1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gyi, J.I. Lane, A.N. Conn, G.L. Brown, T. 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 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 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking US Biochemistry BICHAW 0033 0006-2960 37 73 10.1021/bi9719713 9425027 Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. 1998 US Biochemistry BICHAW 0033 0006-2960 35 12538 Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes 1996 10.2210/pdb1axp/pdb pdb_00001axp 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3127.082 DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC)) 1 syn polymer 2961.940 DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC)) 1 syn polymer DR10.DY10 DR10.DY10 no no (DG)(DA)(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DC) GAAGAGAAGC A polydeoxyribonucleotide no no (DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DT)(DC) GCTTCTCTTC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 8.951 1 19 A 1 B 10 -3.160 A_DG1:DC10_B 1 -11.160 -0.385 0.399 -0.124 4.635 1 20 A 2 B 9 -3.128 A_DA2:DT9_B 2 -15.631 -0.198 0.342 -0.106 6.464 1 20 A 3 B 8 -3.633 A_DA3:DT8_B 3 -15.260 -0.188 0.529 -0.137 3.664 1 19 A 4 B 7 -4.232 A_DG4:DC7_B 4 -14.344 -0.372 0.498 -0.192 6.365 1 20 A 5 B 6 -3.791 A_DA5:DT6_B 5 -13.574 -0.209 0.602 -0.153 6.249 1 19 A 6 B 5 -4.352 A_DG6:DC5_B 6 -14.140 -0.375 0.531 -0.191 6.104 1 20 A 7 B 4 -4.106 A_DA7:DT4_B 7 -16.075 -0.197 0.483 -0.131 6.985 1 20 A 8 B 3 -4.797 A_DA8:DT3_B 8 -17.467 -0.208 0.646 -0.172 0.297 1 19 A 9 B 2 -4.061 A_DG9:DC2_B 9 -17.747 -0.348 0.520 -0.198 -9.051 1 19 A 10 B 1 -3.521 A_DC10:DG1_B 10 -12.361 0.667 0.615 -0.244 3.139 37.933 A A 1 2 0.464 B B 10 9 3.147 0.302 -0.047 -1.017 AA_DG1DA2:DT9DC10_BB 1 -0.326 0.501 37.930 -1.602 0.032 2.998 34.916 A A 2 3 -1.894 B B 9 8 2.968 -1.136 0.001 -1.058 AA_DA2DA3:DT8DT9_BB 2 -1.339 2.233 34.873 -1.606 -0.186 3.055 33.753 A A 3 4 1.269 B B 8 7 3.083 0.737 0.049 -1.216 AA_DA3DG4:DC7DT8_BB 3 -0.664 1.143 33.739 -2.206 -0.185 3.005 36.493 A A 4 5 -2.619 B B 7 6 2.961 -1.640 0.098 -1.114 AA_DG4DA5:DT6DC7_BB 4 -0.401 0.641 36.455 -1.572 -0.207 3.053 33.604 A A 5 6 -0.684 B B 6 5 3.039 -0.395 0.027 -1.306 AA_DA5DG6:DC5DT6_BB 5 -0.076 0.132 33.602 -2.199 -0.059 3.032 35.601 A A 6 7 -0.163 B B 5 4 3.029 -0.099 -0.089 -1.102 AA_DG6DA7:DT4DC5_BB 6 0.063 -0.103 35.600 -1.789 0.154 3.011 35.348 A A 7 8 -2.625 B B 4 3 2.972 -1.593 -0.003 -1.007 AA_DA7DA8:DT3DT4_BB 7 -1.296 2.136 35.290 -1.444 -0.171 3.179 34.822 A A 8 9 0.201 B B 3 2 3.183 0.120 0.048 -1.143 AA_DA8DG9:DC2DT3_BB 8 0.488 -0.815 34.819 -1.927 -0.008 3.381 41.509 A A 9 10 -1.219 B B 2 1 3.361 -0.863 -0.039 -1.018 AA_DG9DC10:DG1DC2_BB 9 -0.897 1.266 41.491 -1.342 -0.043 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1998-04-22 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name Y BNL 1997-10-17 REL REL THE ASSIGNMENTS, NOES AND COUPLING CONSTANTS DETERMINED FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE. LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY 32 6 NOESY COSY 7.0 303 K DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, DEOXYRIBOSE PSEUDOROTATIONAL PHASE ANGLES AND AMPLITUDES CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST SQUARES/GRID-SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCEFIELD AND A DISTANCE DEPENDENT DIELECTRIC CONSTANT. simulated annealing MOLECULAR SIMULATIONS INC. refinement Discover 95.0 structure solution Felix 95.0 structure solution NUCFIT structure solution pfit structure solution DISCOVER 95.0 (INSIGHT II) II) 500 Varian UNITY 600 Varian UNITYPLUS G 1 n 1 DG 1 A A 2 n 2 DA 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A A 7 n 7 DA 7 A A 8 n 8 DA 8 A G 9 n 9 DG 9 A C 10 n 10 DC 10 A G 1 n 1 DG 1 B C 2 n 2 DC 2 B T 3 n 3 DT 3 B T 4 n 4 DT 4 B C 5 n 5 DC 5 B T 6 n 6 DT 6 B C 7 n 7 DC 7 B T 8 n 8 DT 8 B T 9 n 9 DT 9 B C 10 n 10 DC 10 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 3 A DG 1 0.080 SIDE CHAIN 4 B DG 1 0.050 SIDE CHAIN 4 B DT 3 0.069 SIDE CHAIN 5 B DG 1 0.051 SIDE CHAIN 5 B DT 9 0.062 SIDE CHAIN 1 2.07 0.30 108.30 110.37 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 2.52 0.30 108.30 110.82 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 1.98 0.30 108.30 110.28 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 2.98 0.30 108.30 111.28 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 2.22 0.30 108.30 110.52 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 1.99 0.30 108.30 110.29 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 1.98 0.30 108.30 110.28 B B B O4' C1' N1 DC DC DC 2 2 2 N 1 1.97 0.30 108.30 110.27 B B B O4' C1' N1 DT DT DT 3 3 3 N 1 2.17 0.30 108.30 110.47 B B B O4' C1' N1 DT DT DT 4 4 4 N 1 2.70 0.30 108.30 111.00 B B B O4' C1' N1 DC DC DC 5 5 5 N 1 2.20 0.30 108.30 110.50 B B B O4' C1' N1 DT DT DT 6 6 6 N 1 2.44 0.30 108.30 110.74 B B B O4' C1' N1 DC DC DC 7 7 7 N 1 2.14 0.30 108.30 110.44 B B B O4' C1' N1 DT DT DT 8 8 8 N 1 2.61 0.30 108.30 110.91 B B B O4' C1' N1 DT DT DT 9 9 9 N 1 2.35 0.30 108.30 110.65 B B B O4' C1' N1 DC DC DC 10 10 10 N 2 2.07 0.30 108.30 110.37 A A A O4' C1' N9 DA DA DA 3 3 3 N 2 2.94 0.30 108.30 111.24 A A A O4' C1' N9 DG DG DG 4 4 4 N 2 2.03 0.30 108.30 110.33 A A A O4' C1' N9 DG DG DG 6 6 6 N 2 2.22 0.30 108.30 110.52 A A A O4' C1' N9 DA DA DA 8 8 8 N 2 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DC DC DC 10 10 10 N 2 1.98 0.30 108.30 110.28 B B B O4' C1' N9 DG DG DG 1 1 1 N 2 2.01 0.30 108.30 110.31 B B B O4' C1' N1 DT DT DT 3 3 3 N 2 2.35 0.30 108.30 110.65 B B B O4' C1' N1 DT DT DT 4 4 4 N 2 2.64 0.30 108.30 110.94 B B B O4' C1' N1 DT DT DT 6 6 6 N 2 1.86 0.30 108.30 110.16 B B B O4' C1' N1 DC DC DC 7 7 7 N 2 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DT DT DT 8 8 8 N 2 2.61 0.30 108.30 110.91 B B B O4' C1' N1 DT DT DT 9 9 9 N 2 2.37 0.30 108.30 110.67 B B B O4' C1' N1 DC DC DC 10 10 10 N 3 2.21 0.30 108.30 110.51 A A A O4' C1' N9 DG DG DG 1 1 1 N 3 2.26 0.30 108.30 110.56 A A A O4' C1' N9 DA DA DA 3 3 3 N 3 3.07 0.30 108.30 111.37 A A A O4' C1' N9 DG DG DG 4 4 4 N 3 1.86 0.30 108.30 110.16 A A A O4' C1' N9 DA DA DA 5 5 5 N 3 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DG DG DG 6 6 6 N 3 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DA DA DA 7 7 7 N 3 3.46 0.30 108.30 111.76 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 2.84 0.30 108.30 111.14 B B B O4' C1' N1 DC DC DC 5 5 5 N 3 2.09 0.30 108.30 110.39 B B B O4' C1' N1 DT DT DT 6 6 6 N 3 1.92 0.30 108.30 110.22 B B B O4' C1' N1 DC DC DC 7 7 7 N 3 2.04 0.30 108.30 110.34 B B B O4' C1' N1 DC DC DC 10 10 10 N 4 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DA DA DA 3 3 3 N 4 2.89 0.30 108.30 111.19 A A A O4' C1' N9 DG DG DG 4 4 4 N 4 3.00 0.30 108.30 111.30 A A A O4' C1' N9 DA DA DA 8 8 8 N 4 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 2.62 0.30 108.30 110.92 B B B O4' C1' N1 DC DC DC 2 2 2 N 4 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DT DT DT 4 4 4 N 4 1.88 0.30 108.30 110.18 B B B O4' C1' N1 DC DC DC 5 5 5 N 4 2.67 0.30 108.30 110.97 B B B O4' C1' N1 DT DT DT 6 6 6 N 4 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DT DT DT 8 8 8 N 4 1.82 0.30 108.30 110.12 B B B O4' C1' N1 DT DT DT 9 9 9 N 4 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DC DC DC 10 10 10 N 5 1.83 0.30 108.30 110.13 A A A O4' C1' N9 DA DA DA 3 3 3 N 5 2.44 0.30 108.30 110.74 A A A O4' C1' N9 DG DG DG 4 4 4 N 5 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DA DA DA 5 5 5 N 5 2.24 0.30 108.30 110.54 A A A O4' C1' N9 DG DG DG 6 6 6 N 5 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DA DA DA 7 7 7 N 5 2.47 0.30 108.30 110.77 A A A O4' C1' N9 DA DA DA 8 8 8 N 5 2.99 0.30 108.30 111.29 A A A O4' C1' N9 DG DG DG 9 9 9 N 5 2.13 0.30 108.30 110.43 B B B O4' C1' N1 DC DC DC 2 2 2 N 5 1.80 0.30 108.30 110.10 B B B O4' C1' N1 DT DT DT 3 3 3 N 5 2.10 0.30 108.30 110.40 B B B O4' C1' N1 DT DT DT 4 4 4 N 5 2.82 0.30 108.30 111.12 B B B O4' C1' N1 DC DC DC 5 5 5 N 5 2.58 0.30 108.30 110.88 B B B O4' C1' N1 DT DT DT 6 6 6 N 5 2.84 0.30 108.30 111.14 B B B O4' C1' N1 DT DT DT 8 8 8 N 5 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DC DC DC 10 10 10 N 6 2.03 0.30 108.30 110.33 A A A O4' C1' N9 DA DA DA 3 3 3 N 6 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DG DG DG 4 4 4 N 6 1.93 0.30 108.30 110.23 A A A O4' C1' N9 DA DA DA 5 5 5 N 6 2.24 0.30 108.30 110.54 A A A O4' C1' N9 DG DG DG 6 6 6 N 6 1.80 0.30 108.30 110.10 A A A O4' C1' N9 DA DA DA 7 7 7 N 6 2.48 0.30 108.30 110.78 A A A O4' C1' N9 DA DA DA 8 8 8 N 6 3.05 0.30 108.30 111.35 A A A O4' C1' N9 DG DG DG 9 9 9 N 6 2.10 0.30 108.30 110.40 B B B O4' C1' N1 DC DC DC 2 2 2 N 6 1.84 0.30 108.30 110.14 B B B O4' C1' N1 DT DT DT 3 3 3 N 6 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DT DT DT 4 4 4 N 6 2.72 0.30 108.30 111.02 B B B O4' C1' N1 DC DC DC 5 5 5 N 6 2.24 0.30 108.30 110.54 B B B O4' C1' N1 DT DT DT 6 6 6 N 6 2.47 0.30 108.30 110.77 B B B O4' C1' N1 DC DC DC 7 7 7 N 6 2.14 0.30 108.30 110.44 B B B O4' C1' N1 DT DT DT 8 8 8 N 6 2.61 0.30 108.30 110.91 B B B O4' C1' N1 DT DT DT 9 9 9 N 6 2.32 0.30 108.30 110.62 B B B O4' C1' N1 DC DC DC 10 10 10 N refinement AMBER DNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 6 STRUCTURES 1 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 9 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 7 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 7 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 7 B N4 DC 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 6 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 6 B O4 DT 6 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 5 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 5 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 5 B N4 DC 5 1_555 hydrog DA-DT PAIR A DA 7 A N6 DA 7 1_555 B DT 3 B O4 DT 3 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 4 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 4 B O4 DT 4 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 3 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 3 B O4 DT 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 1 B N2 DG 1 1_555 DNA DNA DUPLEX, PURINE/PYRIMIDINE-RICH STRANDS, B-FORM, DEOXYRIBONUCLEIC ACID, DNA 1AXP PDB 1 1AXP 1AXP PDB 2 1AXP 1 10 1AXP 1 10 1AXP A 1 1 10 1 10 1AXP 1 10 1AXP B 2 1 10 1 P 1