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/pdb1d18/pdb pdb_00001d18 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(*CP*AP*TP*GP*CP*AP*TP*G)-3') 2 syn polymer DEOXYRIBONUCLEIC ACID no no (DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) CATGCATG A,B polydeoxyribonucleotide n n n n n n n n 8.975 1 19 A 1 B 16 -4.433 A_DC1:DG16_B 1 -7.563 0.221 0.203 -0.181 10.611 1 20 A 2 B 15 -6.807 A_DA2:DT15_B 2 -12.379 -0.442 0.286 -0.205 9.548 1 20 A 3 B 14 -7.203 A_DT3:DA14_B 3 -8.908 0.253 0.421 -0.167 3.437 1 19 A 4 B 13 -4.865 A_DG4:DC13_B 4 -17.219 -0.398 0.365 -0.253 -3.784 1 19 A 5 B 12 -4.120 A_DC5:DG12_B 5 -17.230 0.456 0.342 -0.243 -8.844 1 20 A 6 B 11 -6.738 A_DA6:DT11_B 6 -7.882 -0.255 0.471 -0.177 -10.605 1 20 A 7 B 10 -6.654 A_DT7:DA10_B 7 -12.799 0.425 0.240 -0.205 -7.449 1 19 A 8 B 9 -4.776 A_DG8:DC9_B 8 -6.345 -0.184 0.198 -0.189 3.034 30.083 A A 1 2 15.652 B B 16 15 3.173 8.029 -0.749 -0.177 AA_DC1DA2:DT15DG16_BB 1 -0.735 1.432 29.007 -1.930 1.298 3.382 32.998 A A 2 3 6.564 B B 15 14 3.412 3.721 0.018 -0.084 AA_DA2DT3:DA14DT15_BB 2 0.155 -0.273 32.793 -0.806 -0.005 3.306 34.984 A A 3 4 5.842 B B 14 13 3.339 3.503 0.444 -0.419 AA_DT3DG4:DC13DA14_BB 3 2.699 -4.502 34.712 -1.235 -0.324 3.492 44.416 A A 4 5 -8.047 B B 13 12 3.473 -6.066 0.039 -0.372 AA_DG4DC5:DG12DC13_BB 4 0.294 -0.390 44.020 0.108 -0.022 3.268 34.205 A A 5 6 5.863 B B 12 11 3.301 3.439 -0.454 -0.448 AA_DC5DA6:DT11DG12_BB 5 -3.010 5.133 33.908 -1.310 0.292 3.419 32.898 A A 6 7 7.924 B B 11 10 3.452 4.474 0.011 -0.025 AA_DA6DT7:DA10DT11_BB 6 0.047 -0.084 32.600 -0.850 -0.012 2.990 30.620 A A 7 8 16.770 B B 10 9 3.124 8.738 0.696 -0.093 AA_DT7DG8:DC9DA10_BB 7 0.763 -1.464 29.366 -1.825 -1.174 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 REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 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 C 1 n 1 DC 1 A A 2 n 2 DA 2 A T 3 n 3 DT 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A G 8 n 8 DG 8 A C 9 n 1 DC 9 B A 10 n 2 DA 10 B T 11 n 3 DT 11 B G 12 n 4 DG 12 B C 13 n 5 DC 13 B A 14 n 6 DA 14 B T 15 n 7 DT 15 B G 16 n 8 DG 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 DC 1 0.068 SIDE CHAIN 1 A DA 2 0.077 SIDE CHAIN 1 A DC 5 0.095 SIDE CHAIN 1 A DA 6 0.135 SIDE CHAIN 1 B DC 9 0.090 SIDE CHAIN 1 B DA 10 0.062 SIDE CHAIN 1 B DG 12 0.066 SIDE CHAIN 1 B DC 13 0.092 SIDE CHAIN 1 B DA 14 0.121 SIDE CHAIN 1 -6.98 0.50 129.30 122.32 A A A N1 C2 N3 DA DA DA 2 2 2 N 1 8.81 0.50 110.60 119.41 A A A C2 N3 C4 DA DA DA 2 2 2 N 1 -6.59 0.70 126.80 120.21 A A A N3 C4 C5 DA DA DA 2 2 2 N 1 3.24 0.50 103.90 107.14 A A A C5 N7 C8 DA DA DA 2 2 2 N 1 -3.82 0.50 113.80 109.98 A A A N7 C8 N9 DA DA DA 2 2 2 N 1 5.57 0.80 127.40 132.97 A A A N3 C4 N9 DA DA DA 2 2 2 N 1 5.06 0.60 114.60 119.66 A A A N1 C2 N3 DT DT DT 3 3 3 N 1 -5.76 0.60 127.20 121.44 A A A C2 N3 C4 DT DT DT 3 3 3 N 1 4.12 0.60 115.20 119.32 A A A N3 C4 C5 DT DT DT 3 3 3 N 1 -3.71 0.60 122.30 118.59 A A A N3 C2 O2 DT DT DT 3 3 3 N 1 -4.56 0.60 122.90 118.34 A A A C6 C5 C7 DT DT DT 3 3 3 N 1 -4.54 0.60 125.10 120.56 A A A C6 N1 C2 DG DG DG 4 4 4 N 1 -4.02 0.60 123.90 119.88 A A A N1 C2 N3 DG DG DG 4 4 4 N 1 8.97 0.50 111.90 120.87 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 -7.21 0.50 128.60 121.39 A A A N3 C4 C5 DG DG DG 4 4 4 N 1 6.51 0.50 111.50 118.01 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 -2.54 0.40 110.80 108.26 A A A C4 C5 N7 DG DG DG 4 4 4 N 1 5.66 0.60 126.00 131.66 A A A N3 C4 N9 DG DG DG 4 4 4 N 1 -8.19 0.60 128.60 120.41 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 3.08 0.50 119.90 122.98 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 -6.65 0.50 129.30 122.65 A A A N1 C2 N3 DA DA DA 6 6 6 N 1 9.27 0.50 110.60 119.87 A A A C2 N3 C4 DA DA DA 6 6 6 N 1 -7.58 0.70 126.80 119.22 A A A N3 C4 C5 DA DA DA 6 6 6 N 1 -3.04 0.50 110.70 107.66 A A A C4 C5 N7 DA DA DA 6 6 6 N 1 3.43 0.50 103.90 107.33 A A A C5 N7 C8 DA DA DA 6 6 6 N 1 -3.38 0.50 113.80 110.42 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 6.15 0.80 127.40 133.55 A A A N3 C4 N9 DA DA DA 6 6 6 N 1 -6.66 1.00 110.10 103.44 A A A C1' O4' C4' DT DT DT 7 7 7 N 1 4.84 0.60 114.60 119.44 A A A N1 C2 N3 DT DT DT 7 7 7 N 1 -5.98 0.60 127.20 121.22 A A A C2 N3 C4 DT DT DT 7 7 7 N 1 4.36 0.60 115.20 119.56 A A A N3 C4 C5 DT DT DT 7 7 7 N 1 -4.26 0.60 122.30 118.04 A A A N3 C2 O2 DT DT DT 7 7 7 N 1 -5.03 0.60 122.90 117.87 A A A C6 C5 C7 DT DT DT 7 7 7 N 1 2.38 0.30 108.30 110.68 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 -5.03 0.60 125.10 120.07 A A A C6 N1 C2 DG DG DG 8 8 8 N 1 -4.05 0.60 123.90 119.85 A A A N1 C2 N3 DG DG DG 8 8 8 N 1 9.11 0.50 111.90 121.01 A A A C2 N3 C4 DG DG DG 8 8 8 N 1 -6.96 0.50 128.60 121.64 A A A N3 C4 C5 DG DG DG 8 8 8 N 1 6.71 0.50 111.50 118.21 A A A C5 C6 N1 DG DG DG 8 8 8 N 1 -2.55 0.40 110.80 108.25 A A A C4 C5 N7 DG DG DG 8 8 8 N 1 -3.56 0.50 113.10 109.54 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 5.50 0.60 126.00 131.50 A A A N3 C4 N9 DG DG DG 8 8 8 N 1 -8.10 0.60 128.60 120.50 A A A C5 C6 O6 DG DG DG 8 8 8 N 1 -6.90 0.50 129.30 122.40 B B B N1 C2 N3 DA DA DA 10 10 10 N 1 9.32 0.50 110.60 119.92 B B B C2 N3 C4 DA DA DA 10 10 10 N 1 -7.32 0.70 126.80 119.48 B B B N3 C4 C5 DA DA DA 10 10 10 N 1 -3.70 0.50 113.80 110.10 B B B N7 C8 N9 DA DA DA 10 10 10 N 1 6.12 0.80 127.40 133.52 B B B N3 C4 N9 DA DA DA 10 10 10 N 1 4.70 0.60 114.60 119.30 B B B N1 C2 N3 DT DT DT 11 11 11 N 1 -5.72 0.60 127.20 121.48 B B B C2 N3 C4 DT DT DT 11 11 11 N 1 4.13 0.60 115.20 119.33 B B B N3 C4 C5 DT DT DT 11 11 11 N 1 -3.76 0.60 122.30 118.54 B B B N3 C2 O2 DT DT DT 11 11 11 N 1 3.64 0.60 119.00 122.64 B B B C4 C5 C7 DT DT DT 11 11 11 N 1 -5.27 0.60 122.90 117.63 B B B C6 C5 C7 DT DT DT 11 11 11 N 1 -5.30 0.60 125.10 119.80 B B B C6 N1 C2 DG DG DG 12 12 12 N 1 -4.01 0.60 123.90 119.89 B B B N1 C2 N3 DG DG DG 12 12 12 N 1 9.13 0.50 111.90 121.03 B B B C2 N3 C4 DG DG DG 12 12 12 N 1 -7.25 0.50 128.60 121.35 B B B N3 C4 C5 DG DG DG 12 12 12 N 1 7.14 0.50 111.50 118.64 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 -2.74 0.40 110.80 108.06 B B B C4 C5 N7 DG DG DG 12 12 12 N 1 5.67 0.60 126.00 131.67 B B B N3 C4 N9 DG DG DG 12 12 12 N 1 -7.54 0.60 128.60 121.06 B B B C5 C6 O6 DG DG DG 12 12 12 N 1 -6.23 0.50 129.30 123.07 B B B N1 C2 N3 DA DA DA 14 14 14 N 1 9.05 0.50 110.60 119.65 B B B C2 N3 C4 DA DA DA 14 14 14 N 1 -7.39 0.70 126.80 119.41 B B B N3 C4 C5 DA DA DA 14 14 14 N 1 3.06 0.50 103.90 106.96 B B B C5 N7 C8 DA DA DA 14 14 14 N 1 -3.39 0.50 113.80 110.41 B B B N7 C8 N9 DA DA DA 14 14 14 N 1 6.38 0.80 127.40 133.78 B B B N3 C4 N9 DA DA DA 14 14 14 N 1 -6.28 1.00 110.10 103.82 B B B C1' O4' C4' DT DT DT 15 15 15 N 1 4.50 0.60 114.60 119.10 B B B N1 C2 N3 DT DT DT 15 15 15 N 1 -5.71 0.60 127.20 121.49 B B B C2 N3 C4 DT DT DT 15 15 15 N 1 4.13 0.60 115.20 119.33 B B B N3 C4 C5 DT DT DT 15 15 15 N 1 -3.66 0.60 122.30 118.64 B B B N3 C2 O2 DT DT DT 15 15 15 N 1 -5.56 0.60 122.90 117.34 B B B C6 C5 C7 DT DT DT 15 15 15 N 1 2.78 0.30 108.30 111.08 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 -5.01 0.60 125.10 120.09 B B B C6 N1 C2 DG DG DG 16 16 16 N 1 -4.10 0.60 123.90 119.80 B B B N1 C2 N3 DG DG DG 16 16 16 N 1 9.64 0.50 111.90 121.54 B B B C2 N3 C4 DG DG DG 16 16 16 N 1 -7.43 0.50 128.60 121.17 B B B N3 C4 C5 DG DG DG 16 16 16 N 1 6.91 0.50 111.50 118.41 B B B C5 C6 N1 DG DG DG 16 16 16 N 1 -2.78 0.40 110.80 108.02 B B B C4 C5 N7 DG DG DG 16 16 16 N 1 5.99 0.60 126.00 131.99 B B B N3 C4 N9 DG DG DG 16 16 16 N 1 -8.69 0.60 128.60 119.91 B B B C5 C6 O6 DG DG DG 16 16 16 N 1 A A N1 C6 DC DC 1 1 0.040 0.006 1.367 1.407 N 1 A A C5 N7 DA DA 2 2 -0.069 0.006 1.388 1.319 N 1 A A N9 C4 DA DA 2 2 -0.042 0.006 1.374 1.332 N 1 A A C5 C6 DT DT 3 3 0.043 0.007 1.339 1.382 N 1 A A C5 N7 DG DG 4 4 -0.062 0.006 1.388 1.326 N 1 A A N1 C6 DC DC 5 5 0.038 0.006 1.367 1.405 N 1 A A C5 N7 DA DA 6 6 -0.063 0.006 1.388 1.325 N 1 A A N9 C4 DA DA 6 6 -0.048 0.006 1.374 1.326 N 1 A A C4 C5 DT DT 7 7 -0.057 0.009 1.445 1.388 N 1 A A C5 C6 DT DT 7 7 0.052 0.007 1.339 1.391 N 1 A A C5 N7 DG DG 8 8 -0.066 0.006 1.388 1.322 N 1 A A N9 C4 DG DG 8 8 -0.054 0.008 1.375 1.321 N 1 B B N1 C6 DC DC 9 9 0.039 0.006 1.367 1.406 N 1 B B C5 N7 DA DA 10 10 -0.062 0.006 1.388 1.326 N 1 B B N9 C4 DA DA 10 10 -0.051 0.006 1.374 1.323 N 1 B B C5 C6 DT DT 11 11 0.047 0.007 1.339 1.386 N 1 B B C5 C7 DT DT 11 11 0.036 0.006 1.496 1.532 N 1 B B C5 N7 DG DG 12 12 -0.063 0.006 1.388 1.325 N 1 B B C8 N9 DG DG 12 12 -0.045 0.007 1.374 1.329 N 1 B B C5 N7 DA DA 14 14 -0.059 0.006 1.388 1.329 N 1 B B N9 C4 DA DA 14 14 -0.044 0.006 1.374 1.330 N 1 B B C4 C5 DT DT 15 15 -0.060 0.009 1.445 1.385 N 1 B B C5 C6 DT DT 15 15 0.053 0.007 1.339 1.392 N 1 B B C5 N7 DG DG 16 16 -0.056 0.006 1.388 1.332 N 1 B B N9 C4 DG DG 16 16 -0.053 0.008 1.375 1.322 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 DC 1 A N3 DC 1 1_555 B DG 16 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 16 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 16 B N2 DG 8 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 15 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 15 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 14 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 14 B N6 DA 6 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 13 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 13 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 13 B N4 DC 5 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 12 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 12 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 12 B N2 DG 4 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 11 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 11 B O4 DT 3 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 10 B N1 DA 2 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 10 B N6 DA 2 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 9 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 9 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 9 B N4 DC 1 1_555 DNA DNA, DOUBLE HELIX 1D18 PDB 1 1D18 1 8 1D18 1 8 1D18 A 1 1 8 9 16 1D18 9 16 1D18 B 1 1 8 1 P 1