1MXK - Header Asymmetric Unit

HEADER DNA 02-OCT-02 1MXK

TITLE NMR STRUCTURE OF HO2-CO(III)BLEOMYCIN A(2) BOUND TO TITLE 2 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)

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 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, JRNL AUTH 2 W.E.ANTHOLINE,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): JRNL TITL 3 STRUCTURE-REACTIVITY RELATIONSHIPS OF CO AND FE JRNL TITL 4 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 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : AXEL BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 424 REMARK 3 DISTANCE RESTRAINTS (333 INTRAMOLECULAR DNA, 66 INTRAMOLECULAR REMARK 3 BLEOMYCIN AND 25 INTERMOLECULAR).

REMARK 4 REMARK 4 1MXK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB017282.

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 REMARK 210 MM PHOSPHATE BUFFER; 0.1 M REMARK 210 NACL; 2MM BLEOMYCIN/DNA REMARK 210 COMPLEX; 20 MM PHOSPHATE REMARK 210 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 : XWINNMR 1.3, FELIX 2.3 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR 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 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 BLM B 21 NG REMARK 620 2 PEO A 23 O1 89.7 REMARK 620 3 BLM B 21 NC 83.8 90.7 REMARK 620 4 BLM B 21 NB 90.5 177.3 86.6 REMARK 620 5 BLM B 21 NH 84.3 92.2 167.7 90.5 REMARK 620 6 BLM B 21 NJ 173.4 85.4 100.7 94.6 91.5 REMARK 620 7 PEO A 23 O2 72.8 27.3 68.1 150.7 110.9 104.2 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLM B 21 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 BLM B 21 179 HET PEO A 23 3

HETNAM 3CO COBALT (III) ION HETNAM BLM BLEOMYCIN A2 HETNAM PEO HYDROGEN PEROXIDE

HETSYN BLM N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE

FORMUL 3 3CO CO 3+ FORMUL 4 BLM C55 H85 N17 O21 S3 FORMUL 5 PEO H2 O2

LINK NG BLM B 21 CO 3CO A 22 1555 1555 1.84 LINK CO 3CO A 22 O1 PEO A 23 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 LINK CO 3CO A 22 O2 PEO A 23 1555 1555 2.75

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