0.031377 0.000000 0.014036 0.000000 0.038926 0.000000 0.000000 0.000000 0.032022 0.000000 0.000000 0.000000 Lipanov, A. Kopka, M.L. Kaczor-Grzeskowiak, M. Quintana, J. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 114.10 90.00 31.870 25.690 34.210 Ca 2 40.078 CALCIUM ION non-polymer C2 H6 As O2 -1 136.989 CACODYLATE ION dimethylarsinate non-polymer 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 H13 N4 O7 P 332.207 y 2'-DEOXYINOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer US Biochemistry BICHAW 0033 0006-2960 32 1373 1389 10.1021/bi00056a024 8448146 Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. 1993 US Science SCIEAS 0038 0036-8075 238 498 504 Helix Geometry, Hydration, and G.A Mismatch in a B-DNA Decamer 1992 UK J.Mol.Biol. JMOBAK 0070 0022-2836 210 369 381 Crystallographic Study of One Turn of G/C-Rich B-DNA 1992 UK J.Mol.Biol. JMOBAK 0070 0022-2836 217 177 199 Structure of the B-DNA Decamer C-C-A-A-C-G-T-T-G-G and Comparison with Isomorphous Decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G 1992 10.2210/pdb1d61/pdb pdb_00001d61 0.912826 0.000000 0.408327 0.000000 1.000000 0.000000 -0.408337 0.000000 0.912839 0.000000 0.000000 0.000000 248.00 1 DIFFRACTOMETER RIGAKU AFC-5R SINGLE WAVELENGTH M x-ray 1 1.0 ROTATING ANODE 3029.990 DNA (5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3') 1 syn polymer 136.989 CACODYLATE ION 1 syn non-polymer 40.078 CALCIUM ION 1 syn non-polymer 18.015 water 79 nat water no no (DC)(DC)(DA)(DA)(DC)(DI)(DT)(DT)(DG)(DG) CCAACITTGG A polydeoxyribonucleotide n n n n n n n n n n 2.02 39.23 VAPOR DIFFUSION, SITTING DROP 7.10 pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K 277.00 WATER 1 MPD 1 CA CACODYLATE 1 NA CACODYLATE 1 SPERMIDINE 1 WATER 2 MPD 2 -8.515 1 19 A 1 A 10 2.252 A_DC1:DG10_A 1 -13.262 0.160 0.132 -0.082 -0.756 1 19 A 2 A 9 -1.421 A_DC2:DG9_A 2 -11.248 0.308 0.046 -0.176 1.788 1 20 A 3 A 8 -0.482 A_DA3:DT8_A 3 -5.383 0.003 0.234 -0.119 2.186 1 20 A 4 A 7 4.449 A_DA4:DT7_A 4 -14.336 -0.019 0.149 -0.125 -8.515 1 19 A 1 A 10 2.252 A_DC1:DG10_A 5 -13.262 0.160 0.132 -0.082 -0.756 1 19 A 2 A 9 -1.421 A_DC2:DG9_A 6 -11.248 0.308 0.046 -0.176 1.787 1 20 A 3 A 8 -0.482 A_DA3:DT8_A 7 -5.383 0.003 0.234 -0.119 2.186 1 20 A 4 A 7 4.449 A_DA4:DT7_A 8 -14.336 -0.019 0.149 -0.125 3.162 29.710 A A 1 2 18.621 A A 10 9 3.153 9.378 -0.669 0.768 AA_DC1DC2:DG9DG10_AA 1 2.740 -5.441 28.091 -0.460 1.877 2.649 50.864 A A 2 3 -11.644 A A 9 8 3.227 -9.943 0.273 2.806 AA_DC2DA3:DT8DG9_AA 2 -1.685 1.973 49.919 3.899 -0.425 3.223 29.816 A A 3 4 20.669 A A 8 7 3.412 10.417 0.390 0.110 AA_DA3DA4:DT7DT8_AA 3 -1.344 2.666 27.944 -2.063 -1.053 3.162 29.710 A A 1 2 18.622 A A 10 9 3.153 9.378 -0.669 0.768 AA_DC1DC2:DG9DG10_AA 4 2.740 -5.441 28.091 -0.460 1.877 2.649 50.864 A A 2 3 -11.644 A A 9 8 3.227 -9.943 0.273 2.806 AA_DC2DA3:DT8DG9_AA 5 -1.685 1.973 49.919 3.899 -0.425 3.223 29.816 A A 3 4 20.669 A A 8 7 3.412 10.416 0.390 0.110 AA_DA3DA4:DT7DT8_AA 6 -1.344 2.666 27.944 -2.063 -1.053 atom_site atom_sites database_2 database_PDB_matrix pdbx_struct_conn_angle pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond pdbx_validate_symm_contact struct_conn struct_site repository Initial release Coordinates and associated ncs operations (if present) transformed into standard crystal frame repository Remediation Version format compliance Advisory Version format compliance Advisory Atomic model Data collection Database references Derived calculations Other 1 0 1993-04-15 1 1 2008-05-22 1 2 2011-07-13 2 0 2023-07-26 _atom_site.Cartn_x _atom_site.Cartn_z _atom_site.occupancy _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[1][3] _atom_sites.fract_transf_matrix[3][1] _atom_sites.fract_transf_matrix[3][3] _database_2.pdbx_DOI _database_2.pdbx_database_accession _database_PDB_matrix.origx[1][1] _database_PDB_matrix.origx[1][3] _database_PDB_matrix.origx[3][1] _database_PDB_matrix.origx[3][3] _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_symm_contact.site_symmetry_2 _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. BNL Y NDB 1992-02-26 REL REL CAC CACODYLATE ION CA CALCIUM ION HOH water CAC 11 2 CAC CAC 11 A OC7 12 3 CA CA 12 A HOH 13 4 HOH HOH 13 A HOH 14 4 HOH HOH 14 A HOH 15 4 HOH HOH 15 A HOH 16 4 HOH HOH 16 A HOH 17 4 HOH HOH 17 A HOH 18 4 HOH HOH 18 A HOH 19 4 HOH HOH 19 A HOH 20 4 HOH HOH 20 A HOH 21 4 HOH HOH 21 A HOH 22 4 HOH HOH 22 A HOH 23 4 HOH HOH 23 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 26 4 HOH HOH 26 A HOH 27 4 HOH HOH 27 A HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 30 4 HOH HOH 30 A HOH 31 4 HOH HOH 31 A HOH 32 4 HOH HOH 32 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 36 4 HOH HOH 36 A HOH 37 4 HOH HOH 37 A HOH 38 4 HOH HOH 38 A HOH 39 4 HOH HOH 39 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 42 4 HOH HOH 42 A HOH 43 4 HOH HOH 43 A HOH 44 4 HOH HOH 44 A HOH 45 4 HOH HOH 45 A HOH 46 4 HOH HOH 46 A HOH 47 4 HOH HOH 47 A HOH 48 4 HOH HOH 48 A HOH 49 4 HOH HOH 49 A HOH 50 4 HOH HOH 50 A HOH 51 4 HOH HOH 51 A HOH 52 4 HOH HOH 52 A HOH 53 4 HOH HOH 53 A HOH 54 4 HOH HOH 54 A HOH 55 4 HOH HOH 55 A HOH 56 4 HOH HOH 56 A HOH 57 4 HOH HOH 57 A HOH 58 4 HOH HOH 58 A HOH 59 4 HOH HOH 59 A HOH 60 4 HOH HOH 60 A HOH 61 4 HOH HOH 61 A HOH 62 4 HOH HOH 62 A HOH 63 4 HOH HOH 63 A HOH 64 4 HOH HOH 64 A HOH 65 4 HOH HOH 65 A HOH 66 4 HOH HOH 66 A HOH 67 4 HOH HOH 67 A HOH 68 4 HOH HOH 68 A HOH 69 4 HOH HOH 69 A HOH 70 4 HOH HOH 70 A HOH 71 4 HOH HOH 71 A HOH 72 4 HOH HOH 72 A HOH 73 4 HOH HOH 73 A HOH 74 4 HOH HOH 74 A HOH 75 4 HOH HOH 75 A HOH 76 4 HOH HOH 76 A HOH 77 4 HOH HOH 77 A HOH 78 4 HOH HOH 78 A HOH 79 4 HOH HOH 79 A HOH 80 4 HOH HOH 80 A HOH 81 4 HOH HOH 81 A HOH 82 4 HOH HOH 82 A HOH 83 4 HOH HOH 83 A HOH 84 4 HOH HOH 84 A OC7 12 4 HOH HOH 85 A OC7 12 4 HOH HOH 86 A OC7 12 4 HOH HOH 87 A OC7 12 4 HOH HOH 88 A OC7 12 4 HOH HOH 89 A OC7 12 4 HOH HOH 90 A OC7 12 4 HOH HOH 91 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A I 6 n 6 DI 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A author_defined_assembly 2 dimeric A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 86 D O HOH 1_555 91.4 A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 87 D O HOH 1_555 104.7 A HOH 86 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 87 D O HOH 1_555 74.6 A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 88 D O HOH 1_555 88.6 A HOH 86 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 88 D O HOH 1_555 141.3 A HOH 87 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 88 D O HOH 1_555 142.3 A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 89 D O HOH 1_555 78.7 A HOH 86 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 89 D O HOH 1_555 137.8 A HOH 87 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 89 D O HOH 1_555 68.8 A HOH 88 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 89 D O HOH 1_555 80.0 A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 85.0 A HOH 86 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 69.0 A HOH 87 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 142.5 A HOH 88 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 72.4 A HOH 89 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 148.2 A HOH 85 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 172.8 A HOH 86 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 87.3 A HOH 87 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 81.8 A HOH 88 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 87.9 A HOH 89 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 106.9 A HOH 90 D O HOH 1_555 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 87.9 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A HOH 13 D HOH 1 A C1 CAC 11 B C1 CAC 1 1 N 1 A C2 CAC 11 B C2 CAC 1 1 N 1 -7.09 0.80 109.40 102.31 A A A O5' C5' C4' DC DC DC 1 1 1 N 1 9.57 1.20 115.70 125.27 A A A C5' C4' C3' DC DC DC 1 1 1 N 1 -6.37 0.70 108.00 101.63 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 10.52 1.10 110.50 121.02 A A A O3' P OP2 DC DC DC 1 2 2 Y 1 3.53 0.50 119.90 123.43 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 3.76 0.50 121.00 124.76 A A A C5 C6 N1 DC DC DC 2 2 2 N 1 -6.31 0.70 108.00 101.69 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 5.40 0.60 118.60 124.00 A A A C6 N1 C2 DA DA DA 3 3 3 N 1 -5.88 0.50 129.30 123.42 A A A N1 C2 N3 DA DA DA 3 3 3 N 1 7.64 1.20 119.70 127.34 A A A C3' O3' P DA DA DA 3 3 4 Y 1 -4.42 0.70 108.00 103.58 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 -4.54 0.50 117.70 113.16 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -5.94 0.80 109.40 103.46 A A A O5' C5' C4' DC DC DC 5 5 5 N 1 3.04 0.30 108.30 111.34 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 5.43 0.50 119.90 125.33 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 -4.88 0.40 121.90 117.02 A A A N3 C4 C5 DC DC DC 5 5 5 N 1 -6.58 0.80 109.40 102.82 A A A O5' C5' C4' DT DT DT 7 7 7 N 1 10.40 1.50 119.60 130.00 A A A OP1 P OP2 DT DT DT 8 8 8 N 1 -5.30 0.80 109.40 104.10 A A A O5' C5' C4' DT DT DT 8 8 8 N 1 4.37 0.60 114.60 118.97 A A A N1 C2 N3 DT DT DT 8 8 8 N 1 -6.34 0.60 127.20 120.86 A A A C2 N3 C4 DT DT DT 8 8 8 N 1 -4.61 0.60 123.70 119.09 A A A C5 C6 N1 DT DT DT 8 8 8 N 1 -4.12 0.60 122.30 118.18 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 -3.86 0.60 122.90 119.04 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 -5.76 0.60 125.10 119.34 A A A C6 N1 C2 DG DG DG 9 9 9 N 1 6.26 0.50 111.50 117.76 A A A C5 C6 N1 DG DG DG 9 9 9 N 1 -3.66 0.60 119.90 116.24 A A A N1 C6 O6 DG DG DG 9 9 9 N 1 -4.76 0.70 108.00 103.24 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 3.91 0.50 111.90 115.81 A A A C2 N3 C4 DG DG DG 10 10 10 N 1 5.05 0.50 111.50 116.55 A A A C5 C6 N1 DG DG DG 10 10 10 N 1 -3.00 0.40 110.80 107.80 A A A C4 C5 N7 DG DG DG 10 10 10 N 1 3.23 0.50 104.30 107.53 A A A C5 N7 C8 DG DG DG 10 10 10 N 1 5.62 0.60 130.40 136.02 A A A C6 C5 N7 DG DG DG 10 10 10 N 1 -5.37 0.60 119.90 114.53 A A A N1 C6 O6 DG DG DG 10 10 10 N 1 A A P OP1 DC DC 2 2 -0.109 0.017 1.485 1.376 N 1 A A P OP2 DC DC 2 2 -0.236 0.017 1.485 1.249 N 1 A A P O5' DC DC 2 2 0.089 0.010 1.593 1.682 N 1 A A P O5' DC DC 5 5 0.067 0.010 1.593 1.660 N 1 A A O4' C4' DC DC 5 5 -0.063 0.010 1.446 1.383 N 1 A A P OP2 DT DT 8 8 -0.133 0.017 1.485 1.352 N 1 A A O O HOH HOH 14 14 1.70 1_555 2_554 1 A A O2 O CAC HOH 11 44 2.19 1_555 3_556 0.1520000 1.300 8.000 5026 1 2.000 TR isotropic TR isotropic TR isotropic 1.300 8.000 79 284 4 201 0 fix fix fix 1.300 8.000 1D61 5848 5026 2.000 1 refinement NUCLSQ THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINIC FORM 1 N N 2 N N 3 N N 4 N N metalc 2.417 A CA 12 C CA CA 1_555 A HOH 85 D O HOH 1_555 metalc 2.519 A CA 12 C CA CA 1_555 A HOH 86 D O HOH 1_555 metalc 2.462 A CA 12 C CA CA 1_555 A HOH 87 D O HOH 1_555 metalc 2.479 A CA 12 C CA CA 1_555 A HOH 88 D O HOH 1_555 metalc 2.318 A CA 12 C CA CA 1_555 A HOH 89 D O HOH 1_555 metalc 2.625 A CA 12 C CA CA 1_555 A HOH 90 D O HOH 1_555 metalc 2.406 A CA 12 C CA CA 1_555 A HOH 91 D O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 10 A N1 DG 10 2_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 10 A O6 DG 10 2_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 10 A N2 DG 10 2_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 9 A N1 DG 9 2_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 9 A O6 DG 9 2_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 9 A N2 DG 9 2_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 8 A N3 DT 8 2_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 8 A O4 DT 8 2_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 A DT 7 A N3 DT 7 2_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 A DT 7 A O4 DT 7 2_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 A DA 4 A N1 DA 4 2_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 A DA 4 A N6 DA 4 2_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 3 A N1 DA 3 2_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 3 A N6 DA 3 2_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 A DC 2 A N3 DC 2 2_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 A DC 2 A O2 DC 2 2_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 A DC 2 A N4 DC 2 2_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 A DC 1 A N3 DC 1 2_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 A DC 1 A O2 DC 1 2_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 A DC 1 A N4 DC 1 2_555 DNA B-DNA, DOUBLE HELIX, MODIFIED, DNA 1D61 PDB 1 1D61 1 10 1D61 1 10 1D61 A 1 1 10 BINDING SITE FOR RESIDUE CAC A 11 A CAC 11 Software 9 BINDING SITE FOR RESIDUE CA A 12 A CA 12 Software 7 A DC 1 A DC 1 9 1_554 A DC 2 A DC 2 9 2_556 A HOH 24 D HOH 9 3_556 A HOH 24 D HOH 9 4_455 A HOH 29 D HOH 9 3_556 A HOH 33 D HOH 9 1_555 A HOH 34 D HOH 9 2_556 A HOH 34 D HOH 9 1_555 A HOH 44 D HOH 9 4_454 A HOH 85 D HOH 7 1_555 A HOH 86 D HOH 7 1_555 A HOH 87 D HOH 7 1_555 A HOH 88 D HOH 7 1_555 A HOH 89 D HOH 7 1_555 A HOH 90 D HOH 7 1_555 A HOH 91 D HOH 7 1_555 5 C 1 2 1