HEADER DNA 02-OCT-02 1MXK TITLE NMR STRUCTURE OF HO2-CO(III)BLEOMYCIN A(2) BOUND TO D(GGAAGCTTCC)(2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*AP*AP*GP*CP*TP*TP*CP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DRUG-DNA COMPLEX, COBALT(III), DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR C.ZHAO,C.XIA,Q.MAO,H.FORSTERLING,E.DEROSE,W.E.ANTHOLINE, AUTHOR 2 W.K.SUBCZYNSKI,D.H.PETERING REVDAT 3 23-FEB-22 1MXK 1 REMARK LINK REVDAT 2 24-FEB-09 1MXK 1 VERSN REVDAT 1 16-OCT-02 1MXK 0 JRNL AUTH C.ZHAO,C.XIA,Q.MAO,H.FORSTERLING,E.DEROSE,W.E.ANTHOLINE, JRNL AUTH 2 W.K.SUBCZYNSKI,D.H.PETERING JRNL TITL STRUCTURES OF HO(2)-CO(III)BLEOMYCIN A(2) BOUND TO JRNL TITL 2 D(GAGCTC)(2) AND D(GGAAGCTTCC)(2): STRUCTURE-REACTIVITY JRNL TITL 3 RELATIONSHIPS OF CO AND FE BLEOMYCINS JRNL REF J.INORG.BIOCHEM. V. 91 259 2002 JRNL REFN ISSN 0162-0134 JRNL PMID 12121784 JRNL DOI 10.1016/S0162-0134(02)00420-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.3, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER INSTR. (XWINNMR), AXEL BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 424 DISTANCE REMARK 3 RESTRAINTS (333 INTRAMOLECULAR DNA, 66 INTRAMOLECULAR BLEOMYCIN REMARK 3 AND 25 INTERMOLECULAR). REMARK 4 REMARK 4 1MXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017282. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.1 M NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM BLEOMYCIN/DNA COMPLEX; 20 MM REMARK 210 PHOSPHATE BUFFER; 0.1 M NACL; REMARK 210 2MM BLEOMYCIN/DNA COMPLEX; 20 MM REMARK 210 PHOSPHATE BUFFER; 0.1 M NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 31P/1H-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2.3 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1 PEO A 23 HNK BLM B 21 1.39 REMARK 500 O2 DC A 9 H21 DG B 12 1.51 REMARK 500 H21 DG A 1 O2 DC B 20 1.56 REMARK 500 O2 DC A 10 H21 DG B 11 1.57 REMARK 500 H21 DG A 2 O2 DC B 19 1.58 REMARK 500 H41 DC A 6 O6 DG B 15 1.59 REMARK 500 O6 DG A 5 H41 DC B 16 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 14 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 3CO A 22 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PEO A 23 O1 REMARK 620 2 PEO A 23 O2 27.3 REMARK 620 3 BLM B 21 NG 89.7 72.8 REMARK 620 4 BLM B 21 NC 90.7 68.1 83.8 REMARK 620 5 BLM B 21 NB 177.3 150.7 90.5 86.6 REMARK 620 6 BLM B 21 NH 92.2 110.9 84.3 167.7 90.5 REMARK 620 7 BLM B 21 NJ 85.4 104.2 173.4 100.7 94.6 91.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3CO A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLM B 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEO A 23 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MTG RELATED DB: PDB REMARK 900 1MTG IS HO2-CO(III)BLEOMYCIN-A(2) BOUND TO D(GAGCTC)(2) DBREF 1MXK A 1 10 PDB 1MXK 1MXK 1 10 DBREF 1MXK B 11 20 PDB 1MXK 1MXK 11 20 SEQRES 1 A 10 DG DG DA DA DG DC DT DT DC DC SEQRES 1 B 10 DG DG DA DA DG DC DT DT DC DC HET 3CO A 22 1 HET PEO A 23 3 HET BLM B 21 179 HETNAM 3CO COBALT (III) ION HETNAM PEO HYDROGEN PEROXIDE HETNAM BLM BLEOMYCIN A2 HETSYN BLM N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE FORMUL 3 3CO CO 3+ FORMUL 4 PEO H2 O2 FORMUL 5 BLM C55 H85 N17 O21 S3 LINK CO 3CO A 22 O1 PEO A 23 1555 1555 1.84 LINK CO 3CO A 22 O2 PEO A 23 1555 1555 2.75 LINK CO 3CO A 22 NG BLM B 21 1555 1555 1.84 LINK CO 3CO A 22 NC BLM B 21 1555 1555 2.06 LINK CO 3CO A 22 NB BLM B 21 1555 1555 2.15 LINK CO 3CO A 22 NH BLM B 21 1555 1555 1.93 LINK CO 3CO A 22 NJ BLM B 21 1555 1555 2.00 SITE 1 AC1 2 PEO A 23 BLM B 21 SITE 1 AC2 12 DG A 5 DC A 6 DT A 7 3CO A 22 SITE 2 AC2 12 PEO A 23 DA B 13 DA B 14 DG B 15 SITE 3 AC2 12 DC B 16 DT B 17 DT B 18 DC B 19 SITE 1 AC3 2 3CO A 22 BLM B 21 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000