2KNK - Header Asymmetric Unit

HEADER DNA 26-AUG-09 2KNK

TITLE STRUCTURE OF THE TRIMETHYLENE N2-DG:N2-DG INTERSTRAND CROSS- TITLE 2 LINK IN 5'-CPG-3' SEQUENCE CONTEXT

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*GP*CP*GP*CP*CP*T)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS INTERSTRAND CROSS-LINK, TRIMETHYLENE, CPG SEQUENCE CONTEXT, KEYWDS 2 DNA

EXPDTA SOLUTION NMR

AUTHOR H.HUANG,P.A.DOOLEY,C.M.HARRIS,T.M.HARRIS,M.P.STONE

REVDAT 2 01-DEC-09 2KNK 1 JRNL REVDAT 1 29-SEP-09 2KNK 0

JRNL AUTH H.HUANG,P.A.DOOLEY,C.M.HARRIS,T.M.HARRIS,M.P.STONE JRNL TITL DIFFERENTIAL BASE STACKING INTERACTIONS INDUCED BY JRNL TITL 2 TRIMETHYLENE INTERSTRAND DNA CROSS-LINKS IN THE JRNL TITL 3 5'-CPG-3' AND 5'-GPC-3' SEQUENCE CONTEXTS. JRNL REF CHEM.RES.TOXICOL. V. 22 1810 2009 JRNL REFN ISSN 0893-228X JRNL PMID 19916525 JRNL DOI 10.1021/TX900225C

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, D.A. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2KNK COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-09. REMARK 100 THE RCSB ID CODE IS RCSB101342.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM DNA (5'-D(*AP*GP*GP*CP* REMARK 210 GP*CP*CP*T)-3'), 2 MM XLK, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 4 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 9 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 9 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA B 9 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 9 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES 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 DG A 2 0.05 SIDE CHAIN REMARK 500 DG A 3 0.09 SIDE CHAIN REMARK 500 DG A 5 0.08 SIDE CHAIN REMARK 500 DG B 11 0.08 SIDE CHAIN REMARK 500 DG B 13 0.08 SIDE CHAIN REMARK 500 DC B 14 0.07 SIDE CHAIN 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 TME A 17

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HZ2 RELATED DB: PDB REMARK 900 PREVIOUSLY REFINED STRUCTURE REMARK 900 RELATED ID: 2KNL RELATED DB: PDB

DBREF 2KNK A 1 8 PDB 2KNK 2KNK 1 8 DBREF 2KNK B 9 16 PDB 2KNK 2KNK 9 16

SEQRES 1 A 8 DA DG DG DC DG DC DC DT SEQRES 1 B 8 DA DG DG DC DG DC DC DT

HET TME A 17 9

HETNAM TME PROPANE

FORMUL 3 TME C3 H8

LINK N2 DG A 5 C1 TME A 17 1555 1555 1.47 LINK N2 DG B 13 C3 TME A 17 1555 1555 1.47

SITE 1 AC1 2 DG A 5 DG B 13

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