1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chou, S.-H. Cheng, J.-W. Reid, B.R. 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 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 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H 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 O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 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 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 228 138 155 10.1016/0022-2836(92)90497-8 1447778 Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups. 1992 10.2210/pdb1d69/pdb pdb_00001d69 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3406.261 DNA (5'-D(P*AP*TP*GP*AP*GP*CP*GP*AP*AP*TP*A)-3') 2 syn polymer no no (DA)(DT)(DG)(DA)(DG)(DC)(DG)(DA)(DA)(DT)(DA) ATGAGCGAATA A,B polydeoxyribonucleotide n n n n n n n n n n n 1.621 1 20 A 1 B 20 -1.081 A_DA1:DT20_B 1 -3.147 0.088 0.072 -0.064 -2.284 1 20 A 2 B 19 1.076 A_DT2:DA19_B 2 4.627 0.170 0.504 -0.142 27.759 A 3 B 18 -10.674 A_DG3:DA18_B 3 10.833 6.760 0.779 -4.529 -28.853 10 11 A 4 B 17 -15.876 A_DA4:DG17_B 4 -0.406 -6.841 0.112 -4.327 -0.979 1 19 A 5 B 16 -0.364 A_DG5:DC16_B 5 4.490 0.121 -0.557 -0.154 1.022 1 19 A 6 B 15 -0.362 A_DC6:DG15_B 6 4.488 -0.122 -0.557 -0.154 28.898 10 11 A 7 B 14 -15.841 A_DG7:DA14_B 7 -0.432 6.841 0.114 -4.326 -27.825 A 8 B 13 -10.662 A_DA8:DG13_B 8 10.775 -6.761 0.775 -4.527 2.214 1 20 A 9 B 12 1.056 A_DA9:DT12_B 9 4.668 -0.169 0.500 -0.143 -1.647 1 20 A 10 B 11 -1.121 A_DT10:DA11_B 10 -3.080 -0.088 0.068 -0.064 3.270 31.859 A A 1 2 8.132 B B 20 19 3.493 4.450 0.031 -1.388 AA_DA1DT2:DA19DT20_BB 1 -0.847 1.549 31.544 -3.371 -0.217 3.350 63.652 A A 2 3 1.904 B B 19 18 3.337 2.007 0.009 0.668 AA_DT2DG3:DA18DA19_BB 2 -3.247 3.080 63.549 0.544 -0.153 3.659 -12.473 A A 3 4 12.366 B B 18 17 4.123 -2.656 -0.394 -1.797 AA_DG3DA4:DG17DA18_BB 3 1.865 8.685 -12.045 12.137 0.903 3.281 60.410 A A 4 5 -0.078 B B 17 16 3.271 -0.079 0.279 1.229 AA_DA4DG5:DC16DG17_BB 4 4.602 -4.577 60.251 1.225 -0.052 2.433 32.273 A A 5 6 24.226 B B 16 15 3.011 13.097 -0.001 -0.833 AA_DG5DC6:DG15DC16_BB 5 -0.037 0.068 29.561 -3.525 -0.004 3.283 60.404 A A 6 7 -0.005 B B 15 14 3.271 -0.005 -0.279 1.229 AA_DC6DG7:DA14DG15_BB 6 -4.610 4.586 60.244 1.222 0.052 3.680 -12.465 A A 7 8 11.894 B B 14 13 4.123 -2.554 0.393 -1.799 AA_DG7DA8:DG13DA14_BB 7 -1.867 -8.695 -12.058 12.015 -0.917 3.351 63.624 A A 8 9 1.944 B B 13 12 3.337 2.048 -0.004 0.664 AA_DA8DA9:DT12DG13_BB 8 3.224 -3.060 63.522 0.539 0.147 3.266 31.838 A A 9 10 8.188 B B 12 11 3.492 4.477 -0.030 -1.391 AA_DA9DT10:DA11DT12_BB 9 0.873 -1.597 31.518 -3.384 0.220 database_2 pdbx_database_status 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 Other Data collection 1 0 1993-04-15 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site Y BNL 1992-04-15 REL CHEMICALLY SYNTHESIZED sample THE 3' OVERHANGING ADENOSINE RESIDUES WERE NOT INCLUDED IN THE BACK-CALCULATION AND NO COORDINATES ARE PRESENTED FOR THEM IN THIS ENTRY. 1 A 1 n 1 DA 1 A T 2 n 2 DT 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A G 5 n 5 DG 5 A C 6 n 6 DC 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A A 9 n 9 DA 9 A T 10 n 10 DT 10 A n 11 11 A A 11 n 1 DA 11 B T 12 n 2 DT 12 B G 13 n 3 DG 13 B A 14 n 4 DA 14 B G 15 n 5 DG 15 B C 16 n 6 DC 16 B G 17 n 7 DG 17 B A 18 n 8 DA 18 B A 19 n 9 DA 19 B T 20 n 10 DT 20 B n 11 21 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 DA 11 A DA 11 1 Y 1 B DA 21 B DA 11 1 Y 1 -10.00 1.50 119.60 109.60 A A A OP1 P OP2 DA DA DA 1 1 1 N 1 16.56 1.20 119.70 136.26 A A A C3' O3' P DA DA DT 1 1 2 Y 1 3.71 0.60 114.60 118.31 A A A N1 C2 N3 DT DT DT 2 2 2 N 1 -4.40 0.60 127.20 122.80 A A A C2 N3 C4 DT DT DT 2 2 2 N 1 -3.74 0.60 123.70 119.96 A A A C5 C6 N1 DT DT DT 2 2 2 N 1 -5.53 0.70 108.00 102.47 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 4.43 0.70 110.30 114.73 A A A C1' O4' C4' DA DA DA 4 4 4 N 1 7.71 0.30 108.30 116.01 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 6.65 1.10 109.80 116.45 A A A C5' C4' O4' DG DG DG 5 5 5 N 1 -6.91 0.70 108.00 101.09 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 15.02 1.20 119.70 134.72 A A A C3' O3' P DG DG DC 5 5 6 Y 1 10.45 1.20 119.70 130.15 A A A C3' O3' P DG DG DA 7 7 8 Y 1 7.67 0.30 108.30 115.97 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 11.59 1.20 119.70 131.29 A A A C3' O3' P DA DA DA 8 8 9 Y 1 7.54 1.10 109.80 117.34 A A A C5' C4' O4' DA DA DA 9 9 9 N 1 -8.29 0.70 108.00 99.71 A A A O4' C1' N9 DA DA DA 9 9 9 N 1 11.22 1.20 119.70 130.92 A A A C3' O3' P DA DA DT 9 9 10 Y 1 -6.17 0.70 108.00 101.83 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 -4.40 0.60 127.20 122.80 A A A C2 N3 C4 DT DT DT 10 10 10 N 1 -3.78 0.60 123.70 119.92 A A A C5 C6 N1 DT DT DT 10 10 10 N 1 -10.10 1.50 119.60 109.50 B B B OP1 P OP2 DA DA DA 11 11 11 N 1 16.50 1.20 119.70 136.20 B B B C3' O3' P DA DA DT 11 11 12 Y 1 3.75 0.60 114.60 118.35 B B B N1 C2 N3 DT DT DT 12 12 12 N 1 -4.39 0.60 127.20 122.81 B B B C2 N3 C4 DT DT DT 12 12 12 N 1 -3.80 0.60 123.70 119.90 B B B C5 C6 N1 DT DT DT 12 12 12 N 1 -5.52 0.70 108.00 102.48 B B B O4' C1' N9 DG DG DG 13 13 13 N 1 4.30 0.70 110.30 114.60 B B B C1' O4' C4' DA DA DA 14 14 14 N 1 7.68 0.30 108.30 115.98 B B B O4' C1' N9 DA DA DA 14 14 14 N 1 6.63 1.10 109.80 116.43 B B B C5' C4' O4' DG DG DG 15 15 15 N 1 -6.93 0.70 108.00 101.07 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 15.05 1.20 119.70 134.75 B B B C3' O3' P DG DG DC 15 15 16 Y 1 10.45 1.20 119.70 130.15 B B B C3' O3' P DG DG DA 17 17 18 Y 1 7.70 0.30 108.30 116.00 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 11.74 1.20 119.70 131.44 B B B C3' O3' P DA DA DA 18 18 19 Y 1 7.52 1.10 109.80 117.32 B B B C5' C4' O4' DA DA DA 19 19 19 N 1 -8.30 0.70 108.00 99.70 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 11.29 1.20 119.70 130.99 B B B C3' O3' P DA DA DT 19 19 20 Y 1 -6.10 0.70 108.00 101.90 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 -4.40 0.60 127.20 122.80 B B B C2 N3 C4 DT DT DT 20 20 20 N 1 -3.78 0.60 123.70 119.92 B B B C5 C6 N1 DT DT DT 20 20 20 N 1 A A P OP2 DA DA 1 1 0.118 0.017 1.485 1.603 N 1 A A P OP3 DA DA 1 1 -0.121 0.012 1.607 1.486 N 1 A A C5 C6 DT DT 2 2 0.054 0.007 1.339 1.393 N 1 A A O3' C3' DG DG 3 3 -0.047 0.006 1.419 1.372 N 1 A A O4' C1' DA DA 4 4 -0.105 0.012 1.418 1.313 N 1 A A C3' C2' DG DG 5 5 0.090 0.012 1.518 1.608 N 1 A A O3' C3' DG DG 7 7 -0.053 0.006 1.419 1.366 N 1 A A O4' C1' DA DA 8 8 -0.112 0.012 1.418 1.306 N 1 A A O3' C3' DA DA 9 9 -0.046 0.006 1.419 1.373 N 1 A A C5 C6 DT DT 10 10 0.052 0.007 1.339 1.391 N 1 B B P OP2 DA DA 11 11 0.119 0.017 1.485 1.604 N 1 B B P OP3 DA DA 11 11 -0.121 0.012 1.607 1.486 N 1 B B C5 C6 DT DT 12 12 0.055 0.007 1.339 1.394 N 1 B B O3' C3' DG DG 13 13 -0.046 0.006 1.419 1.373 N 1 B B O4' C1' DA DA 14 14 -0.105 0.012 1.418 1.313 N 1 B B C3' C2' DG DG 15 15 0.091 0.012 1.518 1.609 N 1 B B O3' C3' DG DG 17 17 -0.052 0.006 1.419 1.367 N 1 B B O4' C1' DA DA 18 18 -0.113 0.012 1.418 1.305 N 1 B B O3' C3' DA DA 19 19 -0.046 0.006 1.419 1.373 N 1 B B C5 C6 DT DT 20 20 0.053 0.007 1.339 1.392 N SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJACENT G:A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND BII PHOSPHATE GROUPS 1 N N 1 N N hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 20 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 20 B O4 DT 10 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 19 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 19 B N6 DA 9 1_555 hydrog DG-DA MISPAIR A DG 3 A N2 DG 3 1_555 B DA 18 B N7 DA 8 1_555 hydrog TYPE_11_PAIR A DA 4 A N6 DA 4 1_555 B DG 17 B N3 DG 7 1_555 hydrog TYPE_11_PAIR A DA 4 A N7 DA 4 1_555 B DG 17 B N2 DG 7 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 16 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 16 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 16 B N4 DC 6 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 15 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 15 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 15 B N2 DG 5 1_555 hydrog TYPE_11_PAIR A DG 7 A N2 DG 7 1_555 B DA 14 B N7 DA 4 1_555 hydrog TYPE_11_PAIR A DG 7 A N3 DG 7 1_555 B DA 14 B N6 DA 4 1_555 hydrog DA-DG MISPAIR A DA 8 A N7 DA 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 9 A N1 DA 9 1_555 B DT 12 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 9 A N6 DA 9 1_555 B DT 12 B O4 DT 2 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 11 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 11 B N6 DA 1 1_555 DNA DNA, DOUBLE HELIX, SHEARED HYDROGEN BONDING 1D69 PDB 1 1D69 1 11 1D69 1 11 1D69 A 1 1 11 11 21 1D69 11 21 1D69 B 1 1 11 1 P 1