10 20 30 40 50 60 70 80 1HZ0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 23-JAN-01 1HZ0
TITLE NMR STRUCTURE OF THE 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5- TITLE 2 B]PYRIDINE (PHIP) C8-DEOXYGUANOSINE ADDUCT IN DUPLEX DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PHIP DNA ADDUCT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA OLIGOMERS SYNTHESIZED ON AN ABI 394 SOURCE 4 DNA/RNA SYNTHESIZER AND CHEMICALLY MODIFIED BY N-ACETOXY- SOURCE 5 PHIP; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES
KEYWDS DNA ADDUCT DUPLEX
EXPDTA SOLUTION NMR
NUMMDL 6
AUTHOR K.BROWN,M.COSMAN
REVDAT 3 24-FEB-09 1HZ0 1 VERSN REVDAT 2 01-APR-03 1HZ0 1 JRNL REVDAT 1 08-AUG-01 1HZ0 0
JRNL AUTH K.BROWN,B.E.HINGERTY,E.A.GUENTHER,V.V.KRISHNAN, JRNL AUTH 2 S.BROYDE,K.W.TURTELTAUB,M.COSMAN JRNL TITL SOLUTION STRUCTURE OF THE 2-AMINO-1- JRNL TITL 2 METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE JRNL TITL 3 C8-DEOXYGUANOSINE ADDUCT IN DUPLEX DNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 8507 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11438709 JRNL DOI 10.1073/PNAS.151251898
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DUPLEX NONE REMARK 3 AUTHORS : HINGERTY AND BROYDE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 266 NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS WERE USED IN THE CALCULATIONS
REMARK 4 REMARK 4 1HZ0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-01. REMARK 100 THE RCSB ID CODE IS RCSB012699.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 293; 274 REMARK 210 PH : 7.00; 7.00; 7.00 REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL; 0.1 M REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 9.1 MG OF [PHIP]DG.DC 11MER REMARK 210 DUPLEX IN 600 UL OF 10 MM REMARK 210 NA2PO4 BUFFER; 9.1 MG OF REMARK 210 [PHIP]DG.DC 11MER DUPLEX IN REMARK 210 600 UL OF 10 MM NA2PO4 BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY 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 : VNMR 6.0, FELIX 97, DUPLEX REMARK 210 NONE REMARK 210 METHOD USED : RESTRAINTED TORSION ANGLE REMARK 210 MINIMIZATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 48 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR 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 1 DG A 6 C8 DG A 6 N9 -0.047 REMARK 500 1 DG B 12 C8 DG B 12 N9 -0.043 REMARK 500 1 DG B 13 C8 DG B 13 N9 -0.045 REMARK 500 1 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 1 DG B 18 C8 DG B 18 N9 -0.044 REMARK 500 1 DG B 21 C8 DG B 21 N9 -0.044 REMARK 500 1 DG B 22 C8 DG B 22 N9 -0.044 REMARK 500 2 DG A 6 C8 DG A 6 N9 -0.047 REMARK 500 2 DG B 12 C8 DG B 12 N9 -0.044 REMARK 500 2 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 2 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 2 DG B 18 C8 DG B 18 N9 -0.044 REMARK 500 2 DG B 21 C8 DG B 21 N9 -0.045 REMARK 500 2 DG B 22 C8 DG B 22 N9 -0.043 REMARK 500 3 DG A 6 C8 DG A 6 N9 -0.047 REMARK 500 3 DG B 12 C8 DG B 12 N9 -0.044 REMARK 500 3 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 3 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 3 DG B 18 C8 DG B 18 N9 -0.044 REMARK 500 3 DG B 21 C8 DG B 21 N9 -0.045 REMARK 500 3 DG B 22 C8 DG B 22 N9 -0.043 REMARK 500 4 DG A 6 C8 DG A 6 N9 -0.046 REMARK 500 4 DG B 12 C8 DG B 12 N9 -0.044 REMARK 500 4 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 4 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 4 DG B 18 C8 DG B 18 N9 -0.044 REMARK 500 4 DG B 21 C8 DG B 21 N9 -0.044 REMARK 500 4 DG B 22 C8 DG B 22 N9 -0.044 REMARK 500 5 DG A 6 C8 DG A 6 N9 -0.047 REMARK 500 5 DG B 12 C8 DG B 12 N9 -0.044 REMARK 500 5 DG B 13 C8 DG B 13 N9 -0.045 REMARK 500 5 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 5 DG B 18 C8 DG B 18 N9 -0.044 REMARK 500 5 DG B 21 C8 DG B 21 N9 -0.044 REMARK 500 5 DG B 22 C8 DG B 22 N9 -0.045 REMARK 500 6 DG A 6 C8 DG A 6 N9 -0.046 REMARK 500 6 DG B 12 C8 DG B 12 N9 -0.044 REMARK 500 6 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 6 DG B 16 C8 DG B 16 N9 -0.044 REMARK 500 6 DG B 18 C8 DG B 18 N9 -0.045 REMARK 500 6 DG B 21 C8 DG B 21 N9 -0.044 REMARK 500 6 DG B 22 C8 DG B 22 N9 -0.045 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 2 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DA A 3 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DT A 4 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DC A 5 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DG A 6 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG A 6 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 6 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DC A 7 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DT A 8 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DA A 9 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DC A 10 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DC A 11 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 12 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 12 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG B 13 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DG B 13 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 13 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 13 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT B 14 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DA B 15 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DG B 16 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 16 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 16 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DC B 17 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 18 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DG B 18 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 18 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 18 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 19 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DT B 20 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 21 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 21 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 21 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 21 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG B 22 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DG B 22 C4 - C5 - N7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG B 22 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DC A 2 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 2 DA A 3 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 2 DT A 4 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 2 DC A 5 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 2 DG A 6 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 2 DG A 6 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG A 6 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 6 N7 - C8 - N9 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DC A 7 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 246 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 PIQ A 23
DBREF 1HZ0 A 1 11 PDB 1HZ0 1HZ0 1 11 DBREF 1HZ0 B 12 22 PDB 1HZ0 1HZ0 12 22
SEQRES 1 A 11 DC DC DA DT DC DG DC DT DA DC DC SEQRES 1 B 11 DG DG DT DA DG DC DG DA DT DG DG
HET PIQ A 23 28
HETNAM PIQ 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE
FORMUL 3 PIQ C13 H12 N4
LINK C8 DG A 6 N PIQ A 23 1555 1555 1.41
SITE 1 AC1 6 DC A 5 DG A 6 DC A 7 DG B 16 SITE 2 AC1 6 DC 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