0.055729 0.000000 0.000000 0.000000 0.031967 0.000000 0.000000 0.000000 0.022371 0.00000 0.00000 0.00000 Schneider, B. Ginell, S.L. Jones, R. Gaffney, B. Berman, H.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 17.944 31.282 44.701 C10 H15 N6 O6 P 346.236 n 2,6-DIAMINOPURINE NUCLEOTIDE 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 C9 H13 N2 O8 P 308.182 y 2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer Y 1 N N Y 2 N C Y 3 N C Y 4 N C Y 5 N C Y 6 N C N 7 N N Y 8 N N Y 9 N N Y 10 N N N 11 N N N 12 N P N 13 N O N 14 N O N 15 N O N 16 N C N 17 R C N 18 N O N 19 R C N 20 N C N 21 S C N 22 N O N 23 N O 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 H N 38 N H N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C Y 85 N N Y 86 N C Y 87 N N Y 88 N C N 89 N C N 90 N O N 91 N N N 92 N C N 93 N N N 94 N N Y 95 N C 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 H N 109 N H N 110 N O N 111 N P N 112 N O N 113 N O N 114 N O N 115 N C N 116 R C N 117 N O N 118 S C N 119 N O N 120 N C N 121 R C N 122 N N N 123 N C N 124 N O N 125 N N N 126 N C N 127 N O N 128 N C N 129 N C 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 O N 144 N H N 145 N H Y 1 N sing Y 2 N doub N 3 N sing Y 4 N doub Y 5 N doub Y 6 N sing Y 7 N sing Y 8 N sing Y 9 N sing N 10 N sing Y 11 N sing Y 12 N doub 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 doub N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N doub 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 sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing Y 99 N sing Y 100 N sing Y 101 N doub N 102 N sing Y 103 N sing N 104 N sing Y 105 N doub N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub 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 sing N 139 N sing N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing US Biochemistry BICHAW 0033 0006-2960 31 9622 9628 10.1021/bi00155a014 1390739 Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers. 1992 10.2210/pdb1d76/pdb pdb_00001d76 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 DIFFRACTOMETER ENRAF-NONIUS CAD4 x-ray 1 1.0 ROTATING ANODE 1810.205 DNA (5'-D(*CP*GP*UP*(1AP)P*CP*G)-3') 2 syn polymer 18.015 water 84 nat water no yes (DC)(DG)(DU)(1AP)(DC)(DG) CGUACG A,B polydeoxyribonucleotide n n n n n n 1.73 27.6000 VAPOR DIFFUSION 7.00 pH 7.00, VAPOR DIFFUSION, temperature 277.00K 277.00 WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE_HCL 1 WATER 2 MPD 2 1.199 1 19 A 1 B 12 2.298 A_DC1:DG12_B 1 0.566 -0.258 0.090 -0.142 -5.450 1 19 A 2 B 11 3.438 A_DG2:DC11_B 2 -0.212 0.266 0.100 -0.158 5.544 A 3 B 10 5.325 A_DU3:1AP10_B 3 -3.439 -0.074 0.030 -0.162 -6.623 A 4 B 9 6.117 A_1AP4:DU9_B 4 1.048 0.009 0.109 -0.132 1.226 1 19 A 5 B 8 2.197 A_DC5:DG8_B 5 -0.885 -0.180 0.069 -0.111 1.000 1 19 A 6 B 7 1.770 A_DG6:DC7_B 6 2.959 0.217 0.078 -0.083 5.675 -7.255 A A 1 2 25.961 B B 12 11 3.710 -3.169 0.197 5.356 AA_DC1DG2:DC11DG12_BB 1 -0.677 -5.547 -6.492 -25.245 -2.095 3.186 -49.718 A A 2 3 3.958 B B 11 10 3.259 -3.325 -0.048 -1.073 AA_DG2DU3:1AP10DC11_BB 2 0.501 0.597 -49.612 1.517 -0.021 5.720 -10.389 A A 3 4 24.618 B B 10 9 3.842 -4.319 0.083 5.373 AA_DU31AP4:DU91AP10_BB 3 -0.722 -4.116 -9.424 -18.188 -1.460 3.306 -51.709 A A 4 5 2.628 B B 9 8 3.346 -2.292 -0.280 -0.932 AA_1AP4DC5:DG8DU9_BB 4 0.354 0.406 -51.661 1.226 -0.297 4.609 -9.422 A A 5 6 13.558 B B 8 7 3.533 -2.198 0.088 5.265 AA_DC5DG6:DC7DG8_BB 5 1.401 8.639 -9.055 -26.168 4.288 diffrn_detector chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Data collection Database references Derived calculations 1 0 1992-09-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2018-04-18 1 4 2024-02-07 _diffrn_detector.detector _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag BNL Y NDB 1992-05-19 REL REL HOH water HOH 18 2 HOH HOH 18 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 22 2 HOH HOH 22 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 33 2 HOH HOH 33 A HOH 36 2 HOH HOH 36 A HOH 39 2 HOH HOH 39 A HOH 40 2 HOH HOH 40 A HOH 41 2 HOH HOH 41 A HOH 44 2 HOH HOH 44 A HOH 46 2 HOH HOH 46 A HOH 53 2 HOH HOH 53 A HOH 55 2 HOH HOH 55 A HOH 56 2 HOH HOH 56 A HOH 60 2 HOH HOH 60 A HOH 61 2 HOH HOH 61 A HOH 62 2 HOH HOH 62 A HOH 64 2 HOH HOH 64 A HOH 67 2 HOH HOH 67 A HOH 68 2 HOH HOH 68 A HOH 69 2 HOH HOH 69 A HOH 71 2 HOH HOH 71 A HOH 72 2 HOH HOH 72 A HOH 75 2 HOH HOH 75 A HOH 76 2 HOH HOH 76 A HOH 77 2 HOH HOH 77 A HOH 78 2 HOH HOH 78 A HOH 79 2 HOH HOH 79 A HOH 81 2 HOH HOH 81 A HOH 82 2 HOH HOH 82 A HOH 83 2 HOH HOH 83 A HOH 84 2 HOH HOH 84 A HOH 91 2 HOH HOH 91 A HOH 92 2 HOH HOH 92 A HOH 95 2 HOH HOH 95 A HOH 96 2 HOH HOH 96 A HOH 13 2 HOH HOH 13 B HOH 14 2 HOH HOH 14 B HOH 15 2 HOH HOH 15 B HOH 16 2 HOH HOH 16 B HOH 17 2 HOH HOH 17 B HOH 21 2 HOH HOH 21 B HOH 23 2 HOH HOH 23 B HOH 24 2 HOH HOH 24 B HOH 25 2 HOH HOH 25 B HOH 26 2 HOH HOH 26 B HOH 29 2 HOH HOH 29 B HOH 30 2 HOH HOH 30 B HOH 31 2 HOH HOH 31 B HOH 32 2 HOH HOH 32 B HOH 34 2 HOH HOH 34 B HOH 35 2 HOH HOH 35 B HOH 37 2 HOH HOH 37 B HOH 38 2 HOH HOH 38 B HOH 42 2 HOH HOH 42 B HOH 43 2 HOH HOH 43 B HOH 45 2 HOH HOH 45 B HOH 47 2 HOH HOH 47 B HOH 48 2 HOH HOH 48 B HOH 49 2 HOH HOH 49 B HOH 50 2 HOH HOH 50 B HOH 51 2 HOH HOH 51 B HOH 52 2 HOH HOH 52 B HOH 54 2 HOH HOH 54 B HOH 57 2 HOH HOH 57 B HOH 58 2 HOH HOH 58 B HOH 59 2 HOH HOH 59 B HOH 63 2 HOH HOH 63 B HOH 65 2 HOH HOH 65 B HOH 66 2 HOH HOH 66 B HOH 70 2 HOH HOH 70 B HOH 73 2 HOH HOH 73 B HOH 74 2 HOH HOH 74 B HOH 80 2 HOH HOH 80 B HOH 85 2 HOH HOH 85 B HOH 86 2 HOH HOH 86 B HOH 87 2 HOH HOH 87 B HOH 88 2 HOH HOH 88 B HOH 89 2 HOH HOH 89 B HOH 90 2 HOH HOH 90 B HOH 93 2 HOH HOH 93 B HOH 94 2 HOH HOH 94 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A U 3 n 3 DU 3 A +A 4 n 4 1AP 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A C 7 n 1 DC 7 B G 8 n 2 DG 8 B U 9 n 3 DU 9 B +A 10 n 4 1AP 10 B C 11 n 5 DC 11 B G 12 n 6 DG 12 B author_defined_assembly 2 dimeric A 1AP 4 2,6-DIAMINOPURINE NUCLEOTIDE A 1AP 4 DA B 1AP 10 2,6-DIAMINOPURINE NUCLEOTIDE B 1AP 4 DA 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 A OP2 O DU HOH 3 75 2.18 1 3.34 0.30 108.30 111.64 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.65 0.50 119.90 124.55 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -3.13 0.40 121.90 118.77 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 3.20 0.50 121.00 124.20 A A A C5 C6 N1 DC DC DC 1 1 1 N 1 4.92 0.70 118.00 122.92 A A A N3 C4 N4 DC DC DC 1 1 1 N 1 -5.58 0.80 109.40 103.82 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 -3.88 0.60 128.60 124.72 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 -4.39 0.60 127.00 122.61 A A A C2 N3 C4 DU DU DU 3 3 3 N 1 4.35 0.60 114.60 118.95 A A A N3 C4 C5 DU DU DU 3 3 3 N 1 3.66 0.60 118.90 122.56 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 -6.37 0.80 109.40 103.03 A A A O5' C5' C4' DG DG DG 6 6 6 N 1 -3.31 0.40 121.90 118.59 B B B N3 C4 C5 DC DC DC 7 7 7 N 1 5.47 0.70 120.20 125.67 B B B C5 C4 N4 DC DC DC 7 7 7 N 1 3.27 0.50 106.80 110.07 B B B O4' C1' C2' DG DG DG 8 8 8 N 1 2.68 0.40 105.40 108.08 B B B N9 C4 C5 DG DG DG 8 8 8 N 1 2.73 0.30 108.30 111.03 B B B O4' C1' N1 DU DU DU 9 9 9 N 1 3.64 0.60 114.90 118.54 B B B N1 C2 N3 DU DU DU 9 9 9 N 1 -5.56 0.60 127.00 121.44 B B B C2 N3 C4 DU DU DU 9 9 9 N 1 4.80 0.60 114.60 119.40 B B B N3 C4 C5 DU DU DU 9 9 9 N 1 -2.45 0.40 121.90 119.45 B B B N3 C4 C5 DC DC DC 11 11 11 N 1 3.89 0.50 121.00 124.89 B B B C5 C6 N1 DC DC DC 11 11 11 N 1 6.44 0.70 118.00 124.44 B B B N3 C4 N4 DC DC DC 11 11 11 N 1 -4.33 0.70 120.20 115.87 B B B C5 C4 N4 DC DC DC 11 11 11 N 1 3.16 0.50 111.50 114.66 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 -4.10 0.60 128.60 124.50 B B B C5 C6 O6 DG DG DG 12 12 12 N 1 A A O4' C4' DG DG 2 2 -0.062 0.010 1.446 1.384 N 1 B B N3 C4 DC DC 7 7 0.046 0.007 1.335 1.381 N 0.138 1.300 8.000 4588 1 4.000 TR isotropic TR isotropic TR isotropic 1.300 8.000 84 324 2 238 0 fix fix ref 1.020 45.000 1D76 13324 5790 2.000 1 refinement NUCLSQ CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT CONTAINING A 2-AMINO ADENINE MODIFICATION: THE RELATIONSHIP BETWEEN CONFORMATION, PACKING, AND HYDRATION IN Z-DNA HEXAMERS 1 N N 1 N N 2 N N 2 N N covale 1.573 both A DU 3 A O3' DU 3 1_555 A 1AP 4 A P 1AP 4 1_555 covale 1.624 one A 1AP 4 A O3' 1AP 4 1_555 A DC 5 A P DC 5 1_555 covale 1.564 both B DU 9 B O3' DU 3 1_555 B 1AP 10 B P 1AP 4 1_555 covale 1.614 one B 1AP 10 B O3' 1AP 4 1_555 B DC 11 B P DC 5 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 5 1_555 hydrog DU-1AP MISPAIR A DU 3 A O2 DU 3 1_555 B 1AP 10 B N2 1AP 4 1_555 hydrog 1AP-DU MISPAIR A 1AP 4 A N2 1AP 4 1_555 B DU 9 B O2 DU 3 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 8 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 7 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 7 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 7 B N4 DC 1 1_555 DNA Z-DNA, DOUBLE HELIX, MODIFIED, DNA 1D76 PDB 1 1D76 1 6 1D76 1 6 1D76 A 1 1 6 7 12 1D76 7 12 1D76 B 1 1 6 19 P 21 21 21