1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Baleja, J.D. Sykes, B.D. 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 215 411 428 10.1016/S0022-2836(05)80361-4 2231713 Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. 1990 US J.Magn.Reson. JOMRA4 0624 0022-2364 87 375 Distance Measurement and Structure Refinement with Noe Data 1990 10.2210/pdb1d19/pdb pdb_00001d19 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2426.617 DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3') 2 syn polymer DEOXYRIBONUCLEIC ACID no no (DG)(DT)(DA)(DC)(DG)(DT)(DA)(DC) GTACGTAC A,B polydeoxyribonucleotide n n n n n n n n -7.468 1 19 A 1 B 16 -3.005 A_DG1:DC16_B 1 -10.997 -0.538 0.064 -0.175 -1.169 1 20 A 2 B 15 -4.753 A_DT2:DA15_B 2 -10.841 0.055 0.165 -0.086 9.027 1 20 A 3 B 14 -6.784 A_DA3:DT14_B 3 -7.003 0.269 0.288 -0.001 10.847 1 19 A 4 B 13 -4.003 A_DC4:DG13_B 4 -16.637 0.650 0.210 -0.216 -8.705 1 19 A 5 B 12 -3.781 A_DG5:DC12_B 5 -17.765 -0.689 0.212 -0.241 -8.641 1 20 A 6 B 11 -6.979 A_DT6:DA11_B 6 -9.726 -0.292 0.264 -0.006 0.462 1 20 A 7 B 10 -4.125 A_DA7:DT10_B 7 -13.198 -0.042 0.159 -0.065 4.511 1 19 A 8 B 9 -4.152 A_DC8:DG9_B 8 -14.031 0.698 0.217 -0.229 3.167 33.421 A A 1 2 1.170 B B 16 15 3.168 0.673 -0.217 -0.372 AA_DG1DT2:DA15DC16_BB 1 -1.736 3.020 33.371 -0.754 0.099 3.157 34.492 A A 2 3 8.429 B B 15 14 3.077 4.980 -0.636 0.621 AA_DT2DA3:DT14DA15_BB 2 -1.450 2.453 34.112 0.307 0.856 3.258 33.429 A A 3 4 -3.996 B B 14 13 3.261 -2.296 -0.097 -0.165 AA_DA3DC4:DG13DT14_BB 3 1.307 -2.274 33.327 0.092 0.384 3.103 38.694 A A 4 5 16.963 B B 13 12 3.416 11.093 0.055 -0.650 AA_DC4DG5:DC12DG13_BB 4 0.221 -0.338 37.127 -2.369 -0.055 3.285 33.938 A A 5 6 -4.246 B B 12 11 3.276 -2.476 -0.002 -0.268 AA_DG5DT6:DA11DC12_BB 5 -1.050 1.801 33.835 -0.061 -0.166 3.147 36.975 A A 6 7 6.953 B B 11 10 3.053 4.399 0.471 0.863 AA_DT6DA7:DT10DA11_BB 6 1.398 -2.210 36.696 0.797 -0.564 3.169 35.101 A A 7 8 -1.068 B B 10 9 3.160 -0.644 0.252 -0.269 AA_DA7DC8:DG9DT10_BB 7 0.651 -1.079 35.089 -0.354 -0.324 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1991-07-15 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 Y BNL 1990-08-01 REL REL CHEMICALLY SYNTHESIZED sample 1 THE STRUCTURE WAS THEN REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.19 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1. ENERGY MINIMIZATION, MOLECULAR DYNAMICS DE VLIEG ET AL. refinement GROMOS G 1 n 1 DG 1 A T 2 n 2 DT 2 A A 3 n 3 DA 3 A C 4 n 4 DC 4 A G 5 n 5 DG 5 A T 6 n 6 DT 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 1 DG 9 B T 10 n 2 DT 10 B A 11 n 3 DA 11 B C 12 n 4 DC 12 B G 13 n 5 DG 13 B T 14 n 6 DT 14 B A 15 n 7 DA 15 B C 16 n 8 DC 16 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 DG 1 0.077 SIDE CHAIN 1 A DT 2 0.086 SIDE CHAIN 1 A DA 3 0.050 SIDE CHAIN 1 A DC 4 0.077 SIDE CHAIN 1 A DG 5 0.101 SIDE CHAIN 1 A DT 6 0.099 SIDE CHAIN 1 B DG 9 0.092 SIDE CHAIN 1 B DT 10 0.110 SIDE CHAIN 1 B DC 12 0.078 SIDE CHAIN 1 B DG 13 0.099 SIDE CHAIN 1 B DT 14 0.092 SIDE CHAIN 1 -5.24 0.60 125.10 119.86 A A A C6 N1 C2 DG DG DG 1 1 1 N 1 -3.76 0.60 123.90 120.14 A A A N1 C2 N3 DG DG DG 1 1 1 N 1 9.11 0.50 111.90 121.01 A A A C2 N3 C4 DG DG DG 1 1 1 N 1 -7.15 0.50 128.60 121.45 A A A N3 C4 C5 DG DG DG 1 1 1 N 1 6.98 0.50 111.50 118.48 A A A C5 C6 N1 DG DG DG 1 1 1 N 1 -2.97 0.40 110.80 107.83 A A A C4 C5 N7 DG DG DG 1 1 1 N 1 -3.29 0.50 113.10 109.81 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 5.16 0.60 126.00 131.16 A A A N3 C4 N9 DG DG DG 1 1 1 N 1 -7.80 0.60 128.60 120.80 A A A C5 C6 O6 DG DG DG 1 1 1 N 1 5.32 0.60 114.60 119.92 A A A N1 C2 N3 DT DT DT 2 2 2 N 1 -5.95 0.60 127.20 121.25 A A A C2 N3 C4 DT DT DT 2 2 2 N 1 4.16 0.60 115.20 119.36 A A A N3 C4 C5 DT DT DT 2 2 2 N 1 -3.78 0.60 122.30 118.52 A A A N3 C2 O2 DT DT DT 2 2 2 N 1 -4.68 0.60 122.90 118.22 A A A C6 C5 C7 DT DT DT 2 2 2 N 1 -6.90 0.50 129.30 122.40 A A A N1 C2 N3 DA DA DA 3 3 3 N 1 9.02 0.50 110.60 119.62 A A A C2 N3 C4 DA DA DA 3 3 3 N 1 -6.91 0.70 126.80 119.89 A A A N3 C4 C5 DA DA DA 3 3 3 N 1 3.26 0.50 103.90 107.16 A A A C5 N7 C8 DA DA DA 3 3 3 N 1 -3.42 0.50 113.80 110.38 A A A N7 C8 N9 DA DA DA 3 3 3 N 1 5.68 0.80 127.40 133.08 A A A N3 C4 N9 DA DA DA 3 3 3 N 1 -5.46 0.60 125.10 119.64 A A A C6 N1 C2 DG DG DG 5 5 5 N 1 8.41 0.50 111.90 120.31 A A A C2 N3 C4 DG DG DG 5 5 5 N 1 -7.32 0.50 128.60 121.28 A A A N3 C4 C5 DG DG DG 5 5 5 N 1 7.55 0.50 111.50 119.05 A A A C5 C6 N1 DG DG DG 5 5 5 N 1 -3.38 0.40 110.80 107.42 A A A C4 C5 N7 DG DG DG 5 5 5 N 1 3.28 0.50 104.30 107.58 A A A C5 N7 C8 DG DG DG 5 5 5 N 1 -3.09 0.50 113.10 110.01 A A A N7 C8 N9 DG DG DG 5 5 5 N 1 5.38 0.60 126.00 131.38 A A A N3 C4 N9 DG DG DG 5 5 5 N 1 -8.35 0.60 128.60 120.25 A A A C5 C6 O6 DG DG DG 5 5 5 N 1 2.39 0.30 108.30 110.69 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 4.58 0.60 114.60 119.18 A A A N1 C2 N3 DT DT DT 6 6 6 N 1 -6.27 0.60 127.20 120.93 A A A C2 N3 C4 DT DT DT 6 6 6 N 1 4.94 0.60 115.20 120.14 A A A N3 C4 C5 DT DT DT 6 6 6 N 1 -3.73 0.60 122.30 118.57 A A A N3 C2 O2 DT DT DT 6 6 6 N 1 -4.50 0.60 122.90 118.40 A A A C6 C5 C7 DT DT DT 6 6 6 N 1 -6.70 0.50 129.30 122.60 A A A N1 C2 N3 DA DA DA 7 7 7 N 1 8.73 0.50 110.60 119.33 A A A C2 N3 C4 DA DA DA 7 7 7 N 1 -7.04 0.70 126.80 119.76 A A A N3 C4 C5 DA DA DA 7 7 7 N 1 3.11 0.50 103.90 107.01 A A A C5 N7 C8 DA DA DA 7 7 7 N 1 -3.48 0.50 113.80 110.32 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 5.09 0.80 127.40 132.49 A A A N3 C4 N9 DA DA DA 7 7 7 N 1 -5.57 0.60 125.10 119.53 B B B C6 N1 C2 DG DG DG 9 9 9 N 1 -3.69 0.60 123.90 120.21 B B B N1 C2 N3 DG DG DG 9 9 9 N 1 9.57 0.50 111.90 121.47 B B B C2 N3 C4 DG DG DG 9 9 9 N 1 -8.18 0.50 128.60 120.42 B B B N3 C4 C5 DG DG DG 9 9 9 N 1 7.13 0.50 111.50 118.63 B B B C5 C6 N1 DG DG DG 9 9 9 N 1 -3.51 0.40 110.80 107.29 B B B C4 C5 N7 DG DG DG 9 9 9 N 1 3.37 0.50 104.30 107.67 B B B C5 N7 C8 DG DG DG 9 9 9 N 1 6.12 0.60 126.00 132.12 B B B N3 C4 N9 DG DG DG 9 9 9 N 1 -7.90 0.60 128.60 120.70 B B B C5 C6 O6 DG DG DG 9 9 9 N 1 -3.08 0.50 121.30 118.22 B B B C6 N1 C2 DT DT DT 10 10 10 N 1 5.19 0.60 114.60 119.79 B B B N1 C2 N3 DT DT DT 10 10 10 N 1 -5.81 0.60 127.20 121.39 B B B C2 N3 C4 DT DT DT 10 10 10 N 1 3.92 0.60 115.20 119.12 B B B N3 C4 C5 DT DT DT 10 10 10 N 1 -3.85 0.60 122.30 118.45 B B B N3 C2 O2 DT DT DT 10 10 10 N 1 -4.57 0.60 122.90 118.33 B B B C6 C5 C7 DT DT DT 10 10 10 N 1 -6.53 0.50 129.30 122.77 B B B N1 C2 N3 DA DA DA 11 11 11 N 1 9.00 0.50 110.60 119.60 B B B C2 N3 C4 DA DA DA 11 11 11 N 1 -7.15 0.70 126.80 119.65 B B B N3 C4 C5 DA DA DA 11 11 11 N 1 6.06 0.80 127.40 133.46 B B B N3 C4 N9 DA DA DA 11 11 11 N 1 -5.73 0.60 125.10 119.37 B B B C6 N1 C2 DG DG DG 13 13 13 N 1 9.20 0.50 111.90 121.10 B B B C2 N3 C4 DG DG DG 13 13 13 N 1 -7.48 0.50 128.60 121.12 B B B N3 C4 C5 DG DG DG 13 13 13 N 1 7.53 0.50 111.50 119.03 B B B C5 C6 N1 DG DG DG 13 13 13 N 1 -3.02 0.40 110.80 107.78 B B B C4 C5 N7 DG DG DG 13 13 13 N 1 3.07 0.50 104.30 107.37 B B B C5 N7 C8 DG DG DG 13 13 13 N 1 -3.15 0.50 113.10 109.95 B B B N7 C8 N9 DG DG DG 13 13 13 N 1 5.67 0.60 126.00 131.67 B B B N3 C4 N9 DG DG DG 13 13 13 N 1 -8.43 0.60 128.60 120.17 B B B C5 C6 O6 DG DG DG 13 13 13 N 1 5.08 0.60 114.60 119.68 B B B N1 C2 N3 DT DT DT 14 14 14 N 1 -6.18 0.60 127.20 121.02 B B B C2 N3 C4 DT DT DT 14 14 14 N 1 4.17 0.60 115.20 119.37 B B B N3 C4 C5 DT DT DT 14 14 14 N 1 -4.36 0.60 122.30 117.94 B B B N3 C2 O2 DT DT DT 14 14 14 N 1 -4.68 0.60 122.90 118.22 B B B C6 C5 C7 DT DT DT 14 14 14 N 1 -6.15 0.50 129.30 123.15 B B B N1 C2 N3 DA DA DA 15 15 15 N 1 8.52 0.50 110.60 119.12 B B B C2 N3 C4 DA DA DA 15 15 15 N 1 -6.67 0.70 126.80 120.13 B B B N3 C4 C5 DA DA DA 15 15 15 N 1 3.49 0.50 103.90 107.39 B B B C5 N7 C8 DA DA DA 15 15 15 N 1 -3.49 0.50 113.80 110.31 B B B N7 C8 N9 DA DA DA 15 15 15 N 1 5.28 0.80 127.40 132.68 B B B N3 C4 N9 DA DA DA 15 15 15 N 1 A A C5 N7 DG DG 1 1 -0.062 0.006 1.388 1.326 N 1 A A N9 C4 DG DG 1 1 -0.050 0.008 1.375 1.325 N 1 A A C4 C5 DT DT 2 2 -0.057 0.009 1.445 1.388 N 1 A A C5 C6 DT DT 2 2 0.054 0.007 1.339 1.393 N 1 A A C5 C7 DT DT 2 2 0.037 0.006 1.496 1.533 N 1 A A C5 N7 DA DA 3 3 -0.067 0.006 1.388 1.321 N 1 A A N9 C4 DA DA 3 3 -0.041 0.006 1.374 1.333 N 1 A A N1 C6 DC DC 4 4 0.038 0.006 1.367 1.405 N 1 A A C5 C6 DC DC 4 4 0.049 0.008 1.339 1.388 N 1 A A C5 N7 DG DG 5 5 -0.057 0.006 1.388 1.331 N 1 A A C5 C6 DT DT 6 6 0.048 0.007 1.339 1.387 N 1 A A C5 N7 DA DA 7 7 -0.059 0.006 1.388 1.329 N 1 A A N9 C4 DA DA 7 7 -0.051 0.006 1.374 1.323 N 1 B B C5 N7 DG DG 9 9 -0.063 0.006 1.388 1.325 N 1 B B N9 C4 DG DG 9 9 -0.050 0.008 1.375 1.325 N 1 B B C5 C6 DT DT 10 10 0.042 0.007 1.339 1.381 N 1 B B C5 N7 DA DA 11 11 -0.059 0.006 1.388 1.329 N 1 B B N9 C4 DA DA 11 11 -0.041 0.006 1.374 1.333 N 1 B B C5 C6 DC DC 12 12 0.051 0.008 1.339 1.390 N 1 B B C5 N7 DG DG 13 13 -0.062 0.006 1.388 1.326 N 1 B B N9 C4 DG DG 13 13 -0.049 0.008 1.375 1.326 N 1 B B C5 C6 DT DT 14 14 0.044 0.007 1.339 1.383 N 1 B B C5 N7 DA DA 15 15 -0.062 0.006 1.388 1.326 N 1 B B N9 C4 DA DA 15 15 -0.047 0.006 1.374 1.327 N 1 B B N1 C6 DC DC 16 16 0.037 0.006 1.367 1.404 N SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT 1 N N 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 16 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 16 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 16 B N4 DC 8 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 15 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 15 B N6 DA 7 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 14 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 14 B O4 DT 6 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 13 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 13 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 13 B N2 DG 5 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 12 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 12 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 12 B N4 DC 4 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 11 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 11 B N6 DA 3 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 10 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 10 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 9 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 9 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 9 B N2 DG 1 1_555 DNA DNA, DOUBLE HELIX 1D19 PDB 1 1D19 1 8 1D19 1 8 1D19 A 1 1 8 9 16 1D19 9 16 1D19 B 1 1 8 1 P 1