0.035804 0.000000 0.000000 0.000000 0.035804 0.000000 0.000000 0.000000 0.017340 0.00000 0.00000 0.00000 Chen, X. Ramakrishnan, B. Rao, S.T. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 27.930 27.930 57.670 C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H13 N4 O7 P 332.207 y 2'-DEOXYINOSINE-5'-MONOPHOSPHATE DNA linking C22 H27 N9 O4 481.508 DISTAMYCIN A DISTAMYCIN; STALLIMYCIN non-polymer H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION 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 N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N H N 22 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N Y 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 C N 71 N O N 72 N N Y 73 N C Y 74 N C Y 75 N C Y 76 N N Y 77 N C N 78 N C N 79 N C N 80 N O N 81 N N Y 82 N C Y 83 N C Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N C N 89 N O N 90 N N Y 91 N C Y 92 N C Y 93 N C Y 94 N N Y 95 N C N 96 N C N 97 N C N 98 N O N 99 N N N 100 N C N 101 N C N 102 N C N 103 N N N 104 N N N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N O N 133 N H N 134 N H N 135 N MG 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 N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing 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 Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N doub 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 Y 78 N sing Y 79 N doub Y 80 N doub N 81 N sing Y 82 N sing N 83 N sing Y 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 doub N 91 N sing N 92 N sing N 93 N sing Y 94 N sing Y 95 N doub Y 96 N doub N 97 N sing Y 98 N sing N 99 N sing Y 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing Y 110 N sing Y 111 N doub Y 112 N doub N 113 N sing Y 114 N sing N 115 N sing Y 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 doub 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 doub N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing US Nat.Struct.Biol. NSBIEW 2024 1072-8368 1 169 175 10.1038/nsb0394-169 7656035 Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. 1994 10.2210/pdb159d/pdb pdb_0000159d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 AREA DETECTOR SIEMENS x-ray 1 1.0 ROTATING ANODE 2368.537 DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3') 1 syn polymer 481.508 DISTAMYCIN A 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 65 nat water no no (DI)(DC)(DI)(DC)(DI)(DC)(DI)(DC) ICICICIC A polydeoxyribonucleotide n n n n n n n n 2.37 48.19 VAPOR DIFFUSION, HANGING DROP 7.00 pH 7.00, VAPOR DIFFUSION, HANGING DROP ROOM TEMPERATURE WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 WATER 2 MPD 2 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1995-02-07 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _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 BNL Y NDB 1994-02-10 REL REL DMY DISTAMYCIN A MG MAGNESIUM ION HOH water DMY 9 2 DMY DMY 9 A MG 10 3 MG MG 10 A HOH 11 4 HOH HOH 11 A HOH 12 4 HOH HOH 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 I 1 n 1 DI 1 A C 2 n 2 DC 2 A I 3 n 3 DI 3 A C 4 n 4 DC 4 A I 5 n 5 DI 5 A C 6 n 6 DC 6 A I 7 n 7 DI 7 A C 8 n 8 DC 8 A author_defined_assembly 2 dimeric A DC 6 A OP2 DC 6 1_555 A MG 10 C MG MG 1_555 A HOH 11 D O HOH 1_555 89.4 A DC 6 A OP2 DC 6 1_555 A MG 10 C MG MG 1_555 A HOH 19 D O HOH 1_555 87.1 A HOH 11 D O HOH 1_555 A MG 10 C MG MG 1_555 A HOH 19 D O HOH 1_555 91.9 A DC 6 A OP2 DC 6 1_555 A MG 10 C MG MG 1_555 A HOH 20 D O HOH 1_555 98.4 A HOH 11 D O HOH 1_555 A MG 10 C MG MG 1_555 A HOH 20 D O HOH 1_555 171.6 A HOH 19 D O HOH 1_555 A MG 10 C MG MG 1_555 A HOH 20 D O HOH 1_555 91.5 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 6_555 x,-y,-z+1/2 crystal symmetry operation 0.0000000000 0.0000000000 28.8350000000 1 A DI 3 0.074 SIDE CHAIN 1 A DI 5 0.089 SIDE CHAIN 1 A DC 6 0.056 SIDE CHAIN 1 3.24 0.30 108.30 111.54 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 7.87 1.10 110.50 118.37 A A A O3' P OP1 DC DI DI 2 3 3 Y 1 -5.09 0.80 105.90 100.81 A A A O4' C1' C2' DC DC DC 4 4 4 N 1 3.65 0.60 118.90 122.55 A A A N1 C2 O2 DC DC DC 4 4 4 N 1 4.07 0.60 118.90 122.97 A A A N1 C2 O2 DC DC DC 6 6 6 N 1 7.55 1.10 110.50 118.05 A A A O3' P OP2 DC DI DI 6 7 7 Y 1 9.22 1.10 110.50 119.72 A A A O3' P OP2 DI DC DC 7 8 8 Y 1 A A O O HOH HOH 41 41 1.83 1_555 8_555 0.1500000 0.1500000 1.800 10.000 2254 1 2.000 TR isotropic TR isotropic 1.800 10.000 65 258 36 157 0 0.011 3.50 38.4 15.30 fix fix 1.800 16.000 159D 10245 2423 1 refinement X-PLOR SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX 1 N N 2 N N 3 N N 4 N N metalc 1.933 A DC 6 A OP2 DC 6 1_555 A MG 10 C MG MG 1_555 metalc 2.049 A MG 10 C MG MG 1_555 A HOH 11 D O HOH 1_555 metalc 2.018 A MG 10 C MG MG 1_555 A HOH 19 D O HOH 1_555 metalc 2.085 A MG 10 C MG MG 1_555 A HOH 20 D O HOH 1_555 DNA B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA 159D PDB 1 159D 1 8 159D 1 8 159D A 1 1 8 BINDING SITE FOR RESIDUE DMY A 9 A DMY 9 Software 16 BINDING SITE FOR RESIDUE MG A 10 A MG 10 Software 6 A DC 2 A DC 2 16 1_555 A DI 3 A DI 3 16 1_555 A DI 3 A DI 3 16 6_555 A DC 4 A DC 4 16 6_555 A DI 5 A DI 5 16 6_555 A DC 6 A DC 6 16 6_555 A DC 6 A DC 6 16 8_565 A DI 7 A DI 7 16 6_555 A DC 8 A DC 8 16 6_555 A HOH 14 D HOH 16 1_555 A HOH 22 D HOH 16 6_555 A HOH 33 D HOH 16 6_555 A HOH 33 D HOH 16 1_555 A HOH 49 D HOH 16 1_555 A HOH 53 D HOH 16 6_555 A HOH 67 D HOH 16 1_555 A DC 6 A DC 6 6 1_555 A HOH 11 D HOH 6 1_555 A HOH 13 D HOH 6 4_554 A HOH 16 D HOH 6 4_554 A HOH 19 D HOH 6 1_555 A HOH 20 D HOH 6 1_555 91 P 41 2 2