10 20 30 40 50 60 70 80 2OEY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 01-JAN-07 2OEY
TITLE SOLUTION STRUCTURE OF A DESIGNED SPIROCYCLIC HELICAL LIGAND TITLE 2 BINDING AT A TWO-BASE BULGE SITE IN DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (25-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS IS AN ARTIFICAL SEQUENCE
KEYWDS DESIGNED SPIROCYCLIC HELICAL LIGAND-BULGED DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR N.ZHANG,Y.LIN,Z.XIAO,G.B.JONES,I.H.GOLDBERG
REVDAT 3 24-FEB-09 2OEY 1 VERSN REVDAT 2 01-MAY-07 2OEY 1 JRNL REVDAT 1 10-APR-07 2OEY 0
JRNL AUTH N.ZHANG,Y.LIN,Z.XIAO,G.B.JONES,I.H.GOLDBERG JRNL TITL SOLUTION STRUCTURE OF A DESIGNED SPIROCYCLIC JRNL TITL 2 HELICAL LIGAND BINDING AT A TWO-BASE BULGE SITE IN JRNL TITL 3 DNA. JRNL REF BIOCHEMISTRY V. 46 4793 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17388570 JRNL DOI 10.1021/BI602599D
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG REMARK 1 TITL SOLUTION STRUCTURE OF A TWO-BASE DNA BULGE REMARK 1 TITL 2 COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOGUE REMARK 1 REF SCIENCE V. 272 1943 1996 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 8658168 REMARK 1 DOI 10.1126/SCIENCE.272.5270.1943 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.GAO,A.STASSINOPOLOUS,J.JI,Y.KWON,S.BARE, REMARK 1 AUTH 2 I.H.GOLDBERG REMARK 1 TITL INDUCED FORMATION OF A DNA BULGE STRUCTURE BY A REMARK 1 TITL 2 MOLECULAR WEDGE LIGAND-POST ACTIVATED REMARK 1 TITL 3 NEOCARZINOSTATIN CHROMOPHORE REMARK 1 REF BIOCHEMISTRY V. 41 5131 2002 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 11955061 REMARK 1 DOI 10.1021/BI012112O
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 531 RESTRAINTS, 506 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 25 DIHEDRAL ANGLE RESTRAINTS,40 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS.
REMARK 4 REMARK 4 2OEY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-07. REMARK 100 THE RCSB ID CODE IS RCSB041050.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 283; 298; 303 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL; 100 REMARK 210 MM NACL; 100 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM PHOSPHATE BUFFER; 100 MM REMARK 210 NACL; 10MM PHOSPHATE BUFFER; REMARK 210 100 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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: THIS STRUCTURE WAS DETERMINED USING STANDARD METHODS REMARK 210 FOR DNA-DRUG COMPLEX.
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 1 DC A 1 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 2 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 3 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT A 4 C1' - O4' - C4' ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 5 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG A 6 C3' - C2' - C1' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 7 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT A 7 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 8 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 9 C3' - C2' - C1' ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 11 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 12 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 12 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 12 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 13 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DT A 13 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 14 O4' - C4' - C3' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 14 C3' - C2' - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DT A 14 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 15 C3' - C2' - C1' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DT A 15 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG A 17 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 17 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 17 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 18 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 19 C3' - C2' - C1' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 DA A 19 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 513 ANGLE DEVIATIONS. 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 S2A A 26
DBREF 2OEY A 1 25 PDB 2OEY 2OEY 1 25
SEQRES 1 A 25 DC DC DA DT DC DG DT DC DT DA DC DC DT SEQRES 2 A 25 DT DT DG DG DT DA DG DG DA DT DG DG
HET S2A A 26 73
HETNAM S2A (1R,3A'S,10'S,10A'R)-7-METHOXY-2-OXO-10',10A'-DIHYDRO- HETNAM 2 S2A 2H,3A'H-SPIRO[NAPHTHALENE-1,3'-PENTALENO[1,2- HETNAM 3 S2A B]NAPHTHALEN]-10'-YL 2,6-DIDEOXY-2-(METHYLAMINO)- HETNAM 4 S2A ALPHA-D-GALACTOPYRANOSIDE
HETSYN S2A SPIROCYCLIC ALKENE
FORMUL 2 S2A C33 H33 N O6
SITE 1 AC1 5 DG A 6 DT A 7 DC A 8 DG A 20 SITE 2 AC1 5 DG A 21
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