0.031949 0.000000 0.000000 0.000000 0.031949 0.000000 0.000000 0.000000 0.007262 0.00000 0.00000 0.00000 Horton, N.C. Finzel, B.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 31.300 31.300 137.700 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 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 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER 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 N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N N N 20 N C N 21 N C N 22 N H N 23 N H 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 O N 37 N P N 38 N O N 39 N O N 40 N O N 41 N C N 42 R C N 43 N O N 44 S C N 45 N O N 46 N C N 47 R C Y 48 N N Y 49 N C Y 50 N N Y 51 N C Y 52 N C N 53 N N Y 54 N N Y 55 N C Y 56 N N Y 57 N C N 58 N H 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 O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C N 84 N N N 85 N C N 86 N O N 87 N N N 88 N C N 89 N N N 90 N C N 91 N C N 92 N H N 93 N H 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 O N 107 N P N 108 N O N 109 N O N 110 N O N 111 N C N 112 R C N 113 N O N 114 S C N 115 N O N 116 N C N 117 R C Y 118 N N Y 119 N C Y 120 N N Y 121 N C N 122 N C N 123 N O N 124 N N N 125 N C N 126 N N N 127 N N Y 128 N C N 129 N H 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 O N 144 N P N 145 N O N 146 N O N 147 N O N 148 N C N 149 R C N 150 N O N 151 S C N 152 N O N 153 R C N 154 N O N 155 R C Y 156 N N Y 157 N C Y 158 N N Y 159 N C N 160 N C N 161 N O N 162 N N N 163 N C N 164 N N N 165 N N Y 166 N C 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 H N 183 N H N 184 N O N 185 N P N 186 N O N 187 N O N 188 N O N 189 N C N 190 R C N 191 N O N 192 S C N 193 N O N 194 R C N 195 N O N 196 R C N 197 N N N 198 N C N 199 N O N 200 N N N 201 N C N 202 N O N 203 N C N 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 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 N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N doub N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub 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 Y 60 N sing Y 61 N sing Y 62 N doub N 63 N sing Y 64 N sing Y 65 N sing Y 66 N doub N 67 N sing Y 68 N doub N 69 N sing N 70 N sing Y 71 N sing Y 72 N doub N 73 N sing Y 74 N sing N 75 N sing N 76 N sing N 77 N doub N 78 N sing 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 doub N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub 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 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 Y 133 N sing Y 134 N sing Y 135 N doub N 136 N sing Y 137 N sing N 138 N sing Y 139 N doub N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing 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 Y 173 N sing Y 174 N sing Y 175 N doub N 176 N sing Y 177 N sing N 178 N sing Y 179 N doub N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N doub 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 doub 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 doub N 218 N sing N 219 N sing N 220 N sing N 221 N doub N 222 N sing N 223 N doub N 224 N sing N 225 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 264 521 533 10.1006/jmbi.1996.0658 8969302 The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase. 1996 10.2210/pdb1fix/pdb pdb_00001fix 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 AREA DETECTOR 1994-10-01 SIEMENS M x-ray 1 1.0 3168.925 RNA (5'-R(*UP*UP*CP*GP*GP*GP*CP*GP*CP*C)-3') 1 syn polymer 3055.006 DNA (5'-D(*GP*GP*CP*GP*CP*CP*CP*GP*AP*A)-3') 1 syn polymer 18.015 water 72 nat water no no UUCGGGCGCC UUCGGGCGCC A polyribonucleotide no no (DG)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DA)(DA) GGCGCCCGAA B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 1 2.64 46.5000 VAPOR DIFFUSION, HANGING DROP 4.50 pH 4.50, VAPOR DIFFUSION, HANGING DROP ROOM TEMPERATURE WATER 1 MPD 1 CACL2 1 NA ACETATE 1 -0.816 1 20 A 1 B 20 -1.761 A_U1:DA20_B 1 -18.085 0.212 -0.128 -0.284 5.424 1 20 A 2 B 19 3.450 A_U2:DA19_B 2 -19.443 -0.163 -0.379 -0.188 -6.727 1 19 A 3 B 18 -3.063 A_C3:DG18_B 3 -16.172 0.132 0.319 -0.257 -8.560 1 19 A 4 B 17 3.867 A_G4:DC17_B 4 -17.579 -0.539 -0.005 -0.153 -17.608 1 19 A 5 B 16 -3.315 A_G5:DC16_B 5 -11.474 -0.573 -0.335 -0.349 -9.687 1 19 A 6 B 15 -2.135 A_G6:DC15_B 6 -14.621 -0.511 -0.249 -0.325 -3.795 1 19 A 7 B 14 2.779 A_C7:DG14_B 7 -8.436 0.168 0.136 -0.172 -9.449 1 19 A 8 B 13 2.093 A_G8:DC13_B 8 -11.290 -0.396 -0.156 -0.137 0.781 1 19 A 9 B 12 2.972 A_C9:DG12_B 9 -10.375 0.144 -0.134 -0.289 2.086 1 19 A 10 B 11 -0.960 A_C10:DG11_B 10 7.245 0.078 0.025 -0.318 2.786 34.955 A A 1 2 15.675 B B 20 19 2.994 9.291 0.308 -0.472 AA_U1U2:DA19DA20_BB 1 3.842 -6.483 33.521 -2.054 0.012 3.411 37.230 A A 2 3 11.366 B B 19 18 3.737 7.182 0.413 -0.770 AA_U2C3:DG18DA19_BB 2 -6.209 9.827 36.041 -2.267 -1.564 2.386 28.942 A A 3 4 19.793 B B 18 17 3.149 9.702 0.472 -1.853 AA_C3G4:DC17DG18_BB 3 1.751 -3.572 27.244 -5.583 -0.606 2.811 35.513 A A 4 5 19.319 B B 17 16 3.450 11.580 -1.187 -1.541 AA_G4G5:DC16DC17_BB 4 -0.851 1.419 33.619 -4.195 1.823 2.271 29.202 A A 5 6 25.506 B B 16 15 3.255 12.445 1.034 -1.824 AA_G5G6:DC15DC16_BB 5 2.672 -5.477 26.336 -6.028 -1.534 2.878 35.588 A A 6 7 9.859 B B 15 14 3.144 5.997 0.407 -1.221 AA_G6C7:DG14DC15_BB 6 -1.844 3.032 35.049 -2.808 -0.915 2.848 29.325 A A 7 8 15.820 B B 14 13 3.392 7.888 0.403 -1.691 AA_C7G8:DC13DG14_BB 7 4.154 -8.331 27.966 -5.003 0.080 3.024 34.417 A A 8 9 4.638 B B 13 12 3.113 2.741 0.123 -1.066 AA_G8C9:DG12DC13_BB 8 1.113 -1.883 34.294 -2.203 -0.045 3.192 32.291 A A 9 10 8.729 B B 12 11 3.476 4.837 -0.108 -1.679 AA_C9C10:DG11DG12_BB 9 0.603 -1.089 31.931 -3.898 0.305 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Refinement description 1 0 1996-12-11 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession NDB Y NDB 1996-10-24 REL REL HOH water A-form RNA/DNA duplex Other in silico model HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 54 3 HOH HOH 54 A HOH 56 3 HOH HOH 56 A HOH 58 3 HOH HOH 58 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 61 3 HOH HOH 61 A HOH 62 3 HOH HOH 62 A HOH 64 3 HOH HOH 64 A HOH 68 3 HOH HOH 68 A HOH 71 3 HOH HOH 71 A HOH 72 3 HOH HOH 72 A HOH 73 3 HOH HOH 73 A HOH 75 3 HOH HOH 75 A HOH 76 3 HOH HOH 76 A HOH 78 3 HOH HOH 78 A HOH 80 3 HOH HOH 80 A HOH 82 3 HOH HOH 82 A HOH 83 3 HOH HOH 83 A HOH 84 3 HOH HOH 84 A HOH 85 3 HOH HOH 85 A HOH 86 3 HOH HOH 86 A HOH 88 3 HOH HOH 88 A HOH 89 3 HOH HOH 89 A HOH 90 3 HOH HOH 90 A HOH 91 3 HOH HOH 91 A HOH 92 3 HOH HOH 92 A HOH 30 3 HOH HOH 30 B HOH 39 3 HOH HOH 39 B HOH 42 3 HOH HOH 42 B HOH 43 3 HOH HOH 43 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 46 3 HOH HOH 46 B HOH 47 3 HOH HOH 47 B HOH 48 3 HOH HOH 48 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 51 3 HOH HOH 51 B HOH 52 3 HOH HOH 52 B HOH 53 3 HOH HOH 53 B HOH 55 3 HOH HOH 55 B HOH 57 3 HOH HOH 57 B HOH 63 3 HOH HOH 63 B HOH 65 3 HOH HOH 65 B HOH 66 3 HOH HOH 66 B HOH 67 3 HOH HOH 67 B HOH 69 3 HOH HOH 69 B HOH 70 3 HOH HOH 70 B HOH 74 3 HOH HOH 74 B HOH 77 3 HOH HOH 77 B HOH 79 3 HOH HOH 79 B HOH 81 3 HOH HOH 81 B HOH 87 3 HOH HOH 87 B U 1 n 1 U 1 A U 2 n 2 U 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A G 6 n 6 G 6 A C 7 n 7 C 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A C 10 n 10 C 10 A G 11 n 1 DG 11 B G 12 n 2 DG 12 B C 13 n 3 DC 13 B G 14 n 4 DG 14 B C 15 n 5 DC 15 B C 16 n 6 DC 16 B C 17 n 7 DC 17 B G 18 n 8 DG 18 B A 19 n 9 DA 19 B A 20 n 10 DA 20 B 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 U 2 0.084 SIDE CHAIN 1 A G 5 0.057 SIDE CHAIN 1 -2.58 0.40 104.50 101.92 B B B O4' C4' C3' DC DC DC 15 15 15 N NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64 0.1450000 0.1450000 2.300 5.000 2457 80.000 1 2.000 MIR A-FORM DUPLEX TR isotropic TR isotropic 2.300 5.000 72 484 0 412 0 0.019 2.20 0.2720000 2.39 117 8 30.00 fix fix 2.300 5.000 1FIX 20393 3315 2.000 0.0810000 0.0810000 1 94.400 model building XTAL refinement X-PLOR data reduction XENGEN data scaling XENGEN phasing XTAL THE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEASE ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE 1 N N 2 N N 3 N N 3 N N hydrog WATSON-CRICK A U 1 A N3 U 1 1_555 B DA 20 B N1 DA 10 1_555 hydrog WATSON-CRICK A U 1 A O4 U 1 1_555 B DA 20 B N6 DA 10 1_555 hydrog WATSON-CRICK A U 2 A N3 U 2 1_555 B DA 19 B N1 DA 9 1_555 hydrog WATSON-CRICK A U 2 A O4 U 2 1_555 B DA 19 B N6 DA 9 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B DG 18 B N1 DG 8 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B DG 18 B O6 DG 8 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B DG 18 B N2 DG 8 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B DC 17 B N3 DC 7 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B DC 17 B O2 DC 7 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B DC 17 B N4 DC 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 G 6 A N1 G 6 1_555 B DC 15 B N3 DC 5 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B DC 15 B O2 DC 5 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B DC 15 B N4 DC 5 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 B DG 14 B N1 DG 4 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 B DG 14 B O6 DG 4 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 B DG 14 B N2 DG 4 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 B DC 13 B N3 DC 3 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 B DC 13 B O2 DC 3 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 B DC 13 B N4 DC 3 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B DG 12 B N1 DG 2 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B DG 12 B O6 DG 2 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B DG 12 B N2 DG 2 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 B DG 11 B N2 DG 1 1_555 DNA-RNA HYBRID RIGHT HANDED DNA/RNA HYBRID, DOUBLE HELIX, HIV-1 PRIMER BINDING SITE, DNA-RNA HYBRID 1FIX PDB 1 1FIX 1FIX PDB 2 1FIX 1 10 1FIX 1 10 1FIX A 1 1 10 11 20 1FIX 11 20 1FIX B 2 1 10 95 P 43 2 2