HEADER DNA 18-MAR-08 2K1Y TITLE SOLUTION STRUCTURE OF DUPLEX DNA CONTAINING THE MUTAGENIC LESION: 1, TITLE 2 N2-ETHENO-2'-DEOXYGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DCP*DGP*DTP*DAP*DCP*(GNE)P*DCP*DAP*DTP*DGP*DC)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*DGP*DCP*DAP*DTP*DGP*DCP*DGP*DTP*DAP*DCP*DG)-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 DAMAGED DNA STRUCTURE, EXOCYCLIC DNA LESIONS, EXTRAHELICAL BASE, BER KEYWDS 2 RECOGNITION, DNA EXPDTA SOLUTION NMR NUMMDL 9 MDLTYP MINIMIZED AVERAGE AUTHOR T.ZALIZNYAK,M.LUKIN,F.JOHNSON,C.DE LOS SANTOS REVDAT 2 16-MAR-22 2K1Y 1 REMARK LINK REVDAT 1 03-FEB-09 2K1Y 0 JRNL AUTH T.ZALIZNYAK,M.LUKIN,F.JOHNSON,C.DE LOS SANTOS JRNL TITL SOLUTION STRUCTURE OF DUPLEX DNA CONTAINING THE MUTAGENIC JRNL TITL 2 LESION 1,N(2)-ETHENO-2'-DEOXYGUANINE. JRNL REF BIOCHEMISTRY V. 47 4606 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18373352 JRNL DOI 10.1021/BI7022514 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.85, X-PLOR 3.85 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MD SIMULATION REMARK 4 REMARK 4 2K1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000100573. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 278 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50MM NACL; 50MM NACL REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT MBAR REMARK 210 SAMPLE CONTENTS : 4.2MM DUPLEX DNA, 1,N2-ETHENO-2 REMARK 210 -DEOXYGUANOSINE, 100% D2O; 4.2MM REMARK 210 DUPLEX DNA, 1,N2-ETHENO-2 - REMARK 210 DEOXYGUANOSINE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-1H COSY; 2D REMARK 210 1H-1H NOESY H2O; 1H-32P PHCORR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, VNMR 5.2 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 1 DT A 3 C5 DT A 3 C7 0.041 REMARK 500 1 DT B 4 C5 DT B 4 C7 0.037 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.042 REMARK 500 3 DT A 3 C5 DT A 3 C7 0.039 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.039 REMARK 500 5 DT A 3 C3' DT A 3 C2' 0.125 REMARK 500 5 DT A 3 C5 DT A 3 C7 0.060 REMARK 500 5 DC A 7 C2' DC A 7 C1' 0.070 REMARK 500 5 DT A 9 C5 DT A 9 C7 0.038 REMARK 500 5 DG A 10 C5' DG A 10 C4' 0.051 REMARK 500 5 DT B 4 C5 DT B 4 C7 0.036 REMARK 500 5 DC B 6 C2' DC B 6 C1' 0.071 REMARK 500 5 DG B 11 C8 DG B 11 N9 0.055 REMARK 500 6 DT A 3 C5 DT A 3 C7 0.039 REMARK 500 7 DT A 3 C5 DT A 3 C7 0.041 REMARK 500 8 DT A 3 C5 DT A 3 C7 0.041 REMARK 500 9 DC A 1 O5' DC A 1 C5' -1.199 REMARK 500 9 DC A 1 C5' DC A 1 C4' -0.111 REMARK 500 9 DC A 1 C4' DC A 1 C3' -0.061 REMARK 500 9 DC A 1 C2' DC A 1 C1' -0.071 REMARK 500 9 DC A 1 O4' DC A 1 C1' -0.095 REMARK 500 9 DC A 1 O4' DC A 1 C4' -0.113 REMARK 500 9 DG A 2 C2' DG A 2 C1' -0.066 REMARK 500 9 DC A 5 O3' GNE A 6 P -0.134 REMARK 500 9 DG B 1 O5' DG B 1 C5' -0.960 REMARK 500 9 DG B 5 O3' DC B 6 P -0.239 REMARK 500 9 DC B 6 P DC B 6 OP1 -0.519 REMARK 500 9 DC B 6 P DC B 6 OP2 -0.553 REMARK 500 9 DC B 6 P DC B 6 O5' -0.259 REMARK 500 9 DC B 6 O5' DC B 6 C5' -0.408 REMARK 500 9 DC B 6 C3' DC B 6 C2' -0.061 REMARK 500 9 DC B 6 O3' DC B 6 C3' -0.056 REMARK 500 9 DC B 6 C2 DC B 6 O2 -0.131 REMARK 500 9 DC B 6 C4 DC B 6 N4 -0.068 REMARK 500 9 DC B 6 N1 DC B 6 C2 -0.069 REMARK 500 9 DC B 6 N1 DC B 6 C6 -0.126 REMARK 500 9 DC B 6 C2 DC B 6 N3 -0.063 REMARK 500 9 DC B 6 N3 DC B 6 C4 -0.134 REMARK 500 9 DC B 6 C4 DC B 6 C5 -0.074 REMARK 500 9 DC B 6 C5 DC B 6 C6 -0.059 REMARK 500 9 DG B 7 P DG B 7 O5' -0.087 REMARK 500 9 DG B 7 O5' DG B 7 C5' -0.281 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 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 10 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 4 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 10 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT B 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 7 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA B 9 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 10 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DG B 1 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT B 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 3 DC B 6 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 206 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2K1Y A 1 11 PDB 2K1Y 2K1Y 1 11 DBREF 2K1Y B 1 11 PDB 2K1Y 2K1Y 1 11 SEQRES 1 A 11 DC DG DT DA DC GNE DC DA DT DG DC SEQRES 1 B 11 DG DC DA DT DG DC DG DT DA DC DG HET GNE A 6 35 HETNAM GNE 1,N2-ETHENOGUANINE FORMUL 1 GNE C12 H14 N5 O7 P LINK O3' DC A 5 P GNE A 6 1555 1555 1.62 LINK O3' GNE A 6 P DC A 7 1555 1555 1.62 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