HEADER DNA 16-APR-14 2MNX TITLE MAJOR GROOVE ORIENTATION OF THE (2S)-N6-(2-HYDROXY-3-BUTEN-1-YL)-2'- TITLE 2 DEOXYADENOSINE DNA ADDUCT INDUCED BY 1,2-EPOXY-3-BUTENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-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 B-FORM, 11-MER, DNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR E.A.KOWAL,S.KOTAPATI,M.TURO,N.TRETYAKOVA,M.P.STONE REVDAT 3 01-MAY-24 2MNX 1 REMARK LINK REVDAT 2 05-NOV-14 2MNX 1 JRNL REVDAT 1 08-OCT-14 2MNX 0 JRNL AUTH E.A.KOWAL,S.WICKRAMARATNE,S.KOTAPATI,M.TURO,N.TRETYAKOVA, JRNL AUTH 2 M.P.STONE JRNL TITL MAJOR GROOVE ORIENTATION OF THE JRNL TITL 2 (2S)-N(6)-(2-HYDROXY-3-BUTEN-1-YL)-2'-DEOXYADENOSINE DNA JRNL TITL 3 ADDUCT INDUCED BY 1,2-EPOXY-3-BUTENE. JRNL REF CHEM.RES.TOXICOL. V. 27 1675 2014 JRNL REFN ISSN 0893-228X JRNL PMID 25238403 JRNL DOI 10.1021/TX500159W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000103841. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 283 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.100; 0.100 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.51 MM 5' REMARK 210 -D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 MM 5'-D(*CP*TP* REMARK 210 TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 MM SODIUM CHLORIDE, 50 UM REMARK 210 EDTA, 10 MM SODIUM PHOSPHATE PH 7.0, 100% D2O; 0.51 MM 5'-D(*CP* REMARK 210 GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 MM 5'-D(*CP*TP*TP*CP* REMARK 210 TP*TP*GP*TP*CP*CP*G)-3', 100 MM SODIUM CHLORIDE, 50 UM EDTA, 10 REMARK 210 MM SODIUM PHOSPHATE PH 7.0, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-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 : TOPSPIN, SPARKY, AMBER, CORMA, REMARK 210 MARDIGRAS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY 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 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 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 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 10 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 15 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 15 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 17 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 21 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DA A 10 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 10 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 286 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19912 RELATED DB: BMRB DBREF 2MNX A 1 11 PDB 2MNX 2MNX 1 11 DBREF 2MNX B 12 22 PDB 2MNX 2MNX 12 22 SEQRES 1 A 11 DC DG DG DA DC 6HB DA DG DA DA DG SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG MODRES 2MNX 6HB A 6 DA HET 6HB A 6 43 HETNAM 6HB 2'-DEOXY-N-[(2S)-2-HYDROXYBUT-3-EN-1-YL]ADENOSINE 5'- HETNAM 2 6HB (DIHYDROGEN PHOSPHATE) FORMUL 1 6HB C14 H20 N5 O7 P LINK O3' DC A 5 P 6HB A 6 1555 1555 1.62 LINK O3' 6HB A 6 P DA 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 MODEL 1