10 20 30 40 50 60 70 80 2KH8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 24-MAR-09 2KH8
TITLE SOLUTION STRUCTURE OF CIS-5R,6S-THYMINE GLYCOL OPPOSITE TITLE 2 COMPLEMENTARY GUANINE IN DUPLEX DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS THYMINE GLYCOL, DNA, NMR
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR K.L.BROWN
REVDAT 1 01-DEC-09 2KH8 0
JRNL AUTH K.L.BROWN,A.K.BASU,M.P.STONE JRNL TITL THE CIS-(5R,6S)-THYMINE GLYCOL LESION OCCUPIES THE JRNL TITL 2 WOBBLE POSITION WHEN MISMATCHED WITH DEOXYGUANOSINE JRNL TITL 3 IN DNA JRNL REF BIOCHEMISTRY V. 48 9722 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19772348 JRNL DOI 10.1021/BI900695E
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 2KH8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-09. REMARK 100 THE RCSB ID CODE IS RCSB101117.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 278 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE-1, 100 REMARK 210 MM SODIUM CHLORIDE-2, 10 UM REMARK 210 SODIUM AZIDE-3, 50 UM EDTA-4, REMARK 210 100% D2O; 20 MM SODIUM REMARK 210 PHOSPHATE-5, 100 MM SODIUM REMARK 210 CHLORIDE-6, 10 UM SODIUM AZIDE REMARK 210 -7, 50 UM EDTA-8, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 COSY; 2D 31P-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, MARDIGRAS, REMARK 210 CORMA, CURVES, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 2 DA B 13 C6 DA B 13 N1 -0.049 REMARK 500 2 DC B 14 C2 DC B 14 O2 -0.054 REMARK 500 2 DC B 14 N3 DC B 14 C4 -0.050 REMARK 500 2 DC B 24 C3' DC B 24 C2' -0.103 REMARK 500 3 DC B 24 C4 DC B 24 N4 -0.055 REMARK 500 4 DT A 9 C3' DT A 9 C2' -0.050 REMARK 500 4 DT A 12 C3' DT A 12 C2' -0.049 REMARK 500 4 DT A 12 O3' DT A 12 C3' -0.041 REMARK 500 4 DC B 20 C4 DC B 20 N4 -0.057 REMARK 500 5 DT A 9 C3' DT A 9 C2' -0.098 REMARK 500 5 DA B 13 C6 DA B 13 N1 -0.044 REMARK 500 6 DA B 13 C6 DA B 13 N1 -0.051 REMARK 500 6 DC B 14 C2 DC B 14 O2 -0.055 REMARK 500 6 DC B 14 N3 DC B 14 C4 -0.045 REMARK 500 6 DC B 24 N3 DC B 24 C4 -0.046 REMARK 500 7 DA B 13 C6 DA B 13 N1 -0.044 REMARK 500 8 DA B 15 O3' DA B 15 C3' -0.049 REMARK 500 9 DT A 12 C3' DT A 12 C2' -0.110 REMARK 500 9 DC B 24 N3 DC B 24 C4 -0.044 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 2 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 3 OP1 - P - OP2 ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DC A 4 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 OP1 - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 8 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 9 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 10 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 11 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 12 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA B 13 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 13 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC B 14 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA B 15 OP1 - P - OP2 ANGL. DEV. = -11.7 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA B 16 OP1 - P - OP2 ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DA B 16 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 16 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DA B 17 OP1 - P - OP2 ANGL. DEV. = -11.1 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC B 18 OP1 - P - OP2 ANGL. DEV. = -12.8 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 19 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 19 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 20 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC B 20 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 633 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DC A 4 0.08 SIDE CHAIN REMARK 500 1 DG B 21 0.06 SIDE CHAIN REMARK 500 2 DC A 4 0.07 SIDE CHAIN REMARK 500 2 DG A 5 0.07 SIDE CHAIN REMARK 500 3 DC A 4 0.07 SIDE CHAIN REMARK 500 3 DG A 5 0.07 SIDE CHAIN REMARK 500 3 DA B 23 0.07 SIDE CHAIN REMARK 500 4 DC A 4 0.09 SIDE CHAIN REMARK 500 4 DA B 23 0.08 SIDE CHAIN REMARK 500 5 DT A 2 0.07 SIDE CHAIN REMARK 500 5 DC A 4 0.07 SIDE CHAIN REMARK 500 6 DC A 4 0.10 SIDE CHAIN REMARK 500 6 DA B 23 0.06 SIDE CHAIN REMARK 500 7 DC A 4 0.08 SIDE CHAIN REMARK 500 7 DG A 7 0.06 SIDE CHAIN REMARK 500 7 DA B 16 0.06 SIDE CHAIN REMARK 500 7 DA B 23 0.08 SIDE CHAIN REMARK 500 8 DC A 4 0.07 SIDE CHAIN REMARK 500 8 DA B 15 0.07 SIDE CHAIN REMARK 500 8 DA B 23 0.06 SIDE CHAIN REMARK 500 9 DC A 4 0.07 SIDE CHAIN REMARK 500 9 DA B 15 0.06 SIDE CHAIN REMARK 500 9 DA B 23 0.08 SIDE CHAIN REMARK 500 10 DC A 4 0.08 SIDE CHAIN REMARK 500 10 DA B 15 0.07 SIDE CHAIN REMARK 500 10 DG B 19 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KH7 RELATED DB: PDB REMARK 900 RELATED ID: 16227 RELATED DB: BMRB
DBREF 2KH8 A 1 12 PDB 2KH8 2KH8 1 12 DBREF 2KH8 B 13 24 PDB 2KH8 2KH8 13 24
SEQRES 1 A 12 DG DT DG DC DG CTG DG DT DT DT DG DT SEQRES 1 B 12 DA DC DA DA DA DC DG DC DG DC DA DC
MODRES 2KH8 CTG A 6 DT
HET CTG A 6 36
HETNAM CTG (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'- HETNAM 2 CTG MONOPHOSPHATE
FORMUL 1 CTG C10 H17 N2 O10 P
LINK O3' DG A 5 P CTG A 6 1555 1555 1.61 LINK O3' CTG A 6 P DG A 7 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