HEADER DNA 23-SEP-08 2K8T TITLE SOLUTION NMR STRUCTURE OF TRANS-4-HYDROXYNONENAL DERIVED DG ADDUCT OF TITLE 2 (6R,8S,11R)-CONFIGURATION OPPOSITE DC 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*DCP*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: DNA STRAND A; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: DNA STRAND B KEYWDS HNE-DG (6R, 8S, 11R), HNE DERIVED DG ADDUCT, TRANS-4-HYDROXYNONENAL, KEYWDS 2 DNA EXPDTA SOLUTION NMR AUTHOR H.HUANG,H.WANG,N.QI,R.S.LLOYD,C.J.RIZZO,M.P.STONE REVDAT 5 22-MAY-24 2K8T 1 REMARK REVDAT 4 16-MAR-22 2K8T 1 REMARK LINK REVDAT 3 24-FEB-09 2K8T 1 VERSN REVDAT 2 11-NOV-08 2K8T 1 JRNL REVDAT 1 04-NOV-08 2K8T 0 JRNL AUTH H.HUANG,H.WANG,N.QI,R.S.LLOYD,C.J.RIZZO,M.P.STONE JRNL TITL THE STEREOCHEMISTRY OF TRANS-4-HYDROXYNONENAL-DERIVED JRNL TITL 2 EXOCYCLIC 1,N2-2'-DEOXYGUANOSINE ADDUCTS MODULATES FORMATION JRNL TITL 3 OF INTERSTRAND CROSS-LINKS IN THE 5'-CPG-3' SEQUENCE. JRNL REF BIOCHEMISTRY V. 47 11457 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18847226 JRNL DOI 10.1021/BI8011143 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 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 2K8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000100820. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'), 1 MM REMARK 210 DNA (5'-D(*DGP*DGP*DAP*DCP*DTP*DCP*DGP*DCP*DTP*DAP*DGP*DC)-3'), REMARK 210 100% 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 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 18 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.1 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 7 0.06 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 HNB A 125 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K8U RELATED DB: PDB REMARK 900 TRANS-4-HYDROXYNONENAL DERIVED DG ADDUCT OF (6S,8R,11S)- REMARK 900 CONFIGURATION MATCHED WITH DC DBREF 2K8T A 1 12 PDB 2K8T 2K8T 1 12 DBREF 2K8T B 13 24 PDB 2K8T 2K8T 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 DC DG DC DT DA DG DC HET HNB A 125 28 HETNAM HNB (2S,5R)-5-PENTYLTETRAHYDROFURAN-2-OL FORMUL 3 HNB C9 H18 O2 LINK N2 DG A 7 C3 HNB A 125 1555 1555 1.48 SITE 1 AC1 5 DG A 7 DA A 8 DG A 9 DG B 19 SITE 2 AC1 5 DC B 20 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 379 DC A 12 TER 759 DC B 24 HETATM 760 C1 HNB A 125 -1.690 -8.446 14.316 1.00 0.00 C HETATM 761 C2 HNB A 125 -2.095 -7.933 15.690 1.00 0.00 C HETATM 762 C3 HNB A 125 -2.989 -6.758 15.345 1.00 0.00 C HETATM 763 C4 HNB A 125 -3.670 -7.325 14.079 1.00 0.00 C HETATM 764 C5 HNB A 125 -4.418 -6.316 13.187 1.00 0.00 C HETATM 765 C6 HNB A 125 -5.219 -6.953 12.039 1.00 0.00 C HETATM 766 C7 HNB A 125 -6.602 -7.505 12.433 1.00 0.00 C HETATM 767 C8 HNB A 125 -7.635 -6.400 12.709 1.00 0.00 C HETATM 768 C9 HNB A 125 -9.016 -7.003 12.971 1.00 0.00 C HETATM 769 O4 HNB A 125 -2.639 -8.005 13.371 1.00 0.00 O HETATM 770 O1 HNB A 125 -1.871 -9.827 14.210 1.00 0.00 O HETATM 771 H3 HNB A 125 -3.722 -6.609 16.136 1.00 0.00 H HETATM 772 H4 HNB A 125 -4.396 -8.067 14.417 1.00 0.00 H HETATM 773 H1 HNB A 125 -0.681 -8.136 14.039 1.00 0.00 H HETATM 774 HO1 HNB A 125 -2.221 -9.962 13.315 1.00 0.00 H HETATM 775 H12 HNB A 125 -2.672 -8.691 16.220 1.00 0.00 H HETATM 776 H22 HNB A 125 -1.230 -7.634 16.277 1.00 0.00 H HETATM 777 H15 HNB A 125 -3.684 -5.645 12.749 1.00 0.00 H HETATM 778 H25 HNB A 125 -5.098 -5.729 13.798 1.00 0.00 H HETATM 779 H16 HNB A 125 -5.361 -6.200 11.262 1.00 0.00 H HETATM 780 H26 HNB A 125 -4.628 -7.762 11.609 1.00 0.00 H HETATM 781 H17 HNB A 125 -6.967 -8.112 11.604 1.00 0.00 H HETATM 782 H27 HNB A 125 -6.509 -8.147 13.309 1.00 0.00 H HETATM 783 H18 HNB A 125 -7.701 -5.736 11.846 1.00 0.00 H HETATM 784 H28 HNB A 125 -7.336 -5.817 13.578 1.00 0.00 H HETATM 785 H19 HNB A 125 -9.351 -7.559 12.095 1.00 0.00 H HETATM 786 H29 HNB A 125 -8.975 -7.670 13.831 1.00 0.00 H HETATM 787 H39 HNB A 125 -9.727 -6.203 13.177 1.00 0.00 H CONECT 208 762 CONECT 760 761 769 770 773 CONECT 761 760 762 775 776 CONECT 762 208 761 763 771 CONECT 763 762 764 769 772 CONECT 764 763 765 777 778 CONECT 765 764 766 779 780 CONECT 766 765 767 781 782 CONECT 767 766 768 783 784 CONECT 768 767 785 786 787 CONECT 769 760 763 CONECT 770 760 774 CONECT 771 762 CONECT 772 763 CONECT 773 760 CONECT 774 770 CONECT 775 761 CONECT 776 761 CONECT 777 764 CONECT 778 764 CONECT 779 765 CONECT 780 765 CONECT 781 766 CONECT 782 766 CONECT 783 767 CONECT 784 767 CONECT 785 768 CONECT 786 768 CONECT 787 768 MASTER 144 0 1 0 0 0 2 6 497 2 29 2 END