Header list of 1n8c.pdb file
Complete list - 23 20 Bytes
HEADER DNA 20-NOV-02 1N8C
TITLE SOLUTION STRUCTURE OF A CIS-OPENED (10R)-N6-DEOXYADENOSINE ADDUCT OF
TITLE 2 (9S,10R)-(9,10)-EPOXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE IN A DNA
TITLE 3 DUPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*TP*CP*AP*CP*GP*AP*GP*G)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*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
KEYWDS BENZO[A]PYRENE, 7, 8, 9, 10-TETRAHYDROBENZO[A]PYRENE, DNA
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR D.E.VOLK,V.THIVIYANATHAN,J.S.RICE,B.A.LUXON,J.H.SHAH,H.YAGI,
AUTHOR 2 J.M.SAYER,H.J.C.YEH,D.M.JERINA,D.G.GORENSTEIN
REVDAT 3 23-FEB-22 1N8C 1 REMARK LINK
REVDAT 2 24-FEB-09 1N8C 1 VERSN
REVDAT 1 14-FEB-03 1N8C 0
JRNL AUTH D.E.VOLK,V.THIVIYANATHAN,J.S.RICE,B.A.LUXON,J.H.SHAH,H.YAGI,
JRNL AUTH 2 J.M.SAYER,H.J.C.YEH,D.M.JERINA,D.G.GORENSTEIN
JRNL TITL SOLUTION STRUCTURE OF A CIS-OPENED (10R)-N6-DEOXYADENOSINE
JRNL TITL 2 ADDUCT OF (9S,10R)-(9,10)-EPOXY-7,8,9,
JRNL TITL 3 10-TETRAHYDROBENZO[A]PYRENE IN A DNA DUPLEX
JRNL REF BIOCHEMISTRY V. 42 1410 2003
JRNL REFN ISSN 0006-2960
JRNL PMID 12578353
JRNL DOI 10.1021/BI026745U
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 5.0, 6.0, AND 7.0
REMARK 3 AUTHORS :
REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,
REMARK 3 WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1N8C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-02.
REMARK 100 THE DEPOSITION ID IS D_1000017645.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 288
REMARK 210 PH : 6.7; 6.7
REMARK 210 IONIC STRENGTH : 100 MM; 100 MM
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX: 20 MM SODIUM
REMARK 210 PHOSPHATE (PH 6.7); 56 MM NACL;
REMARK 210 50 UM SODIUM AZIDE; 1 MM DUPLEX:
REMARK 210 20 MM SODIUM PHOSPHATE (PH 6.7);
REMARK 210 56 MM NACL; 50 UM SODIUM AZIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D ROESY;
REMARK 210 EXCHANGE-ONLY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1, MORASS 2.51
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 11
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : 10 STRUCTURES AND THEIR
REMARK 210 MINIMIZED AVERAGE WERE DEPOSITED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
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 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: 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 2 DC A 1 C5' DC A 1 C4' 0.048
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' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DC A 5 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DC B 12 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DC A 1 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DG A 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES
REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES
REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DT A 4 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 DT A 4 C5 - C4 - O4 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DA A 6 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DC A 7 N3 - C4 - N4 ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DC A 7 C5 - C4 - N4 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 DA A 9 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES
REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -6.6 DEGREES
REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES
REMARK 500 2 DC B 13 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES
REMARK 500 2 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES
REMARK 500 2 DT B 14 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES
REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DC B 15 N3 - C4 - C5 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DC B 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES
REMARK 500 2 DG B 16 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 251 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 DG A 8 0.07 SIDE CHAIN
REMARK 500 1 DG B 18 0.11 SIDE CHAIN
REMARK 500 2 DG A 3 0.10 SIDE CHAIN
REMARK 500 2 DT A 4 0.10 SIDE CHAIN
REMARK 500 2 DC A 5 0.12 SIDE CHAIN
REMARK 500 2 DA A 6 0.06 SIDE CHAIN
REMARK 500 2 DG A 8 0.07 SIDE CHAIN
REMARK 500 2 DG A 10 0.10 SIDE CHAIN
REMARK 500 2 DG A 11 0.06 SIDE CHAIN
REMARK 500 2 DT B 14 0.10 SIDE CHAIN
REMARK 500 2 DG B 18 0.18 SIDE CHAIN
REMARK 500 3 DC A 1 0.07 SIDE CHAIN
REMARK 500 3 DC A 5 0.10 SIDE CHAIN
REMARK 500 3 DG A 8 0.07 SIDE CHAIN
REMARK 500 3 DG B 18 0.08 SIDE CHAIN
REMARK 500 3 DA B 19 0.09 SIDE CHAIN
REMARK 500 3 DG B 22 0.12 SIDE CHAIN
REMARK 500 4 DT A 4 0.07 SIDE CHAIN
REMARK 500 4 DG A 8 0.08 SIDE CHAIN
REMARK 500 4 DG A 11 0.08 SIDE CHAIN
REMARK 500 4 DC B 12 0.08 SIDE CHAIN
REMARK 500 4 DG B 18 0.09 SIDE CHAIN
REMARK 500 4 DG B 22 0.07 SIDE CHAIN
REMARK 500 5 DG A 2 0.05 SIDE CHAIN
REMARK 500 5 DG A 3 0.07 SIDE CHAIN
REMARK 500 5 DT A 4 0.08 SIDE CHAIN
REMARK 500 5 DA A 6 0.06 SIDE CHAIN
REMARK 500 5 DG A 8 0.09 SIDE CHAIN
REMARK 500 5 DG A 11 0.08 SIDE CHAIN
REMARK 500 5 DC B 15 0.09 SIDE CHAIN
REMARK 500 5 DG B 18 0.13 SIDE CHAIN
REMARK 500 5 DG B 22 0.07 SIDE CHAIN
REMARK 500 6 DT A 4 0.07 SIDE CHAIN
REMARK 500 6 DG A 8 0.08 SIDE CHAIN
REMARK 500 6 DA A 9 0.06 SIDE CHAIN
REMARK 500 6 DC B 15 0.07 SIDE CHAIN
REMARK 500 6 DG B 18 0.13 SIDE CHAIN
REMARK 500 6 DC B 21 0.11 SIDE CHAIN
REMARK 500 7 DG B 18 0.12 SIDE CHAIN
REMARK 500 8 DT A 4 0.10 SIDE CHAIN
REMARK 500 8 DG A 8 0.08 SIDE CHAIN
REMARK 500 8 DA A 9 0.06 SIDE CHAIN
REMARK 500 8 DG B 18 0.14 SIDE CHAIN
REMARK 500 8 DG B 22 0.06 SIDE CHAIN
REMARK 500 9 DG A 2 0.06 SIDE CHAIN
REMARK 500 9 DC A 5 0.06 SIDE CHAIN
REMARK 500 9 DC A 7 0.10 SIDE CHAIN
REMARK 500 9 DA A 9 0.06 SIDE CHAIN
REMARK 500 9 DG A 11 0.07 SIDE CHAIN
REMARK 500 9 DG B 18 0.13 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 61 PLANE 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 TBC A 23
DBREF 1N8C A 1 11 PDB 1N8C 1N8C 1 11
DBREF 1N8C B 12 22 PDB 1N8C 1N8C 12 22
SEQRES 1 A 11 DC DG DG DT DC DA DC DG DA DG DG
SEQRES 1 B 11 DC DC DT DC DG DT DG DA DC DC DG
HET TBC A 23 36
HETNAM TBC (9S,10R)-9-HYDROXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE
FORMUL 3 TBC C20 H16 O
LINK N6 DA A 6 C10 TBC A 23 1555 1555 1.38
SITE 1 AC1 5 DC A 5 DA A 6 DC A 7 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
MODEL 1
Complete list - 23 20 Bytes