Header list of 1y9h.pdb file
Complete list - 2 20 Bytes
HEADER DNA 15-DEC-04 1Y9H
TITLE METHYLATION OF CYTOSINE AT C5 IN A CPG SEQUENCE CONTEXT CAUSES A
TITLE 2 CONFORMATIONAL SWITCH OF A BENZO[A]PYRENE DIOL EPOXIDE-N2-GUANINE
TITLE 3 ADDUCT IN DNA FROM A MINOR GROOVE ALIGNMENT TO INTERCALATION WITH
TITLE 4 BASE DISPLACEMENT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: BP ATTACHED TO G6, METHYLATION OF C5;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES
KEYWDS CONFORMATIONAL SWITCH, CYTOSINE METHYLATION, P53 MUTATION HOT SPOT,
KEYWDS 2 DNA ADDUCT, BENZO[A]PYRENE, BPDE, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR N.ZHANG,C.LIN,X.HUANG,A.KOLBANOVSKIY,B.E.HINGERTY,S.AMIN,S.BROYDE,
AUTHOR 2 N.E.GEACINTOV,D.J.PATEL
REVDAT 3 02-MAR-22 1Y9H 1 REMARK LINK
REVDAT 2 24-FEB-09 1Y9H 1 VERSN
REVDAT 1 22-MAR-05 1Y9H 0
JRNL AUTH N.ZHANG,C.LIN,X.HUANG,A.KOLBANOVSKIY,B.E.HINGERTY,S.AMIN,
JRNL AUTH 2 S.BROYDE,N.E.GEACINTOV,D.J.PATEL
JRNL TITL METHYLATION OF CYTOSINE AT C5 IN A CPG SEQUENCE CONTEXT
JRNL TITL 2 CAUSES A CONFORMATIONAL SWITCH OF A BENZO[A]PYRENE DIOL
JRNL TITL 3 EPOXIDE-N2-GUANINE ADDUCT IN DNA FROM A MINOR GROOVE
JRNL TITL 4 ALIGNMENT TO INTERCALATION WITH BASE DISPLACEMENT.
JRNL REF J.MOL.BIOL. V. 346 951 2005
JRNL REFN ISSN 0022-2836
JRNL PMID 15701509
JRNL DOI 10.1016/J.JMB.2004.12.027
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: NULL
REMARK 4
REMARK 4 1Y9H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000031284.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 273
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 100 MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 11MER DNA DUPLEX WITH MEC5 AND
REMARK 210 [BP]G6 MODIFIED, H2O AND D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR
REMARK 210 DYNAMICS MATRIX RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 9
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED,BACK CALCULATED DATA
REMARK 210 AGREE WITH EXPERIMENTAL NOESY
REMARK 210 SPECTRUM,STRUCTURES WITH
REMARK 210 ACCEPTABLE COVALENT GEOMETRY,
REMARK 210 STRUCTURES WITH FAVORABLE NON-
REMARK 210 BOND ENERGY,STRUCTURES WITH THE
REMARK 210 LEAST RESTRAINT VIOLATIONS,
REMARK 210 STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY,TARGET FUNCTION
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 N2 DG A 6 C4' BAP A 23 1.49
REMARK 500 O2 DC A 11 H21 DG B 12 1.55
REMARK 500 O2 5CM A 5 H21 DG B 18 1.55
REMARK 500
REMARK 500 REMARK: NULL
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 4 C3' DT A 4 C2' -0.070
REMARK 500 1 DT A 4 C5 DT A 4 C7 0.039
REMARK 500 1 DT A 8 C5 DT A 8 C7 0.050
REMARK 500 1 DA A 9 C4' DA A 9 C3' -0.060
REMARK 500 1 DA A 9 C3' DA A 9 C2' -0.051
REMARK 500 1 DC A 11 C3' DC A 11 C2' -0.059
REMARK 500 1 DC A 11 C2' DC A 11 C1' -0.078
REMARK 500 1 DT B 14 C5 DT B 14 C7 0.044
REMARK 500 1 DT B 20 C5 DT B 20 C7 0.055
REMARK 500 2 DT A 4 C3' DT A 4 C2' -0.080
REMARK 500 2 DT A 4 C5 DT A 4 C7 0.039
REMARK 500 2 DT A 8 C5 DT A 8 C7 0.050
REMARK 500 2 DA A 9 C3' DA A 9 C2' -0.051
REMARK 500 2 DT B 14 C5 DT B 14 C7 0.037
REMARK 500 2 DT B 20 C5 DT B 20 C7 0.041
REMARK 500 3 DT A 4 C3' DT A 4 C2' -0.083
REMARK 500 3 DT A 4 C5 DT A 4 C7 0.042
REMARK 500 3 DT A 8 C5 DT A 8 C7 0.049
REMARK 500 3 DA A 9 C3' DA A 9 C2' -0.058
REMARK 500 3 DT B 20 C5 DT B 20 C7 0.046
REMARK 500 4 DC A 2 C3' DC A 2 C2' -0.049
REMARK 500 4 DT A 4 C5 DT A 4 C7 0.043
REMARK 500 4 DT A 8 C5 DT A 8 C7 0.045
REMARK 500 4 DA A 9 C3' DA A 9 C2' -0.051
REMARK 500 4 DT B 14 C5 DT B 14 C7 0.042
REMARK 500 4 DT B 20 C5 DT B 20 C7 0.047
REMARK 500 5 DC A 2 C3' DC A 2 C2' -0.051
REMARK 500 5 DT A 4 C3' DT A 4 C2' -0.074
REMARK 500 5 DT A 8 C5 DT A 8 C7 0.049
REMARK 500 5 DA A 9 C4' DA A 9 C3' -0.064
REMARK 500 5 DA A 9 C3' DA A 9 C2' -0.052
REMARK 500 5 DT B 14 C5 DT B 14 C7 0.038
REMARK 500 5 DT B 20 C5 DT B 20 C7 0.040
REMARK 500 6 DC A 2 C3' DC A 2 C2' -0.051
REMARK 500 6 DT A 4 C3' DT A 4 C2' -0.083
REMARK 500 6 DT A 4 C5 DT A 4 C7 0.042
REMARK 500 6 DT A 8 C5 DT A 8 C7 0.050
REMARK 500 6 DA A 9 C3' DA A 9 C2' -0.052
REMARK 500 6 DT B 14 C5 DT B 14 C7 0.041
REMARK 500 6 DT B 20 C5 DT B 20 C7 0.051
REMARK 500 7 DT A 4 C4' DT A 4 C3' -0.065
REMARK 500 7 DT A 4 C3' DT A 4 C2' -0.053
REMARK 500 7 DT A 4 C5 DT A 4 C7 0.046
REMARK 500 7 DT A 8 C5 DT A 8 C7 0.047
REMARK 500 7 DA A 9 C4' DA A 9 C3' -0.062
REMARK 500 7 DA A 9 C3' DA A 9 C2' -0.056
REMARK 500 7 DC A 11 C3' DC A 11 C2' -0.060
REMARK 500 7 DC A 11 C2' DC A 11 C1' -0.077
REMARK 500 7 DT B 20 C5 DT B 20 C7 0.038
REMARK 500 8 DT A 4 C3' DT A 4 C2' -0.075
REMARK 500
REMARK 500 THIS ENTRY HAS 61 BOND DEVIATIONS.
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. = -9.8 DEGREES
REMARK 500 1 DC A 1 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DT A 4 C5' - C4' - C3' ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DT A 4 C4' - C3' - C2' ANGL. DEV. = -6.4 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -8.9 DEGREES
REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DA A 9 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DA A 9 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES
REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DC A 10 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES
REMARK 500 1 DC A 10 O4' - C1' - C2' ANGL. DEV. = -8.5 DEGREES
REMARK 500 1 DC A 10 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES
REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = -7.6 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 DG B 13 C4' - C3' - C2' ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 DT B 14 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DT B 14 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DG B 16 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DG B 16 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DG B 18 O3' - P - O5' ANGL. DEV. = -12.1 DEGREES
REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DT B 20 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 DT B 20 C5' - C4' - C3' ANGL. DEV. = 9.4 DEGREES
REMARK 500 1 DT B 20 C4' - C3' - C2' ANGL. DEV. = -12.3 DEGREES
REMARK 500 1 DT B 20 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES
REMARK 500 1 DT B 20 N1 - C1' - C2' ANGL. DEV. = 9.3 DEGREES
REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DT B 20 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DG B 21 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 DG B 21 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 DG B 22 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES
REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DC A 1 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 2 DA A 3 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DT A 4 C5' - C4' - C3' ANGL. DEV. = 9.2 DEGREES
REMARK 500 2 DT A 4 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - C2' ANGL. DEV. = -8.9 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 399 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
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 C10 ATOM OF BP IS COVALENTLY BONDED TO N2 ATOM OF G6 IN CHAIN A.
DBREF 1Y9H A 1 11 PDB 1Y9H 1Y9H 1 11
DBREF 1Y9H B 12 22 PDB 1Y9H 1Y9H 12 22
SEQRES 1 A 11 DC DC DA DT 5CM DG DC DT DA DC DC
SEQRES 1 B 11 DG DG DT DA DG DC DG DA DT DG DG
MODRES 1Y9H 5CM A 5 DC
HET 5CM A 5 33
HET BAP A 23 38
HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
FORMUL 1 5CM C10 H16 N3 O7 P
FORMUL 3 BAP C20 H16 O3
LINK O3' DT A 4 P 5CM A 5 1555 1555 1.59
LINK O3' 5CM A 5 P DG A 6 1555 1555 1.61
SITE 1 AC1 6 5CM A 5 DG A 6 DC A 7 DT A 8
SITE 2 AC1 6 DG B 16 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 - 2 20 Bytes