalc 2.125 A CA 33 D CA CA 1_555 A HOH 145 G O HOH 1_555 metalc 2.099 A CA 33 D CA CA 1_555 A HOH 146 G O HOH 1_555 metalc 2.022 A CA 33 D CA CA 1_555 A HOH 147 G O HOH 1_555 metalc 2.132 A CA 33 D CA CA 1_555 A HOH 148 G O HOH 1_555 metalc 2.237 B DT 18 B OP2 DT 8 1_555 B CA 31 E CA CA 1_555 metalc 2.223 B DT 18 B OP1 DT 8 1_555 B CA 34 F CA CA 1_555 metalc 2.757 B B DG 20 B OP1 DG 10 4_567 B CA 34 F CA CA 1_555 metalc 2.288 B CA 31 E CA CA 1_555 B HOH 134 H O HOH 1_555 metalc 2.294 B CA 31 E CA CA 1_555 B HOH 135 H O HOH 1_555 metalc 2.259 B CA 31 E CA CA 1_555 B HOH 136 H O HOH 1_555 metalc 2.284 B CA 31 E CA CA 1_555 B HOH 137 H O HOH 1_555 metalc 2.360 B CA 34 F CA CA 1_555 B HOH 149 H O HOH 1_555 metalc 2.019 B CA 34 F CA CA 1_555 B HOH 150 H O HOH 1_555 metalc 2.462 B CA 34 F CA CA 1_555 B HOH 151 H O HOH 1_555 metalc 2.473 B CA 34 F CA CA 1_555 B HOH 152 H O HOH 1_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; Moleuclar Replacement; sugar conformation, DNA-RNA COMPLEX, DNA-RNA HYBRID 1PJG PDB 1 1PJG 1PJG PDB 2 1PJG 1 10 1PJG 1 10 1PJG A 1 1 10 11 20 1PJG 11 20 1PJG B 2 1 10 BINDING SITE FOR RESIDUE CA B 31 B CA 31 Software 6 BINDING SITE FOR RESIDUE CA A 32 A CA 32 Software 7 BINDING SITE FOR RESIDUE CA A 33 A CA 33 Software 6 BINDING SITE FOR RESIDUE CA B 34 B CA 34 Software 7 A A 9 A A 9 6 3_646 B DT 18 B DT 8 6 1_555 B HOH 134 H HOH 6 1_555 B HOH 135 H HOH 6 1_555 B HOH 136 H HOH 6 1_555 B HOH 137 H HOH 6 1_555 A G 5 A G 5 7 1_555 A HOH 138 G HOH 7 1_555 A HOH 139 G HOH 7 1_555 A HOH 140 G HOH 7 1_555 A HOH 141 G HOH 7 1_555 A HOH 142 G HOH 7 1_555 A HOH 143 G HOH 7 1_555 A A 9 A A 9 6 1_555 A HOH 144 G HOH 6 1_555 A HOH 145 G HOH 6 1_555 A HOH 146 G HOH 6 1_555 A HOH 147 G HOH 6 1_555 A HOH 148 G HOH 6 1_555 A G 10 A G 10 7 3_646 B DT 18 B DT 8 7 1_555 B DG 20 B DG 10 7 4_567 B HOH 149 H HOH 7 1_555 B HOH 150 H HOH 7 1_555 B HOH 151 H HOH 7 1_555 B HOH 152 H HOH 7 1_555 19 P 21 21 21