10 20 30 40 50 60 70 80 2KH4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 24-MAR-09 2KH4
TITLE AFLATOXIN FORMAMIDOPYRIMIDINE ALPHA ANOMER IN SINGLE STRAND TITLE 2 DNA
CAVEAT 2KH4 CHIRALITY ERROR AT C1' CENTER OF FAG IN CHAIN A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*(FAG)P*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS AFLATOXIN, FORMAMIDOPYRIMIDINE, ALPHA ANOMER, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR K.L.BROWN
REVDAT 1 15-DEC-09 2KH4 0
JRNL AUTH K.L.BROWN,M.W.VOEHLER,S.M.MAGEE,C.M.HARRIS, JRNL AUTH 2 T.M.HARRIS,M.P.STONE JRNL TITL STRUCTURAL PERTURBATIONS INDUCED BY THE JRNL TITL 2 ALPHA-ANOMER OF THE AFLATOXIN B(1) JRNL TITL 3 FORMAMIDOPYRIMIDINE ADDUCT IN DUPLEX AND JRNL TITL 4 SINGLE-STRAND DNA JRNL REF J.AM.CHEM.SOC. V. 131 16096 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19831353 JRNL DOI 10.1021/JA902052V
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KH4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-09. REMARK 100 THE RCSB ID CODE IS RCSB101113.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 8.7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM (5'-D(*DCP*DTP*(FAG)P* REMARK 210 DA)-3')-1, 100% D2O; 0.4 MM (5'-D(*DCP*DTP*(FAG)P*DA)-3')-2, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : ADVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, MARDIGRAS, REMARK 210 CORMA, CURVES REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM 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 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 DC A 1 C5 DC A 1 C6 0.087 REMARK 500 1 DT A 2 C5 DT A 2 C6 0.091 REMARK 500 1 DA A 4 P DA A 4 OP1 -0.102 REMARK 500 2 DC A 1 C5 DC A 1 C6 0.085 REMARK 500 2 DT A 2 C5 DT A 2 C6 0.088 REMARK 500 3 DC A 1 O5' DC A 1 C5' -0.448 REMARK 500 3 DC A 1 C5' DC A 1 C4' -0.083 REMARK 500 3 DC A 1 C3' DC A 1 C2' -0.080 REMARK 500 3 DC A 1 O3' DC A 1 C3' -0.039 REMARK 500 3 DC A 1 C5 DC A 1 C6 0.086 REMARK 500 3 DT A 2 C5 DT A 2 C6 0.089 REMARK 500 3 DC A 1 O3' DT A 2 P -0.082 REMARK 500 4 DC A 1 C5 DC A 1 C6 0.085 REMARK 500 4 DT A 2 C5 DT A 2 C6 0.090 REMARK 500 4 DA A 4 C3' DA A 4 C2' -0.115 REMARK 500 4 DA A 4 C2' DA A 4 C1' -0.079 REMARK 500 4 DA A 4 O4' DA A 4 C4' -0.093 REMARK 500 4 DA A 4 O3' DA A 4 C3' -0.116 REMARK 500 5 DC A 1 C5 DC A 1 C6 0.087 REMARK 500 5 DT A 2 C5 DT A 2 C6 0.089 REMARK 500 5 DA A 4 C3' DA A 4 C2' -0.115 REMARK 500 5 DA A 4 O3' DA A 4 C3' -0.136 REMARK 500 6 DC A 1 C5 DC A 1 C6 0.087 REMARK 500 6 DT A 2 C5 DT A 2 C6 0.089 REMARK 500 7 DC A 1 C3' DC A 1 C2' -0.068 REMARK 500 7 DC A 1 C5 DC A 1 C6 0.087 REMARK 500 7 DT A 2 C5 DT A 2 C6 0.090 REMARK 500 8 DC A 1 C5 DC A 1 C6 0.086 REMARK 500 8 DT A 2 C5 DT A 2 C6 0.090 REMARK 500 8 DA A 4 P DA A 4 OP1 -0.145 REMARK 500 8 DA A 4 P DA A 4 OP2 -0.211 REMARK 500 8 DA A 4 P DA A 4 O5' -0.147 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. = 6.5 DEGREES REMARK 500 1 DC A 1 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DC A 1 C3' - C2' - C1' ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 4 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DA A 4 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 4 DA A 4 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.2 DEGREES REMARK 500 5 DA A 4 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 7 DA A 4 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 8 DC A 1 C5' - C4' - C3' ANGL. DEV. = -13.3 DEGREES REMARK 500 8 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 DT A 2 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 DT A 2 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 8 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 FAG A 3 38.4 D L WRONG HAND REMARK 500 2 FAG A 3 37.9 D L WRONG HAND REMARK 500 3 FAG A 3 38.1 D L WRONG HAND REMARK 500 4 FAG A 3 38.1 D L WRONG HAND REMARK 500 5 FAG A 3 38.3 D L WRONG HAND REMARK 500 6 FAG A 3 38.2 D L WRONG HAND REMARK 500 7 FAG A 3 38.4 D L WRONG HAND REMARK 500 8 FAG A 3 38.0 D L WRONG HAND REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KH3 RELATED DB: PDB REMARK 900 RELATED ID: 16223 RELATED DB: BMRB
DBREF 2KH4 A 1 4 PDB 2KH4 2KH4 1 4
SEQRES 1 A 4 DC DT FAG DA
HET FAG A 3 72
HETNAM FAG [1',2'-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]- HETNAM 2 FAG FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]- HETNAM 3 FAG RIBOFURANOSE]-5-MONOPHOSPHATE GROUP
FORMUL 1 FAG C27 H28 N5 O15 P
LINK O3' DT A 2 P FAG A 3 1555 1555 1.61 LINK O3' FAG A 3 P DA A 4 1555 1555 1.61
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