1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Zhao, C. Xia, C. Mao, Q. Forsterling, H. DeRose, E. Antholine, W.E. Subczynski, W.K. Petering, D.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic Co 3 58.933 COBALT (III) ION non-polymer C55 H85 N17 O21 S3 1416.560 BLEOMYCIN A2 N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE 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 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O2 34.015 HYDROGEN PEROXIDE non-polymer US J.Inorg.Biochem. JIBIDJ 0525 0162-0134 91 259 268 10.1016/S0162-0134(02)00420-8 12121784 Structures of HO(2)-Co(III)bleomycin A(2) Bound to d(GAGCTC)(2) and d(GGAAGCTTCC)(2): Structure-Reactivity Relationships of Co and Fe Bleomycins 2002 10.2210/pdb1mxk/pdb pdb_00001mxk 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 SINGLE WAVELENGTH M 1 1.0 3045.005 5'-D(*GP*GP*AP*AP*GP*CP*TP*TP*CP*C)-3' 2 syn polymer 58.933 COBALT (III) ION 1 syn non-polymer 34.015 HYDROGEN PEROXIDE 1 syn non-polymer 1416.560 BLEOMYCIN A2 1 syn non-polymer no no (DG)(DG)(DA)(DA)(DG)(DC)(DT)(DT)(DC)(DC) GGAAGCTTCC A,B polydeoxyribonucleotide n n n n n n n n n n -0.202 1 19 A 1 B 20 1.464 A_DG1:DC20_B 1 -1.191 -0.604 0.039 -0.377 1.945 1 19 A 2 B 19 2.018 A_DG2:DC19_B 2 -2.138 -0.630 -0.063 -0.350 3.656 1 20 A 3 B 18 0.301 A_DA3:DT18_B 3 -5.133 0.005 -0.019 -0.199 2.247 1 20 A 4 B 17 2.320 A_DA4:DT17_B 4 -5.839 -0.158 -0.067 0.159 -4.357 1 19 A 5 B 16 -11.625 A_DG5:DC16_B 5 1.056 0.186 -0.281 -0.088 15.841 1 19 A 6 B 15 -10.751 A_DC6:DG15_B 6 -10.448 -0.629 -0.143 -0.152 -13.072 A 7 B 14 13.680 A_DT7:DA14_B 7 6.348 -0.322 -0.169 0.395 -4.407 1 20 A 8 B 13 -4.803 A_DT8:DA13_B 8 -1.040 -0.041 -0.109 -0.213 2.843 1 19 A 9 B 12 6.420 A_DC9:DG12_B 9 -4.402 0.723 -0.052 -0.189 -2.836 1 19 A 10 B 11 0.980 A_DC10:DG11_B 10 0.335 0.516 0.146 -0.362 3.488 37.140 A A 1 2 -10.977 B B 20 19 3.421 -6.952 0.140 -0.670 AA_DG1DG2:DC19DC20_BB 1 1.020 -1.611 36.492 -0.063 -0.075 3.210 34.889 A A 2 3 -4.092 B B 19 18 3.159 -2.452 -0.365 -0.888 AA_DG2DA3:DT18DC19_BB 2 0.266 -0.444 34.805 -1.119 0.648 3.359 33.716 A A 3 4 -4.799 B B 18 17 3.274 -2.780 -0.030 -1.199 AA_DA3DA4:DT17DT18_BB 3 -0.636 1.098 33.599 -1.609 -0.054 3.204 32.765 A A 4 5 10.817 B B 17 16 3.352 6.064 -1.461 -1.008 AA_DA4DG5:DC16DT17_BB 4 -2.208 3.938 32.140 -2.844 2.205 2.452 29.091 A A 5 6 -0.662 B B 16 15 2.396 -0.333 -1.186 0.061 AA_DG5DC6:DG15DC16_BB 5 -1.519 3.025 29.050 0.175 2.115 6.168 38.326 A A 6 7 20.261 B B 15 14 6.306 13.047 1.938 1.000 AA_DC6DT7:DA14DG15_BB 6 -2.157 3.350 36.052 -1.696 -3.484 2.809 30.038 A A 7 8 25.286 B B 14 13 3.151 12.710 -1.168 -0.138 AA_DT7DT8:DA13DA14_BB 7 0.011 -0.021 27.273 -2.765 2.256 3.216 37.327 A A 8 9 1.503 B B 13 12 3.192 0.961 0.745 -0.131 AA_DT8DC9:DG12DA13_BB 8 1.606 -2.510 37.281 -0.328 -0.957 3.713 41.524 A A 9 10 -14.969 B B 12 11 3.660 -10.462 -0.589 -0.479 AA_DC9DC10:DG11DG12_BB 9 -6.800 9.730 39.684 0.609 -0.004 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-10-16 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1mtg is HO2-Co(III)bleomycin-A(2) bound to d(GAGCTC)(2) RCSB Y RCSB 2002-10-02 REL REL 3CO COBALT (III) ION PEO HYDROGEN PEROXIDE BLM BLEOMYCIN A2 This structure was determined using standard 2D homonuclear techniques 1 2D NOESY 2D TOCSY DQF-COSY 31P/1H-COSY 0.1 M NaCl 7.4 ambient 298 K The structure is based on 424 distance restraints (333 intramolecular DNA, 66 intramolecular bleomycin and 25 intermolecular). Simulated Annealing, Molecular Dynamics minimized average structure 2mM Bleomycin/DNA complex; 20 mM phosphate buffer; 0.1 M NaCl 90% H2O/10% D2O 2mM Bleomycin/DNA complex; 20 mM phosphate buffer; 0.1 M NaCl D2O Bruker Instr. collection XwinNMR 1.3 Biosym data analysis Felix 2.3 Axel Brunger refinement X-PLOR 3.1 500 Bruker DRX 3CO 22 2 3CO 3CO 22 A PEO 23 3 PEO PEO 23 A BLM 21 4 BLM BLM 21 B GUA 1 n 1 DG 1 A GUA 2 n 2 DG 2 A ADE 3 n 3 DA 3 A ADE 4 n 4 DA 4 A GUA 5 n 5 DG 5 A CYT 6 n 6 DC 6 A THY 7 n 7 DT 7 A THY 8 n 8 DT 8 A CYT 9 n 9 DC 9 A CYT 10 n 10 DC 10 A GUA 11 n 1 DG 11 B GUA 12 n 2 DG 12 B ADE 13 n 3 DA 13 B ADE 14 n 4 DA 14 B GUA 15 n 5 DG 15 B CYT 16 n 6 DC 16 B THY 17 n 7 DT 17 B THY 18 n 8 DT 18 B CYT 19 n 9 DC 19 B CYT 20 n 10 DC 20 B author_defined_assembly 2 dimeric A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 A PEO 23 D O2 PEO 1_555 27.3 A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NG BLM 1_555 89.7 A PEO 23 D O2 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NG BLM 1_555 72.8 A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NC BLM 1_555 90.7 A PEO 23 D O2 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NC BLM 1_555 68.1 B BLM 21 E NG BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NC BLM 1_555 83.8 A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NB BLM 1_555 177.3 A PEO 23 D O2 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NB BLM 1_555 150.7 B BLM 21 E NG BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NB BLM 1_555 90.5 B BLM 21 E NC BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NB BLM 1_555 86.6 A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 92.2 A PEO 23 D O2 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 110.9 B BLM 21 E NG BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 84.3 B BLM 21 E NC BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 167.7 B BLM 21 E NB BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 90.5 A PEO 23 D O1 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 85.4 A PEO 23 D O2 PEO 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 104.2 B BLM 21 E NG BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 173.4 B BLM 21 E NC BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 100.7 B BLM 21 E NB BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 94.6 B BLM 21 E NH BLM 1_555 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 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 A B O1 HNK PEO BLM 23 21 1.39 1 A B O2 H21 DC DG 9 12 1.51 1 A B H21 O2 DG DC 1 20 1.56 1 A B O2 H21 DC DG 10 11 1.57 1 A B H21 O2 DG DC 2 19 1.58 1 A B H41 O6 DC DG 6 15 1.59 1 A B O6 H41 DG DC 5 16 1.60 1 2.89 0.30 108.30 111.19 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 4.48 0.50 113.10 117.58 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 DG DG DG 1 1 1 N 1 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.57 0.50 113.10 117.67 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 2.93 0.30 108.30 111.23 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 3.77 0.50 113.80 117.57 A A A N7 C8 N9 DA DA DA 3 3 3 N 1 2.83 0.30 108.30 111.13 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.89 0.50 113.80 117.69 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 4.18 0.30 108.30 112.48 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 4.51 0.50 113.10 117.61 A A A N7 C8 N9 DG DG DG 5 5 5 N 1 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 DG DG DG 5 5 5 N 1 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -3.79 0.60 122.90 119.11 A A A C6 C5 C7 DT DT DT 7 7 7 N 1 3.43 0.30 108.30 111.73 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 2.79 0.30 108.30 111.09 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 2.91 0.30 108.30 111.21 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 4.46 0.50 113.10 117.56 B B B N7 C8 N9 DG DG DG 11 11 11 N 1 -2.57 0.40 106.40 103.83 B B B C8 N9 C4 DG DG DG 11 11 11 N 1 2.59 0.30 108.30 110.89 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 4.62 0.50 113.10 117.72 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 -2.56 0.40 106.40 103.84 B B B C8 N9 C4 DG DG DG 12 12 12 N 1 2.61 0.30 108.30 110.91 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 3.90 0.50 113.80 117.70 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 3.39 0.30 108.30 111.69 B B B O4' C1' N9 DA DA DA 14 14 14 N 1 3.74 0.50 113.80 117.54 B B B N7 C8 N9 DA DA DA 14 14 14 N 1 2.47 0.30 108.30 110.77 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 4.60 0.50 113.10 117.70 B B B N7 C8 N9 DG DG DG 15 15 15 N 1 -2.73 0.40 106.40 103.67 B B B C8 N9 C4 DG DG DG 15 15 15 N 1 3.88 0.30 108.30 112.18 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 3.35 0.30 108.30 111.65 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 2.48 0.30 108.30 110.78 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 3.97 0.30 108.30 112.27 B B B O4' C1' N1 DC DC DC 19 19 19 N 1 2.73 0.30 108.30 111.03 B B B O4' C1' N1 DC DC DC 20 20 20 N minimized average NMR Structure of HO2-Co(III)bleomycin A(2) Bound to d(GGAAGCTTCC)(2) 1 N N 1 N N 2 N N 3 N N 4 N N metalc 1.839 A 3CO 22 C CO 3CO 1_555 A PEO 23 D O1 PEO 1_555 metalc 2.749 A 3CO 22 C CO 3CO 1_555 A PEO 23 D O2 PEO 1_555 metalc 1.837 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NG BLM 1_555 metalc 2.062 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NC BLM 1_555 metalc 2.154 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NB BLM 1_555 metalc 1.928 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NH BLM 1_555 metalc 2.004 A 3CO 22 C CO 3CO 1_555 B BLM 21 E NJ BLM 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 20 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 20 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 20 B N4 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 19 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 19 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 19 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 17 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 17 B O4 DT 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 DT-DA PAIR A DT 7 A N3 DT 7 1_555 B DA 14 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 13 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 13 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 12 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 12 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 12 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA DRUG-DNA COMPLEX, COBALT(III), DNA 1MXK PDB 1 1MXK 1 10 1MXK 1 10 1MXK A 1 1 10 11 20 1MXK 11 20 1MXK B 1 1 10 BINDING SITE FOR RESIDUE 3CO A 22 A 3CO 22 Software 2 BINDING SITE FOR RESIDUE BLM B 21 B BLM 21 Software 12 BINDING SITE FOR RESIDUE PEO A 23 A PEO 23 Software 2 A PEO 23 D PEO 2 1_555 B BLM 21 E BLM 2 1_555 A DG 5 A DG 5 12 1_555 A DC 6 A DC 6 12 1_555 A DT 7 A DT 7 12 1_555 A 3CO 22 C 3CO 12 1_555 A PEO 23 D PEO 12 1_555 B DA 13 B DA 3 12 1_555 B DA 14 B DA 4 12 1_555 B DG 15 B DG 5 12 1_555 B DC 16 B DC 6 12 1_555 B DT 17 B DT 7 12 1_555 B DT 18 B DT 8 12 1_555 B DC 19 B DC 9 12 1_555 A 3CO 22 C 3CO 2 1_555 B BLM 21 E BLM 2 1_555