PDB Short entry for 1Y9H 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 CAVEAT 1Y9H BAP A 23 HAS WRONG CHIRALITY AT ATOM C1' BAP A 23 HAS WRONG CAVEAT 2 1Y9H CHIRALITY AT ATOM C2' BAP A 23 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 1Y9H C3' 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 4 24-APR-24 1Y9H 1 CAVEAT REMARK LINK 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 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 LINK N2 DG A 6 C4' BAP A 23 1555 1555 1.49 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