10 20 30 40 50 60 70 80 1AXV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 21-OCT-97 1AXV
TITLE SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN TITLE 2 A DNA DUPLEX, 6 STRUCTURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DUPLEX D(CTCTC-[BP]A-CTTCC)D(GGAAGTGAGAG); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C10 ATOM OF BP-ADDUCT LINKED TO N6 ATOM OF COMPND 6 DA6; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA DUPLEX D(CTCTC-[BP]A-CTTCC)D(GGAAGTGAGAG); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: C10 ATOM OF BP-ADDUCT LINKED TO N6 ATOM OF COMPND 12 DA6
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS DNA DUPLEX, BENZO[A]PYRENE ADDUCT, CARCINOGEN ADDUCT
EXPDTA SOLUTION NMR
NUMMDL 6
AUTHOR B.MAO,Z.GU,A.A.GORIN,J.CHEN,B.E.HINGERTY,S.AMID,S.BROYDE, AUTHOR 2 N.E.GEACINTOV,D.J.PATEL
REVDAT 3 24-FEB-09 1AXV 1 VERSN REVDAT 2 01-APR-03 1AXV 1 JRNL REVDAT 1 01-JUL-98 1AXV 0
JRNL AUTH B.MAO,Z.GU,A.GORIN,J.CHEN,B.E.HINGERTY,S.AMIN, JRNL AUTH 2 S.BROYDE,N.E.GEACINTOV,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE JRNL TITL 2 (+)-CIS-ANTI-BENZO[A]PYRENE-DA ([BP]DA) ADDUCT JRNL TITL 3 OPPOSITE DT IN A DNA DUPLEX. JRNL REF BIOCHEMISTRY V. 38 10831 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10451380 JRNL DOI 10.1021/BI991212F
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE.
REMARK 4 REMARK 4 1AXV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 322 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN UNITY PLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, DUPLEX, X-PLOR REMARK 210 METHOD USED : RELAXATION MATRIX REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CONFORMERS PRESENTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL
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 1 DT A 2 C5 DT A 2 C7 0.044 REMARK 500 1 DT A 4 C5 DT A 4 C7 0.039 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.045 REMARK 500 1 DT B 17 C5 DT B 17 C7 0.044 REMARK 500 1 DG B 18 C5' DG B 18 C4' 0.051 REMARK 500 2 DT A 2 C5 DT A 2 C7 0.040 REMARK 500 2 DG B 13 C5' DG B 13 C4' 0.045 REMARK 500 2 DA B 14 C5' DA B 14 C4' 0.046 REMARK 500 3 DT A 2 C5 DT A 2 C7 0.045 REMARK 500 3 DA A 6 C5' DA A 6 C4' 0.064 REMARK 500 3 DG B 13 C3' DG B 13 C2' -0.059 REMARK 500 3 DT B 17 C5 DT B 17 C7 0.037 REMARK 500 3 DG B 18 C5' DG B 18 C4' 0.059 REMARK 500 4 DT A 4 C5 DT A 4 C7 0.048 REMARK 500 4 DT A 9 C5' DT A 9 C4' 0.062 REMARK 500 4 DA B 14 C5' DA B 14 C4' 0.042 REMARK 500 5 DT A 2 C5 DT A 2 C7 0.040 REMARK 500 5 DT A 9 C5' DT A 9 C4' 0.049 REMARK 500 5 DT A 9 C5 DT A 9 C7 0.039 REMARK 500 5 DG B 13 C3' DG B 13 C2' -0.053 REMARK 500 5 DA B 14 C3' DA B 14 C2' -0.054 REMARK 500 5 DA B 15 C5' DA B 15 C4' 0.055 REMARK 500 5 DT B 17 C2' DT B 17 C1' 0.061 REMARK 500 6 DT A 2 C5 DT A 2 C7 0.041 REMARK 500 6 DT A 4 C5 DT A 4 C7 0.045 REMARK 500 6 DT B 17 C5 DT B 17 C7 0.045 REMARK 500 6 DG B 18 P DG B 18 O5' 0.066 REMARK 500 6 DG B 18 C5' DG B 18 C4' 0.064 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 1 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 2 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 3 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC A 5 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N6 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 7 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DT A 8 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 8 N1 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DT A 8 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 15 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG B 16 C1' - O4' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT B 17 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT B 17 C4' - C3' - O3' ANGL. DEV. = 12.4 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG B 18 C5' - C4' - C3' ANGL. DEV. = 13.1 DEGREES REMARK 500 1 DG B 18 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT B 17 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG B 18 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DA B 19 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 2 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DC A 3 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA A 6 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DC A 7 C5' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DC A 7 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA A 6 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 2 DT A 8 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DT A 8 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DA B 15 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT B 17 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 169 ANGLE DEVIATIONS. 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 BAP A 23
DBREF 1AXV A 1 11 PDB 1AXV 1AXV 1 11 DBREF 1AXV B 12 22 PDB 1AXV 1AXV 12 22
SEQRES 1 A 11 DC DT DC DT DC DA DC DT DT DC DC SEQRES 1 B 11 DG DG DA DA DG DT DG DA DG DA DG
HET BAP A 23 38
HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
FORMUL 3 BAP C20 H16 O3
LINK C4' BAP A 23 N6 DA A 6 1555 1555 1.49
SITE 1 AC1 4 DC A 5 DA A 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