HEADER DNA 27-APR-99 1QBY TITLE THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE TITLE 2 OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN TITLE 3 OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 TITLE 4 SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP* G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL SOURCE 6 METHOD KEYWDS BENZ[A]ANTHRACENE-DNA DUPLEX, INTERCALATION EXPDTA SOLUTION NMR AUTHOR Z.LI,H.MAO,H.-Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS, AUTHOR 2 M.P.STONE REVDAT 3 24-FEB-09 1QBY 1 VERSN REVDAT 2 01-APR-03 1QBY 1 JRNL REVDAT 1 06-MAY-99 1QBY 0 JRNL AUTH Z.LI,H.MAO,H.Y.KIM,P.J.TAMURA,C.M.HARRIS, JRNL AUTH 2 T.M.HARRIS,M.P.STONE JRNL TITL INTERCALATION OF THE (-)-(1R,2S,3R, JRNL TITL 2 4S)-N6-[1-BENZ[A]ANTHRACENYL]-2'-DEOXYADENOSYL JRNL TITL 3 ADDUCT IN AN OLIGODEOXYNUCLEOTIDE CONTAINING THE JRNL TITL 4 HUMAN N-RAS CODON 61 SEQUENCE. JRNL REF BIOCHEMISTRY V. 38 2969 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10074349 JRNL DOI 10.1021/BI982072X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CORMA 5.2 REMARK 3 AUTHORS : BORGIAS,B.A., THOMAS,P.D., LI,H., KUMAR,A., AND REMARK 3 TONELLI,M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 509 NOE-DERIVED DISTANCE CONSTRAINTS, 95 EMPIRICAL SUGAR REMARK 3 PUCKER RESTRAINTS, 36 EMPIRICAL BACKBONE ANGLE DIHEDRAL REMARK 3 RESTRAINTS, AND 16 EMPIRICAL PLANARITY RESTRAINTS. REMARK 4 REMARK 4 1QBY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB ON 30-APR-99. REMARK 100 THE RCSB ID CODE IS RCSB009054. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL; 0.1 M REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM OLIGODEOXYNUCLEOTIDE; REMARK 210 10 MM PHOSPHATE BUFFER; 0.05 REMARK 210 MM EDTA; 0.1 M NACL; 1.6 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 : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, X-PLOR 3.1, 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: STRUCTURE WAS DETERMINED USING STANDARD 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT B 13 C5 DT B 13 C7 0.036 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 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.8 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 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.6 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 BZA A 66 DBREF 1QBY A 1 11 PDB 1QBY 1QBY 1 11 DBREF 1QBY B 12 22 PDB 1QBY 1QBY 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 BZA A 66 36 HETNAM BZA 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL FORMUL 3 BZA C18 H16 O3 LINK N6 DA A 6 C4C BZA A 66 1555 1555 1.34 SITE 1 AC1 6 DC A 5 DA A 6 DA A 7 DT B 16 SITE 2 AC1 6 DT B 17 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 MASTER 137 0 1 0 0 0 2 6 0 0 0 2 END