0.021645 0.012497 0.000000 0.000000 0.024994 0.000000 0.000000 0.000000 0.013986 0.00000 0.00000 0.00000 Bingman, C.A. Zon, G. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 46.200 46.200 71.500 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 H2 O 18.015 WATER non-polymer 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 144 N O N 145 N H N 146 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 N 150 N sing N 151 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 227 738 756 10.1016/0022-2836(92)90221-5 1404387 Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. 1992 UK Nucleic Acids Res. NARHAD 0389 0305-1048 20 6637 6647 Crystal and Molecular Structure of the Alternating Dodecamer d(GCGTACGTACGC) in the A-DNA Form: Comparison with the Isomorphous Non-Alternating Dodecamer d(CCGTACGTACGG) 1992 10.2210/pdb116d/pdb pdb_0000116d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 277.00 1 OSCILLATION CAMERA ENRAF-NONIUS x-ray 1 1.0 3663.392 DNA (5'-D(*CP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*G)-3') 1 syn polymer 18.015 water 40 nat water no no (DC)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DG) CCGTACGTACGG A polydeoxyribonucleotide n n n n n n n n n n n n 3.01 59.09 VAPOR DIFFUSION 6.50 pH 6.50, VAPOR DIFFUSION WATER 1 [CO(NH3)6]3+ 1 SPERMINE 1 NA CACODYLATE 1 WATER 2 -6.191 1 19 A 1 A 12 -0.609 A_DC1:DG12_A 1 -4.220 -0.136 0.086 -0.053 -0.885 1 19 A 2 A 11 -2.608 A_DC2:DG11_A 2 -5.317 0.095 0.227 -0.152 0.261 1 19 A 3 A 10 -1.989 A_DG3:DC10_A 3 -7.162 0.008 0.196 -0.120 0.846 1 20 A 4 A 9 -3.223 A_DT4:DA9_A 4 -10.398 0.180 -0.046 -0.163 2.445 1 20 A 5 A 8 0.737 A_DA5:DT8_A 5 -14.140 -0.682 0.051 -0.314 5.742 1 19 A 6 A 7 -0.324 A_DC6:DG7_A 6 -11.967 0.054 -0.515 -0.180 -5.742 1 19 A 7 A 6 -0.324 A_DG7:DC6_A 7 -11.967 -0.054 -0.515 -0.180 -2.445 1 20 A 8 A 5 0.737 A_DT8:DA5_A 8 -14.140 0.682 0.051 -0.314 -0.846 1 20 A 9 A 4 -3.223 A_DA9:DT4_A 9 -10.398 -0.180 -0.046 -0.163 -0.261 1 19 A 10 A 3 -1.989 A_DC10:DG3_A 10 -7.162 -0.008 0.196 -0.120 0.885 1 19 A 11 A 2 -2.608 A_DG11:DC2_A 11 -5.317 -0.095 0.227 -0.152 6.191 1 19 A 12 A 1 -0.609 A_DG12:DC1_A 12 -4.220 0.136 0.086 -0.053 3.184 29.759 A A 1 2 2.409 A A 12 11 3.261 1.236 -0.060 -1.726 AA_DC1DC2:DG11DG12_AA 1 -2.111 4.115 29.660 -3.616 -0.320 3.092 32.022 A A 2 3 6.934 A A 11 10 3.335 3.816 0.101 -1.889 AA_DC2DG3:DC10DG11_AA 2 -0.356 0.647 31.797 -4.103 -0.247 3.000 33.553 A A 3 4 8.518 A A 10 9 3.248 4.899 -0.407 -1.372 AA_DG3DT4:DA9DC10_AA 3 1.468 -2.553 33.172 -3.148 0.937 2.723 28.579 A A 4 5 19.177 A A 9 8 3.323 9.301 0.086 -1.332 AA_DT4DA5:DT8DA9_AA 4 -0.248 0.511 27.052 -4.707 -0.228 2.751 36.308 A A 5 6 17.862 A A 8 7 3.296 10.960 0.112 -1.370 AA_DA5DC6:DG7DT8_AA 5 2.431 -3.961 34.585 -3.652 0.142 2.096 35.249 A A 6 7 38.990 A A 7 6 3.674 21.965 0.000 -1.330 AA_DC6DG7:DC6DG7_AA 6 0.000 0.000 27.741 -5.444 0.000 2.751 36.308 A A 7 8 17.862 A A 6 5 3.296 10.960 -0.112 -1.370 AA_DG7DT8:DA5DC6_AA 7 -2.431 3.961 34.585 -3.652 -0.142 2.723 28.579 A A 8 9 19.177 A A 5 4 3.323 9.301 -0.086 -1.332 AA_DT8DA9:DT4DA5_AA 8 0.248 -0.511 27.052 -4.707 0.228 3.000 33.553 A A 9 10 8.518 A A 4 3 3.248 4.899 0.407 -1.372 AA_DA9DC10:DG3DT4_AA 9 -1.468 2.553 33.172 -3.148 -0.937 3.092 32.022 A A 10 11 6.934 A A 3 2 3.335 3.816 -0.101 -1.889 AA_DC10DG11:DC2DG3_AA 10 0.356 -0.647 31.797 -4.103 0.247 3.184 29.759 A A 11 12 2.409 A A 2 1 3.261 1.236 0.060 -1.726 AA_DG11DG12:DC1DC2_AA 11 2.111 -4.115 29.660 -3.616 0.320 chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Data collection Database references 1 0 1993-04-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession BNL Y NDB 1993-02-10 REL REL HOH water HOH 13 2 HOH HOH 13 A HOH 14 2 HOH HOH 14 A HOH 15 2 HOH HOH 15 A HOH 16 2 HOH HOH 16 A HOH 17 2 HOH HOH 17 A HOH 18 2 HOH HOH 18 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 21 2 HOH HOH 21 A HOH 22 2 HOH HOH 22 A HOH 23 2 HOH HOH 23 A HOH 24 2 HOH HOH 24 A HOH 25 2 HOH HOH 25 A HOH 26 2 HOH HOH 26 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 30 2 HOH HOH 30 A HOH 31 2 HOH HOH 31 A HOH 32 2 HOH HOH 32 A HOH 33 2 HOH HOH 33 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 37 2 HOH HOH 37 A HOH 38 2 HOH HOH 38 A HOH 39 2 HOH HOH 39 A HOH 40 2 HOH HOH 40 A HOH 41 2 HOH HOH 41 A HOH 42 2 HOH HOH 42 A HOH 43 2 HOH HOH 43 A HOH 44 2 HOH HOH 44 A HOH 45 2 HOH HOH 45 A HOH 46 2 HOH HOH 46 A HOH 47 2 HOH HOH 47 A HOH 48 2 HOH HOH 48 A HOH 49 2 HOH HOH 49 A HOH 50 2 HOH HOH 50 A HOH 51 2 HOH HOH 51 A HOH 52 2 HOH HOH 52 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A C 6 n 6 DC 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A A 9 n 9 DA 9 A C 10 n 10 DC 10 A G 11 n 11 DG 11 A G 12 n 12 DG 12 A 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 0.5000000000 0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 12_565 x,x-y+1,-z+1/6 crystal symmetry operation -23.1000000000 40.0103736548 11.9166666667 1 -8.03 1.20 119.70 111.67 A A A C3' O3' P DC DC DC 1 1 2 Y 1 -10.94 1.20 119.70 108.76 A A A C3' O3' P DC DC DG 2 2 3 Y 1 -9.97 1.20 119.70 109.73 A A A C3' O3' P DG DG DT 3 3 4 Y 1 -5.32 0.80 109.40 104.08 A A A O5' C5' C4' DT DT DT 4 4 4 N 1 -5.30 0.60 127.20 121.90 A A A C2 N3 C4 DT DT DT 4 4 4 N 1 4.85 0.60 115.20 120.05 A A A N3 C4 C5 DT DT DT 4 4 4 N 1 -8.40 1.20 119.70 111.30 A A A C3' O3' P DT DT DA 4 4 5 Y 1 4.50 0.30 108.30 112.80 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 3.69 0.60 118.60 122.29 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 -8.78 1.20 119.70 110.92 A A A C3' O3' P DA DA DC 5 5 6 Y 1 7.30 1.20 110.70 118.00 A A A O5' P OP1 DC DC DC 6 6 6 N 1 4.87 0.30 108.30 113.17 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 3.04 0.50 111.50 114.54 A A A C5 C6 N1 DG DG DG 7 7 7 N 1 9.79 1.20 110.70 120.49 A A A O5' P OP1 DT DT DT 8 8 8 N 1 -4.36 0.60 127.20 122.84 A A A C2 N3 C4 DT DT DT 8 8 8 N 1 4.14 0.60 115.20 119.34 A A A N3 C4 C5 DT DT DT 8 8 8 N 1 -5.07 0.60 119.90 114.83 A A A N3 C4 O4 DT DT DT 8 8 8 N 1 -9.77 1.50 119.60 109.83 A A A OP1 P OP2 DA DA DA 9 9 9 N 1 8.08 1.20 110.70 118.78 A A A O5' P OP1 DA DA DA 9 9 9 N 1 2.79 0.30 108.30 111.09 A A A O4' C1' N9 DA DA DA 9 9 9 N 1 -3.79 0.50 129.30 125.51 A A A N1 C2 N3 DA DA DA 9 9 9 N 1 -7.86 1.20 119.70 111.84 A A A C3' O3' P DA DA DC 9 9 10 Y 1 9.39 1.20 110.70 120.09 A A A O5' P OP2 DC DC DC 10 10 10 N 1 3.79 0.30 108.30 112.09 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 -5.52 0.80 109.40 103.88 A A A O5' C5' C4' DG DG DG 11 11 11 N 1 3.86 0.50 111.50 115.36 A A A C5 C6 N1 DG DG DG 11 11 11 N 1 9.86 1.20 110.70 120.56 A A A O5' P OP1 DG DG DG 12 12 12 N 1 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 3.11 0.50 111.50 114.61 A A A C5 C6 N1 DG DG DG 12 12 12 N 1 A A O3' P DG DT 3 4 0.074 0.012 1.607 1.681 Y 0.1500000 2.500 8.000 1664 1 2.000 TR isotropic TR isotropic 2.500 8.000 40 283 0 243 0 1.750 3.000 2.650 4.500 1.790 3.000 2.670 4.500 0.006 0.025 0.016 0.050 0.027 0.050 0.038 0.075 0.027 0.040 0.057 0.100 0.089 0.090 0.206 0.090 fix fix 2.500 116D 4971 1664 2.000 1 refinement NUCLSQ CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGTACGG): CHOICE OF FRAGMENT HELICAL AXIS 1 N N 2 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 12 A N1 DG 12 12_565 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 12 A O6 DG 12 12_565 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 12 A N2 DG 12 12_565 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 11 A N1 DG 11 12_565 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 11 A O6 DG 11 12_565 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 11 A N2 DG 11 12_565 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 A DC 10 A N3 DC 10 12_565 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 A DC 10 A O2 DC 10 12_565 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 A DC 10 A N4 DC 10 12_565 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 9 A N1 DA 9 12_565 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 9 A N6 DA 9 12_565 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 A DT 8 A N3 DT 8 12_565 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 A DT 8 A O4 DT 8 12_565 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 7 A N1 DG 7 12_565 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 7 A O6 DG 7 12_565 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 7 A N2 DG 7 12_565 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 A DC 6 A N3 DC 6 12_565 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 A DC 6 A O2 DC 6 12_565 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 A DC 6 A N4 DC 6 12_565 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 5 A N1 DA 5 12_565 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 5 A N6 DA 5 12_565 hydrog WATSON-CRICK A DA 9 A N1 DA 9 1_555 A DT 4 A N3 DT 4 12_565 hydrog WATSON-CRICK A DA 9 A N6 DA 9 1_555 A DT 4 A O4 DT 4 12_565 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 A DG 3 A N1 DG 3 12_565 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 A DG 3 A O6 DG 3 12_565 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 A DG 3 A N2 DG 3 12_565 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 A DC 2 A N3 DC 2 12_565 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 A DC 2 A O2 DC 2 12_565 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 A DC 2 A N4 DC 2 12_565 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 A DC 1 A N3 DC 1 12_565 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 A DC 1 A O2 DC 1 12_565 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 A DC 1 A N4 DC 1 12_565 DNA A-DNA, DOUBLE HELIX, DNA 116D PDB 1 116D 1 12 116D 1 12 116D A 1 1 12 178 P 61 2 2