HEADER DNA 13-NOV-08 2KAS TITLE HNE-DG ADDUCT MISMATCHED WITH DA IN BASIC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE DNA OLIGOMER IS CHEMICALLY SYNTHESIZED.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THE DNA OLIGOMER IS CHEMICALLY SYNTHESIZED. KEYWDS HNE-DG, MISMATCH, HYDROXYNONENAL, DNA EXPDTA SOLUTION NMR AUTHOR H.HUANG,H.WANG,R.S.LLOYD,C.J.RIZZO,M.P.STONE REVDAT 3 22-MAY-24 2KAS 1 REMARK REVDAT 2 16-MAR-22 2KAS 1 REMARK LINK REVDAT 1 26-MAY-09 2KAS 0 JRNL AUTH H.HUANG,H.WANG,R.S.LLOYD,C.J.RIZZO,M.P.STONE JRNL TITL CONFORMATIONAL INTERCONVERSION OF THE JRNL TITL 2 TRANS-4-HYDROXYNONENAL-DERIVED (6S,8R,11S) JRNL TITL 3 1,N(2)-DEOXYGUANOSINE ADDUCT WHEN MISMATCHED WITH JRNL TITL 4 DEOXYADENOSINE IN DNA JRNL REF CHEM.RES.TOXICOL. V. 22 187 2009 JRNL REFN ISSN 0893-228X JRNL PMID 19053179 JRNL DOI 10.1021/TX800320M 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 2KAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000100890. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 8.9 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM DNA (5' REMARK 210 -D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'), 1.0 MM REMARK 210 DNA (5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'), REMARK 210 1.0 MM (2E,4R)-4-HYDROXYNON-2-ENAL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 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 : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 7 C6 - N1 - C2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 7 N3 - C2 - N2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 17 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 18 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA B 18 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC B 20 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT REMARK 600 POSITION 7 OF CHAIN A. THIS LIGAND IS FORMED BY CHEMICAL REACTION REMARK 600 OF ANOTHER LIGAND HNE. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HND A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KAR RELATED DB: PDB DBREF 2KAS A 1 12 PDB 2KAS 2KAS 1 12 DBREF 2KAS B 13 24 PDB 2KAS 2KAS 13 24 SEQRES 1 A 12 DG DC DT DA DG DC DG DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DA DG DC DT DA DG DC HET HND A 25 29 HETNAM HND (4S)-NONANE-1,4-DIOL FORMUL 3 HND C9 H20 O2 LINK N2 DG A 7 C3 HND A 25 1555 1555 1.45 LINK N1 DG A 7 C1 HND A 25 1555 1555 1.49 SITE 1 AC1 5 DG A 7 DA A 8 DG A 9 DA B 18 SITE 2 AC1 5 DG B 19 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 TER 378 DC A 12 TER 760 DC B 24 HETATM 761 C1 HND A 25 -0.432 -0.520 22.248 1.00 0.00 C HETATM 762 C2 HND A 25 -0.790 -2.016 22.259 1.00 0.00 C HETATM 763 C3 HND A 25 -2.040 -2.408 21.462 1.00 0.00 C HETATM 764 C4 HND A 25 -2.696 -3.710 21.991 1.00 0.00 C HETATM 765 C5 HND A 25 -1.828 -4.937 21.647 1.00 0.00 C HETATM 766 C6 HND A 25 -2.166 -6.201 22.457 1.00 0.00 C HETATM 767 C7 HND A 25 -1.852 -6.039 23.958 1.00 0.00 C HETATM 768 C8 HND A 25 -1.682 -7.391 24.675 1.00 0.00 C HETATM 769 C9 HND A 25 -2.961 -8.242 24.677 1.00 0.00 C HETATM 770 O10 HND A 25 -4.009 -3.882 21.407 1.00 0.00 O HETATM 771 O11 HND A 25 0.801 -0.353 21.572 1.00 0.00 O HETATM 772 H2 HND A 25 0.055 -2.593 21.888 1.00 0.00 H HETATM 773 H3 HND A 25 -1.772 -2.568 20.420 1.00 0.00 H HETATM 774 H4 HND A 25 -2.816 -3.617 23.069 1.00 0.00 H HETATM 775 H5 HND A 25 -0.777 -4.711 21.812 1.00 0.00 H HETATM 776 H5A HND A 25 -1.944 -5.150 20.586 1.00 0.00 H HETATM 777 HO10 HND A 25 -4.434 -4.683 21.764 1.00 0.00 H HETATM 778 H6 HND A 25 -1.563 -7.013 22.060 1.00 0.00 H HETATM 779 H6A HND A 25 -3.213 -6.465 22.318 1.00 0.00 H HETATM 780 H7 HND A 25 -2.643 -5.468 24.443 1.00 0.00 H HETATM 781 H7A HND A 25 -0.920 -5.484 24.072 1.00 0.00 H HETATM 782 H8 HND A 25 -1.392 -7.200 25.707 1.00 0.00 H HETATM 783 H8A HND A 25 -0.878 -7.953 24.202 1.00 0.00 H HETATM 784 H9 HND A 25 -2.789 -9.153 25.249 1.00 0.00 H HETATM 785 H9A HND A 25 -3.239 -8.521 23.662 1.00 0.00 H HETATM 786 H9B HND A 25 -3.781 -7.690 25.136 1.00 0.00 H HETATM 787 H1 HND A 25 -0.234 -0.234 23.272 1.00 0.00 H HETATM 788 HO11 HND A 25 1.016 0.593 21.637 1.00 0.00 H HETATM 789 H2A HND A 25 -0.926 -2.311 23.294 1.00 0.00 H CONECT 206 761 CONECT 208 763 CONECT 761 206 762 771 787 CONECT 762 761 763 772 789 CONECT 763 208 762 764 773 CONECT 764 763 765 770 774 CONECT 765 764 766 775 776 CONECT 766 765 767 778 779 CONECT 767 766 768 780 781 CONECT 768 767 769 782 783 CONECT 769 768 784 785 786 CONECT 770 764 777 CONECT 771 761 788 CONECT 772 762 CONECT 773 763 CONECT 774 764 CONECT 775 765 CONECT 776 765 CONECT 777 770 CONECT 778 766 CONECT 779 766 CONECT 780 767 CONECT 781 767 CONECT 782 768 CONECT 783 768 CONECT 784 769 CONECT 785 769 CONECT 786 769 CONECT 787 761 CONECT 788 771 CONECT 789 762 MASTER 142 0 1 0 0 0 2 6 499 2 31 2 END