HEADER DNA 23-JAN-01 1HZ0 TITLE NMR STRUCTURE OF THE 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE TITLE 2 (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 DNA/RNA SOURCE 4 SYNTHESIZER AND CHEMICALLY MODIFIED BY N-ACETOXY-PHIP; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS DNA ADDUCT DUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR K.BROWN,M.COSMAN REVDAT 4 23-FEB-22 1HZ0 1 REMARK LINK 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,S.BROYDE, JRNL AUTH 2 K.W.TURTELTAUB,M.COSMAN JRNL TITL SOLUTION STRUCTURE OF THE 2-AMINO-1- JRNL TITL 2 METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE C8-DEOXYGUANOSINE JRNL TITL 3 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.0, DUPLEX NONE REMARK 3 AUTHORS : VARIAN (VNMR), HINGERTY AND BROYDE (DUPLEX) 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 DEPOSITION ID IS D_1000012699. 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 NA2PO4 REMARK 210 BUFFER; 9.1 MG OF [PHIP]DG.DC REMARK 210 11MER DUPLEX IN 600 UL OF 10 MM REMARK 210 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 : FELIX 97, DUPLEX 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 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 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. = -3.9 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. = 3.8 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 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