1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Szyperski, T. Goette, M. Billeter, M. Perola, E. Cellai, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 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 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 N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 92 N C 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 H N 107 N O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 N C N 118 R C Y 119 N N Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N N Y 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 O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C N 156 N N N 157 N C N 158 N O N 159 N N N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C N 165 N H 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 O N 181 N P N 182 N O N 183 N O N 184 N O N 185 N C N 186 R C N 187 N O N 188 S C N 189 N O N 190 R C N 191 N O N 192 R C Y 193 N N Y 194 N C Y 195 N N Y 196 N C N 197 N C N 198 N O N 199 N N N 200 N C N 201 N N N 202 N N Y 203 N C 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 O N 219 N P N 220 N O N 221 N O N 222 N O N 223 N C N 224 R C N 225 N O N 226 S C N 227 N O N 228 R C N 229 N O N 230 R C N 231 N N N 232 N C N 233 N O N 234 N N N 235 N C N 236 N O N 237 N C N 238 N C N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 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 doub 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 N 250 N sing N 251 N sing N 252 N sing N 253 N doub N 254 N sing N 255 N sing N 256 N sing N 257 N doub N 258 N sing N 259 N doub N 260 N sing N 261 N sing NE J.Biomol.NMR JBNME9 0800 0925-2738 13 343 355 10.1023/A:1008350604637 10353196 NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription. 1999 10.2210/pdb1byx/pdb pdb_00001byx 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2581.601 RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3') 1 syn polymer CHIMERIC HYBRID RNA/RNA-DNA DUPLEX 2451.580 DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3') 1 syn polymer no no GCAGUGGC GCAGUGGC A polyribonucleotide no no GCCA(DC)(DT)(DG)(DC) GCCACTGC B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n n n n n n -8.025 1 19 A 2 B 107 -3.366 A_C2:DG107_B 1 1.032 -0.139 -0.195 -0.031 2.416 1 20 A 3 B 106 -0.019 A_A3:DT106_B 2 -12.101 -0.288 0.760 -0.280 -10.188 1 19 A 4 B 105 -1.231 A_G4:DC105_B 3 -20.854 0.145 -0.094 -0.102 -6.741 1 20 A 5 B 104 -2.632 A_U5:A104_B 4 -16.433 -0.382 -0.069 -0.034 -8.484 1 19 A 6 B 103 -6.816 A_G6:C103_B 5 1.582 0.584 -0.041 -0.046 -0.608 1 19 A 7 B 102 -2.104 A_G7:C102_B 6 -11.132 0.101 -0.087 -0.049 -5.691 A 8 B 101 -161.699 A_C8:G101_B 7 -5.285 -1.530 2.442 2.367 3.554 29.927 A A 2 3 -23.827 B B 107 106 3.456 -11.950 1.121 -1.315 AA_C2A3:DT106DG107_BB 1 -3.241 6.462 27.299 0.233 -2.925 4.287 37.759 A A 3 4 -10.771 B B 106 105 4.137 -6.854 0.040 -1.972 AA_A3G4:DC105DT106_BB 2 10.095 -15.864 35.802 -1.875 1.665 3.402 34.794 A A 4 5 -10.926 B B 105 104 3.259 -6.498 -0.424 -1.099 AA_G4U5:A104DC105_BB 3 0.155 -0.260 34.200 -0.820 0.734 3.079 32.986 A A 5 6 9.366 B B 104 103 3.379 5.294 0.056 -1.601 AA_U5G6:C103A104_BB 4 -1.928 3.411 32.515 -3.713 -0.424 2.469 31.204 A A 6 7 19.815 B B 103 102 3.127 10.454 0.661 -1.593 AA_G6G7:C102C103_BB 5 2.078 -3.940 29.370 -4.717 -0.881 -0.336 175.750 A A 7 8 70.510 B B 102 101 -0.085 140.513 -4.199 1.474 AA_G7C8:G101C102_BB 6 85.663 -42.986 147.943 0.763 2.086 database_2 pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 1999-10-20 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession BNL Y RCSB 1998-10-20 REL REL THE RNA:RNA-DNA CHIMERIC HYBRID DUPLEX WAS CHEMICALLY SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY VIRUS TYPE 1 (HIV-1). THE DUPLEX IS FORMED DURING THE INITIATION OF (-)DNA STRAND SYNTHESIS IN HIV-1 REPLICATION. sample THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER FORCE FIELD USING THE PROGRAM OPAL DYANA TARGET FUNCTION 100 20 NOESY TOCSY DQF-COSY E H-P HETCOR H-C COSY 7.0 1 atm 298 K REFINEMENT DETAILS ARE DESCRIBED IN THE JRNL CITATION ABOVE distance geometry GUNTERT,WUTHRICH refinement DYANA structure solution DYANA 500 Bruker AMX 600 Bruker AMX 750 Varian UNITY G 1 n 1 G 1 A C 2 n 2 C 2 A A 3 n 3 A 3 A G 4 n 4 G 4 A U 5 n 5 U 5 A G 6 n 6 G 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A G 101 n 1 G 101 B C 102 n 2 C 102 B C 103 n 3 C 103 B A 104 n 4 A 104 B C 105 n 5 DC 105 B T 106 n 6 DT 106 B G 107 n 7 DG 107 B C 108 n 8 DC 108 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 A OP2 HO3' G C 7 8 1.56 15 B B HO5' OP2 G C 101 102 1.59 18 A A OP2 HO3' G C 7 8 1.54 1 A G 4 0.068 SIDE CHAIN 1 A U 5 0.083 SIDE CHAIN 1 A G 7 0.083 SIDE CHAIN 1 B G 101 0.061 SIDE CHAIN 1 B C 102 0.082 SIDE CHAIN 1 B DG 107 0.101 SIDE CHAIN 2 A G 4 0.101 SIDE CHAIN 2 A U 5 0.109 SIDE CHAIN 2 A G 7 0.111 SIDE CHAIN 2 B C 103 0.058 SIDE CHAIN 2 B A 104 0.085 SIDE CHAIN 3 A A 3 0.106 SIDE CHAIN 3 A G 4 0.089 SIDE CHAIN 3 A U 5 0.093 SIDE CHAIN 3 A C 8 0.072 SIDE CHAIN 3 B C 102 0.094 SIDE CHAIN 3 B A 104 0.087 SIDE CHAIN 4 A C 2 0.068 SIDE CHAIN 4 A G 4 0.107 SIDE CHAIN 4 B G 101 0.046 SIDE CHAIN 4 B C 102 0.092 SIDE CHAIN 4 B DT 106 0.102 SIDE CHAIN 5 A G 1 0.071 SIDE CHAIN 5 A G 4 0.128 SIDE CHAIN 5 A U 5 0.084 SIDE CHAIN 5 A C 8 0.081 SIDE CHAIN 5 B G 101 0.107 SIDE CHAIN 5 B A 104 0.071 SIDE CHAIN 5 B DC 105 0.097 SIDE CHAIN 5 B DT 106 0.073 SIDE CHAIN 5 B DC 108 0.105 SIDE CHAIN 6 A G 1 0.071 SIDE CHAIN 6 A G 4 0.146 SIDE CHAIN 6 A U 5 0.109 SIDE CHAIN 6 B G 101 0.060 SIDE CHAIN 6 B C 103 0.145 SIDE CHAIN 6 B A 104 0.073 SIDE CHAIN 7 A C 2 0.187 SIDE CHAIN 7 A G 4 0.066 SIDE CHAIN 7 A U 5 0.083 SIDE CHAIN 7 B G 101 0.144 SIDE CHAIN 7 B C 102 0.077 SIDE CHAIN 7 B DC 105 0.073 SIDE CHAIN 7 B DT 106 0.095 SIDE CHAIN 7 B DG 107 0.094 SIDE CHAIN 8 A G 1 0.067 SIDE CHAIN 8 A C 2 0.101 SIDE CHAIN 8 A G 4 0.124 SIDE CHAIN 8 A U 5 0.081 SIDE CHAIN 8 B A 104 0.088 SIDE CHAIN 8 B DG 107 0.064 SIDE CHAIN 8 B DC 108 0.172 SIDE CHAIN 9 A G 1 0.093 SIDE CHAIN 9 A G 4 0.095 SIDE CHAIN 9 A U 5 0.134 SIDE CHAIN 9 A G 7 0.077 SIDE CHAIN 9 B C 103 0.062 SIDE CHAIN 9 B DT 106 0.090 SIDE CHAIN 9 B DG 107 0.082 SIDE CHAIN 9 B DC 108 0.106 SIDE CHAIN 10 A G 1 0.075 SIDE CHAIN 10 A A 3 0.083 SIDE CHAIN 10 A G 7 0.056 SIDE CHAIN 10 B G 101 0.088 SIDE CHAIN 10 B A 104 0.060 SIDE CHAIN 10 B DC 108 0.111 SIDE CHAIN 11 A G 1 0.079 SIDE CHAIN 11 A A 3 0.108 SIDE CHAIN 11 A G 7 0.138 SIDE CHAIN 11 B G 101 0.094 SIDE CHAIN 11 B C 102 0.085 SIDE CHAIN 11 B DT 106 0.088 SIDE CHAIN 11 B DC 108 0.071 SIDE CHAIN 12 A G 1 0.152 SIDE CHAIN 12 A A 3 0.100 SIDE CHAIN 12 A G 4 0.095 SIDE CHAIN 12 A U 5 0.114 SIDE CHAIN 12 A G 6 0.064 SIDE CHAIN 12 A C 8 0.126 SIDE CHAIN 12 B G 101 0.100 SIDE CHAIN 12 B A 104 0.084 SIDE CHAIN 12 B DC 108 0.141 SIDE CHAIN 13 A G 1 0.195 SIDE CHAIN 13 A A 3 0.096 SIDE CHAIN 13 A G 4 0.119 SIDE CHAIN 13 A U 5 0.102 SIDE CHAIN 13 A G 7 0.059 SIDE CHAIN 13 A C 8 0.154 SIDE CHAIN 13 B G 101 0.092 SIDE CHAIN 13 B C 102 0.063 SIDE CHAIN 13 B A 104 0.059 SIDE CHAIN 13 B DC 105 0.079 SIDE CHAIN 13 B DT 106 0.101 SIDE CHAIN 13 B DG 107 0.049 SIDE CHAIN 13 B DC 108 0.070 SIDE CHAIN 14 A G 4 0.127 SIDE CHAIN 14 A U 5 0.095 SIDE CHAIN 14 B C 102 0.101 SIDE CHAIN 14 B A 104 0.079 SIDE CHAIN 14 B DT 106 0.094 SIDE CHAIN 15 A G 4 0.125 SIDE CHAIN 15 A U 5 0.107 SIDE CHAIN 15 B G 101 0.114 SIDE CHAIN 15 B DC 105 0.066 SIDE CHAIN 16 A G 1 0.079 SIDE CHAIN 16 A A 3 0.060 SIDE CHAIN 16 A G 4 0.128 SIDE CHAIN 16 A U 5 0.082 SIDE CHAIN 16 A G 7 0.063 SIDE CHAIN 16 B G 101 0.137 SIDE CHAIN 16 B C 102 0.065 SIDE CHAIN 16 B C 103 0.074 SIDE CHAIN 16 B DG 107 0.056 SIDE CHAIN 16 B DC 108 0.069 SIDE CHAIN 17 A C 2 0.073 SIDE CHAIN 17 A G 4 0.122 SIDE CHAIN 17 A G 6 0.059 SIDE CHAIN 17 A G 7 0.078 SIDE CHAIN 17 B A 104 0.092 SIDE CHAIN 17 B DT 106 0.094 SIDE CHAIN 18 A G 1 0.076 SIDE CHAIN 18 A A 3 0.111 SIDE CHAIN 18 A G 4 0.129 SIDE CHAIN 18 A U 5 0.128 SIDE CHAIN 18 A G 7 0.075 SIDE CHAIN 18 B G 101 0.059 SIDE CHAIN 18 B A 104 0.071 SIDE CHAIN 18 B DC 108 0.083 SIDE CHAIN 19 A G 1 0.083 SIDE CHAIN 19 A G 4 0.122 SIDE CHAIN 19 A G 7 0.113 SIDE CHAIN 19 B A 104 0.065 SIDE CHAIN 19 B DT 106 0.082 SIDE CHAIN 19 B DG 107 0.058 SIDE CHAIN 19 B DC 108 0.129 SIDE CHAIN 20 A G 1 0.120 SIDE CHAIN 20 A G 4 0.094 SIDE CHAIN 20 A U 5 0.102 SIDE CHAIN 20 A G 7 0.056 SIDE CHAIN 20 B G 101 0.137 SIDE CHAIN 20 B DT 106 0.084 SIDE CHAIN 20 B DC 108 0.109 SIDE CHAIN 1 6.84 0.70 108.50 115.34 A A A O4' C1' N1 C C C 2 2 2 N 1 4.21 0.70 108.50 112.71 A A A O4' C1' N1 U U U 5 5 5 N 1 5.00 0.70 108.50 113.50 A A A O4' C1' N9 G G G 6 6 6 N 1 4.20 0.70 108.50 112.70 B B B O4' C1' N9 G G G 101 101 101 N 1 6.85 0.70 108.50 115.35 B B B O4' C1' N1 C C C 102 102 102 N 1 4.85 0.70 108.50 113.35 B B B O4' C1' N1 C C C 103 103 103 N 1 6.57 0.30 108.30 114.87 B B B O4' C1' N1 DC DC DC 105 105 105 N 1 4.04 0.30 108.30 112.34 B B B O4' C1' N1 DT DT DT 106 106 106 N 1 4.01 0.30 108.30 112.31 B B B O4' C1' N9 DG DG DG 107 107 107 N 1 2.77 0.30 108.30 111.07 B B B O4' C1' N1 DC DC DC 108 108 108 N 2 4.89 0.80 101.50 106.39 A A A C3' C2' C1' C C C 2 2 2 N 2 4.82 0.70 108.50 113.32 A A A O4' C1' N1 C C C 2 2 2 N 2 3.81 0.60 118.90 122.71 A A A N1 C2 O2 C C C 2 2 2 N 2 4.87 0.70 108.50 113.37 A A A O4' C1' N1 U U U 5 5 5 N 2 4.66 0.70 108.50 113.16 A A A O4' C1' N9 G G G 6 6 6 N 2 5.49 0.70 108.50 113.99 B B B O4' C1' N1 C C C 103 103 103 N 2 6.23 0.30 108.30 114.53 B B B O4' C1' N1 DC DC DC 105 105 105 N 2 4.03 0.30 108.30 112.33 B B B O4' C1' N1 DT DT DT 106 106 106 N 2 2.75 0.30 108.30 111.05 B B B O4' C1' N9 DG DG DG 107 107 107 N 2 6.07 0.30 108.30 114.37 B B B O4' C1' N1 DC DC DC 108 108 108 N 3 4.84 0.70 108.50 113.34 A A A O4' C1' N1 C C C 2 2 2 N 3 -4.24 0.70 119.90 115.66 A A A N3 C2 N2 G G G 4 4 4 N 3 8.08 0.70 108.50 116.58 A A A O4' C1' N9 G G G 7 7 7 N 3 4.36 0.70 108.50 112.86 B B B O4' C1' N1 C C C 102 102 102 N 3 5.10 0.70 108.50 113.60 B B B O4' C1' N1 C C C 103 103 103 N 3 3.94 0.30 108.30 112.24 B B B O4' C1' N1 DC DC DC 105 105 105 N 3 5.13 0.30 108.30 113.43 B B B O4' C1' N1 DT DT DT 106 106 106 N 3 1.95 0.30 108.30 110.25 B B B O4' C1' N9 DG DG DG 107 107 107 N 4 -4.94 0.70 119.90 114.96 A A A N3 C2 N2 G G G 1 1 1 N 4 6.80 0.70 108.50 115.30 A A A O4' C1' N1 C C C 2 2 2 N 4 4.61 0.70 108.50 113.11 A A A O4' C1' N9 A A A 3 3 3 N 4 4.20 0.70 108.50 112.70 A A A O4' C1' N1 U U U 5 5 5 N 4 5.76 0.90 109.80 115.56 A A A C5' C4' O4' G G G 6 6 6 N 4 3.89 0.60 118.90 122.79 B B B N1 C2 O2 C C C 102 102 102 N 4 5.14 0.30 108.30 113.44 B B B O4' C1' N1 DC DC DC 105 105 105 N 4 5.69 0.30 108.30 113.99 B B B O4' C1' N1 DT DT DT 106 106 106 N 4 5.48 0.30 108.30 113.78 B B B O4' C1' N9 DG DG DG 107 107 107 N 4 3.21 0.30 108.30 111.51 B B B O4' C1' N1 DC DC DC 108 108 108 N 4 3.75 0.60 118.90 122.65 B B B N1 C2 O2 DC DC DC 108 108 108 N 5 5.16 0.70 108.50 113.66 A A A O4' C1' N1 C C C 2 2 2 N 5 5.74 0.90 109.80 115.54 A A A C5' C4' O4' A A A 3 3 3 N 5 6.01 0.70 108.50 114.51 A A A O4' C1' N9 G G G 4 4 4 N 5 4.29 0.70 108.50 112.79 A A A O4' C1' N9 G G G 6 6 6 N 5 5.77 0.70 108.50 114.27 B B B O4' C1' N1 C C C 102 102 102 N 5 5.43 0.70 108.50 113.93 B B B O4' C1' N1 C C C 103 103 103 N 5 -4.29 0.70 102.20 97.91 B B B C4' C3' C2' DC DC DC 105 105 105 N 5 3.88 0.30 108.30 112.18 B B B O4' C1' N1 DC DC DC 105 105 105 N 5 5.00 0.30 108.30 113.30 B B B O4' C1' N1 DT DT DT 106 106 106 N 5 -3.76 0.60 122.90 119.14 B B B C6 C5 C7 DT DT DT 106 106 106 N 5 3.51 0.30 108.30 111.81 B B B O4' C1' N9 DG DG DG 107 107 107 N 5 5.86 0.30 108.30 114.16 B B B O4' C1' N1 DC DC DC 108 108 108 N 6 6.16 0.70 108.50 114.66 A A A O4' C1' N1 C C C 2 2 2 N 6 -4.58 0.70 119.90 115.32 A A A N3 C2 N2 G G G 4 4 4 N 6 4.61 0.70 108.50 113.11 B B B O4' C1' N1 C C C 102 102 102 N 6 4.87 0.30 108.30 113.17 B B B O4' C1' N1 DC DC DC 105 105 105 N 6 3.11 0.30 108.30 111.41 B B B O4' C1' N1 DT DT DT 106 106 106 N 6 4.28 0.30 108.30 112.58 B B B O4' C1' N9 DG DG DG 107 107 107 N 6 5.44 0.30 108.30 113.74 B B B O4' C1' N1 DC DC DC 108 108 108 N 7 6.00 0.70 108.50 114.50 A A A O4' C1' N1 C C C 2 2 2 N 7 4.78 0.60 118.90 123.68 A A A N1 C2 O2 C C C 2 2 2 N 7 4.35 0.70 108.50 112.85 A A A O4' C1' N9 G G G 4 4 4 N 7 4.51 0.70 108.50 113.01 A A A O4' C1' N9 G G G 6 6 6 N 7 5.67 0.70 108.50 114.17 A A A O4' C1' N9 G G G 7 7 7 N 7 4.55 0.70 108.50 113.05 B B B O4' C1' N9 A A A 104 104 104 N 7 5.37 0.30 108.30 113.67 B B B O4' C1' N1 DC DC DC 105 105 105 N 7 3.90 0.30 108.30 112.20 B B B O4' C1' N1 DT DT DT 106 106 106 N 7 -3.78 0.60 122.90 119.12 B B B C6 C5 C7 DT DT DT 106 106 106 N 7 3.38 0.30 108.30 111.68 B B B O4' C1' N9 DG DG DG 107 107 107 N 7 5.18 0.30 108.30 113.48 B B B O4' C1' N1 DC DC DC 108 108 108 N 7 3.93 0.60 118.90 122.83 B B B N1 C2 O2 DC DC DC 108 108 108 N 7 -4.41 0.70 121.90 117.49 B B B N3 C2 O2 DC DC DC 108 108 108 N 8 6.11 0.70 108.50 114.61 A A A O4' C1' N1 C C C 2 2 2 N 8 5.80 0.90 109.80 115.60 A A A C5' C4' O4' A A A 3 3 3 N 8 5.37 0.70 108.50 113.87 A A A O4' C1' N9 G G G 4 4 4 N 8 5.01 0.70 108.50 113.51 B B B O4' C1' N1 C C C 103 103 103 N 8 5.79 0.30 108.30 114.09 B B B O4' C1' N1 DC DC DC 105 105 105 N 8 6.33 0.30 108.30 114.63 B B B O4' C1' N1 DT DT DT 106 106 106 N 8 3.61 0.30 108.30 111.91 B B B O4' C1' N9 DG DG DG 107 107 107 N 8 7.18 0.30 108.30 115.48 B B B O4' C1' N1 DC DC DC 108 108 108 N 9 5.48 0.70 108.50 113.98 A A A O4' C1' N1 C C C 2 2 2 N 9 6.65 0.90 109.80 116.45 A A A C5' C4' O4' A A A 3 3 3 N 9 4.48 0.70 108.50 112.98 A A A O4' C1' N1 U U U 5 5 5 N 9 5.53 0.70 108.50 114.03 A A A O4' C1' N9 G G G 7 7 7 N 9 5.21 0.70 108.50 113.71 B B B O4' C1' N1 C C C 103 103 103 N 9 5.13 0.30 108.30 113.43 B B B O4' C1' N1 DC DC DC 105 105 105 N 9 4.89 0.30 108.30 113.19 B B B O4' C1' N1 DT DT DT 106 106 106 N 9 5.78 0.30 108.30 114.08 B B B O4' C1' N9 DG DG DG 107 107 107 N 9 6.06 0.30 108.30 114.36 B B B O4' C1' N1 DC DC DC 108 108 108 N 9 -4.20 0.70 121.90 117.70 B B B N3 C2 O2 DC DC DC 108 108 108 N 10 4.56 0.70 108.50 113.06 A A A O4' C1' N9 G G G 1 1 1 N 10 -4.26 0.70 119.90 115.64 A A A N3 C2 N2 G G G 1 1 1 N 10 6.18 0.70 108.50 114.68 A A A O4' C1' N1 C C C 2 2 2 N 10 5.09 0.70 108.50 113.59 A A A O4' C1' N9 G G G 4 4 4 N 10 -4.42 0.70 119.90 115.48 A A A N3 C2 N2 G G G 4 4 4 N 10 4.29 0.70 108.50 112.79 A A A O4' C1' N1 U U U 5 5 5 N 10 4.47 0.70 108.50 112.97 A A A O4' C1' N1 C C C 8 8 8 N 10 6.70 0.70 108.50 115.20 B B B O4' C1' N1 C C C 102 102 102 N 10 5.16 0.70 108.50 113.66 B B B O4' C1' N1 C C C 103 103 103 N 10 -4.25 0.70 121.90 117.65 B B B N3 C2 O2 C C C 103 103 103 N 10 5.80 0.30 108.30 114.10 B B B O4' C1' N1 DC DC DC 105 105 105 N 10 4.79 0.30 108.30 113.09 B B B O4' C1' N1 DT DT DT 106 106 106 N 10 -3.85 0.60 122.90 119.05 B B B C6 C5 C7 DT DT DT 106 106 106 N 10 3.59 0.30 108.30 111.89 B B B O4' C1' N9 DG DG DG 107 107 107 N 11 4.44 0.70 108.50 112.94 A A A O4' C1' N9 G G G 1 1 1 N 11 5.74 0.70 108.50 114.24 A A A O4' C1' N1 C C C 2 2 2 N 11 4.06 0.60 118.90 122.96 A A A N1 C2 O2 C C C 2 2 2 N 11 -4.28 0.70 121.90 117.62 A A A N3 C2 O2 C C C 2 2 2 N 11 4.85 0.70 108.50 113.35 A A A O4' C1' N1 U U U 5 5 5 N 11 5.93 0.90 109.80 115.73 A A A C5' C4' O4' G G G 7 7 7 N 11 4.38 0.70 108.50 112.88 B B B O4' C1' N1 C C C 102 102 102 N 11 4.66 0.70 108.50 113.16 B B B O4' C1' N1 C C C 103 103 103 N 11 4.79 0.30 108.30 113.09 B B B O4' C1' N1 DC DC DC 105 105 105 N 11 4.85 0.30 108.30 113.15 B B B O4' C1' N1 DT DT DT 106 106 106 N 11 -3.79 0.60 122.90 119.11 B B B C6 C5 C7 DT DT DT 106 106 106 N 11 4.60 0.30 108.30 112.90 B B B O4' C1' N9 DG DG DG 107 107 107 N 11 4.36 0.30 108.30 112.66 B B B O4' C1' N1 DC DC DC 108 108 108 N 12 5.89 0.70 108.50 114.39 A A A O4' C1' N1 C C C 2 2 2 N 12 -4.99 0.70 119.90 114.91 A A A N3 C2 N2 G G G 4 4 4 N 12 4.51 0.70 108.50 113.01 A A A O4' C1' N9 G G G 6 6 6 N 12 4.59 0.70 108.50 113.09 A A A O4' C1' N9 G G G 7 7 7 N 12 5.57 0.70 108.50 114.07 B B B O4' C1' N1 C C C 102 102 102 N 12 5.02 0.70 108.50 113.52 B B B O4' C1' N1 C C C 103 103 103 N 12 4.43 0.70 108.50 112.93 B B B O4' C1' N9 A A A 104 104 104 N 12 4.03 0.30 108.30 112.33 B B B O4' C1' N1 DC DC DC 105 105 105 N 12 5.62 0.30 108.30 113.92 B B B O4' C1' N1 DT DT DT 106 106 106 N 12 4.34 0.30 108.30 112.64 B B B O4' C1' N9 DG DG DG 107 107 107 N 12 6.50 0.30 108.30 114.80 B B B O4' C1' N1 DC DC DC 108 108 108 N 13 4.15 0.60 118.90 123.05 A A A N1 C2 O2 C C C 2 2 2 N 13 7.00 0.70 108.50 115.50 A A A O4' C1' N9 G G G 4 4 4 N 13 -4.25 0.70 119.90 115.65 A A A N3 C2 N2 G G G 4 4 4 N 13 5.06 0.70 108.50 113.56 A A A O4' C1' N9 G G G 6 6 6 N 13 4.22 0.70 108.50 112.72 A A A O4' C1' N9 G G G 7 7 7 N 13 5.51 0.70 108.50 114.01 B B B O4' C1' N9 G G G 101 101 101 N 13 5.29 0.70 108.50 113.79 B B B O4' C1' N1 C C C 102 102 102 N 13 4.75 0.70 108.50 113.25 B B B O4' C1' N1 C C C 103 103 103 N 13 3.20 0.30 108.30 111.50 B B B O4' C1' N1 DC DC DC 105 105 105 N 13 3.90 0.30 108.30 112.20 B B B O4' C1' N1 DT DT DT 106 106 106 N 13 6.31 0.30 108.30 114.61 B B B O4' C1' N9 DG DG DG 107 107 107 N 14 6.55 0.70 108.50 115.05 A A A O4' C1' N1 C C C 2 2 2 N 14 -4.44 0.70 121.90 117.46 A A A N3 C2 O2 C C C 8 8 8 N 14 4.32 0.70 108.50 112.82 B B B O4' C1' N9 G G G 101 101 101 N 14 6.50 0.70 108.50 115.00 B B B O4' C1' N1 C C C 103 103 103 N 14 5.55 0.30 108.30 113.85 B B B O4' C1' N1 DC DC DC 105 105 105 N 14 4.29 0.30 108.30 112.59 B B B O4' C1' N1 DT DT DT 106 106 106 N 14 3.62 0.30 108.30 111.92 B B B O4' C1' N9 DG DG DG 107 107 107 N 14 3.28 0.30 108.30 111.58 B B B O4' C1' N1 DC DC DC 108 108 108 N 15 4.66 0.70 108.50 113.16 A A A O4' C1' N1 C C C 2 2 2 N 15 5.84 0.90 109.80 115.64 A A A C5' C4' O4' A A A 3 3 3 N 15 6.82 0.70 108.50 115.32 A A A O4' C1' N9 G G G 4 4 4 N 15 5.57 0.70 108.50 114.07 A A A O4' C1' N9 G G G 7 7 7 N 15 6.16 0.70 108.50 114.66 B B B O4' C1' N1 C C C 103 103 103 N 15 -4.36 0.70 102.20 97.84 B B B C4' C3' C2' DC DC DC 105 105 105 N 15 3.85 0.30 108.30 112.15 B B B O4' C1' N1 DC DC DC 105 105 105 N 15 6.24 0.30 108.30 114.54 B B B O4' C1' N1 DT DT DT 106 106 106 N 15 3.30 0.30 108.30 111.60 B B B O4' C1' N1 DC DC DC 108 108 108 N 16 5.23 0.80 101.50 106.73 A A A C3' C2' C1' C C C 2 2 2 N 16 6.09 0.70 108.50 114.59 A A A O4' C1' N1 C C C 2 2 2 N 16 4.76 0.70 108.50 113.26 A A A O4' C1' N9 G G G 6 6 6 N 16 4.92 0.70 108.50 113.42 A A A O4' C1' N9 G G G 7 7 7 N 16 5.41 0.30 108.30 113.71 B B B O4' C1' N1 DC DC DC 105 105 105 N 16 4.28 0.30 108.30 112.58 B B B O4' C1' N1 DT DT DT 106 106 106 N 16 5.64 0.30 108.30 113.94 B B B O4' C1' N9 DG DG DG 107 107 107 N 17 4.37 0.70 108.50 112.87 A A A O4' C1' N9 G G G 1 1 1 N 17 7.46 0.70 108.50 115.96 A A A O4' C1' N1 C C C 2 2 2 N 17 4.94 0.70 108.50 113.44 A A A O4' C1' N9 A A A 3 3 3 N 17 4.72 0.70 108.50 113.22 A A A O4' C1' N9 G G G 6 6 6 N 17 5.26 0.70 108.50 113.76 A A A O4' C1' N9 G G G 7 7 7 N 17 4.61 0.70 108.50 113.11 B B B O4' C1' N1 C C C 102 102 102 N 17 -4.29 0.70 121.90 117.61 B B B N3 C2 O2 C C C 102 102 102 N 17 5.75 0.70 108.50 114.25 B B B O4' C1' N1 C C C 103 103 103 N 17 5.55 0.30 108.30 113.85 B B B O4' C1' N1 DC DC DC 105 105 105 N 17 3.43 0.30 108.30 111.73 B B B O4' C1' N1 DT DT DT 106 106 106 N 17 2.61 0.30 108.30 110.91 B B B O4' C1' N9 DG DG DG 107 107 107 N 17 1.86 0.30 108.30 110.16 B B B O4' C1' N1 DC DC DC 108 108 108 N 18 5.62 0.70 108.50 114.12 A A A O4' C1' N9 G G G 1 1 1 N 18 4.95 0.70 108.50 113.45 A A A O4' C1' N1 C C C 2 2 2 N 18 4.79 0.70 108.50 113.29 A A A O4' C1' N1 U U U 5 5 5 N 18 4.45 0.70 108.50 112.95 A A A O4' C1' N9 G G G 6 6 6 N 18 8.81 0.70 108.50 117.31 A A A O4' C1' N9 G G G 7 7 7 N 18 4.79 0.70 108.50 113.29 B B B O4' C1' N9 G G G 101 101 101 N 18 5.41 0.70 108.50 113.91 B B B O4' C1' N1 C C C 103 103 103 N 18 4.27 0.30 108.30 112.57 B B B O4' C1' N1 DC DC DC 105 105 105 N 18 4.39 0.30 108.30 112.69 B B B O4' C1' N1 DT DT DT 106 106 106 N 18 -3.63 0.60 122.90 119.27 B B B C6 C5 C7 DT DT DT 106 106 106 N 18 4.43 0.30 108.30 112.73 B B B O4' C1' N9 DG DG DG 107 107 107 N 18 5.37 0.30 108.30 113.67 B B B O4' C1' N1 DC DC DC 108 108 108 N 19 4.89 0.70 108.50 113.39 A A A O4' C1' N9 G G G 1 1 1 N 19 8.32 0.70 108.50 116.82 A A A O4' C1' N1 C C C 2 2 2 N 19 4.57 0.70 108.50 113.07 A A A O4' C1' N1 U U U 5 5 5 N 19 6.24 0.90 109.80 116.04 A A A C5' C4' O4' G G G 7 7 7 N 19 3.64 0.60 118.90 122.54 A A A N1 C2 O2 C C C 8 8 8 N 19 3.69 0.60 118.90 122.59 B B B N1 C2 O2 C C C 102 102 102 N 19 -4.49 0.70 121.90 117.41 B B B N3 C2 O2 C C C 102 102 102 N 19 5.03 0.70 108.50 113.53 B B B O4' C1' N1 C C C 103 103 103 N 19 4.52 0.30 108.30 112.82 B B B O4' C1' N1 DC DC DC 105 105 105 N 19 4.31 0.30 108.30 112.61 B B B O4' C1' N1 DT DT DT 106 106 106 N 19 3.43 0.30 108.30 111.73 B B B O4' C1' N9 DG DG DG 107 107 107 N 19 2.96 0.30 108.30 111.26 B B B O4' C1' N1 DC DC DC 108 108 108 N 20 6.95 0.70 108.50 115.45 A A A O4' C1' N1 C C C 2 2 2 N 20 6.03 0.90 109.80 115.83 A A A C5' C4' O4' G G G 6 6 6 N 20 7.57 0.90 109.80 117.37 A A A C5' C4' O4' G G G 7 7 7 N 20 5.09 0.70 108.50 113.59 B B B O4' C1' N1 C C C 103 103 103 N 20 7.74 0.30 108.30 116.04 B B B O4' C1' N1 DC DC DC 105 105 105 N 20 4.20 0.30 108.30 112.50 B B B O4' C1' N1 DT DT DT 106 106 106 N 20 4.89 0.30 108.30 113.19 B B B O4' C1' N9 DG DG DG 107 107 107 N 20 2.37 0.30 108.30 110.67 B B B O4' C1' N1 DC DC DC 108 108 108 N CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JUNCTION FORMED DURING INITIATION OF HIV-1 REVERSE TRANSCRIPTION 1 N N 2 N N hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B DG 107 B N1 DG 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B DG 107 B O6 DG 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B DG 107 B N2 DG 7 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 B DT 106 B N3 DT 6 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B DT 106 B O4 DT 6 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B DC 105 B N3 DC 5 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B DC 105 B O2 DC 5 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B DC 105 B N4 DC 5 1_555 hydrog WATSON-CRICK A U 5 A N3 U 5 1_555 B A 104 B N1 A 4 1_555 hydrog WATSON-CRICK A U 5 A O4 U 5 1_555 B A 104 B N6 A 4 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 B C 103 B N3 C 3 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B C 103 B O2 C 3 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B C 103 B N4 C 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 102 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 102 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 102 B N4 C 2 1_555 hydrog C-G PAIR A C 8 A N4 C 8 1_555 B G 101 B O6 G 1 1_555 DNA-RNA HYBRID RNA:RNA-DNA CHIMERIC HYBRID, RNASE H, REVERSE TRANSCRIPTASE, DNA-RNA COMPLEX, DNA-RNA HYBRID 1BYX PDB 1 1BYX 1BYX PDB 2 1BYX 1 8 1BYX 1 8 1BYX A 1 1 8 101 108 1BYX 101 108 1BYX B 2 1 8 1 P 1