1DJD - Header Asymmetric Unit

HEADER DNA 02-DEC-99 1DJD

TITLE THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R- TITLE 2 BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF TITLE 3 ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N- TITLE 4 RAS CODON 61 SEQUENCE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA(5'-D(*CT*GT*GT*AT*CT*AT*AT*GT*AT*AT*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA(5'-D(*CT*TT*TT*CT*TT*TT*GT*TT*CT*CT*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OBSERVED IN HUMAN N-RAS CODON 61; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES

KEYWDS BENZ[A]ANTHRACENE-DNA DUPLEX

EXPDTA SOLUTION NMR

AUTHOR Z.LI,H.Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS,M.P.STONE

REVDAT 2 24-FEB-09 1DJD 1 VERSN REVDAT 1 16-DEC-99 1DJD 0

JRNL AUTH Z.LI,H.Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS, JRNL AUTH 2 M.P.STONE JRNL TITL ROLE OF A POLYCYCLIC AROMATIC HYDROCARBON BAY JRNL TITL 2 REGION RING IN MODULATING DNA ADDUCT STRUCTURE: JRNL TITL 3 THE NON-BAY REGION (8S,9R,10S, JRNL TITL 4 11R)-N(6)-[11-(8,9,10,11-TETRAHYDRO-8,9, JRNL TITL 5 10-TRIHYDROXYBENZ[A]ANTHRACENYL)]-2' JRNL TITL 6 -DEOXYADENOSYL ADDUCT IN CODON 61 OF THE HUMAN JRNL TITL 7 N-RAS PROTOONCOGENE JRNL REF BIOCHEMISTRY V. 38 14820 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10555964 JRNL DOI 10.1021/BI991607Z

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CORMA 5.2 REMARK 3 AUTHORS : BORGIAS, THOMAS, LI, KUMAR, TONELLI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 475 NOE DERIVED DISTANCE CONSTRAINTS, 55 EMPIRICAL SUGAR REMARK 3 PUCKER RESTRAINTS, 35 EMPIRICAL BACKBONE ANGLE RESTRAINTS, AND REMARK 3 18 EMPIRICAL PLANARITY RESTRAINTS.

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-99. REMARK 100 THE RCSB ID CODE IS RCSB010129.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 293 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.8 MM OLIGODEOXYNUCLEOTIDE; REMARK 210 10 MM PHOSPHATE BUFFER; 0.05 REMARK 210 MM EDTA; 0.1 M NACL; 1.8 MM REMARK 210 OLIGODEOXYNUCLEOTIDE; 10 MM REMARK 210 PHOSPHATE BUFFER; 0.05 MM REMARK 210 EDTA; 0.1 M NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, X-PLOR 3.851, REMARK 210 FELIX 97.0, MARDIGRAS 3.0 REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR REMARK 210 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBT A 25

DBREF 1DJD A 1 11 PDB 1DJD 1DJD 1 11 DBREF 1DJD B 12 22 PDB 1DJD 1DJD 12 22

SEQRES 1 A 11 DC DG DG DA DC DA DA DG DA DA DG SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG

HET TBT A 25 36

HETNAM TBT 8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL

FORMUL 3 TBT C18 H16 O3

LINK C4C TBT A 25 N6 DA A 6 1555 1555 1.34

SITE 1 AC1 5 DA A 6 DA A 7 DT B 16 DT B 17 SITE 2 AC1 5 DG B 18

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