HEADER DNA 18-JAN-12 2LO8 TITLE STRUCTURAL BASIS FOR BIFUNCTIONAL ZN(II) MACROCYCLIC COMPLEX TITLE 2 RECOGNITION OF THYMINE BULGES IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA_(5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')_; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS THYMINE BULGE, HAIRPIN, BIFUNCTIONAL ZN(II) MACROCYCLIC COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR J.R.MORROW,M.A.FOUNTAIN,I.A.DEL MUNDO,K.E.SITER REVDAT 2 23-MAY-12 2LO8 1 JRNL REVDAT 1 14-MAR-12 2LO8 0 JRNL AUTH I.M.DEL MUNDO,K.E.SITERS,M.A.FOUNTAIN,J.R.MORROW JRNL TITL STRUCTURAL BASIS FOR BIFUNCTIONAL ZINC(II) MACROCYCLIC JRNL TITL 2 COMPLEX RECOGNITION OF THYMINE BULGES IN DNA. JRNL REF INORG.CHEM. V. 51 5444 2012 JRNL REFN ISSN 0020-1669 JRNL PMID 22507054 JRNL DOI 10.1021/IC3004245 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-12. REMARK 100 THE RCSB ID CODE IS RCSB102626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 5 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM DNA (5'-D(*GP*CP*CP*GP* REMARK 210 CP*AP*GP*TP*GP*C)-3'), 100% D2O; 2.0 MM DNA (5'-D(*GP*CP*CP*GP* REMARK 210 CP*AP*GP*TP*GP*C)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY 3.14 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 9 O4' DT A 9 C4' -0.072 REMARK 500 2 DT A 9 O4' DT A 9 C4' -0.072 REMARK 500 2 DG A 10 O4' DG A 10 C4' -0.069 REMARK 500 3 DG A 5 O4' DG A 5 C4' -0.063 REMARK 500 3 DT A 9 O4' DT A 9 C4' -0.074 REMARK 500 3 DG A 10 O4' DG A 10 C4' -0.060 REMARK 500 4 DT A 9 O4' DT A 9 C4' -0.072 REMARK 500 4 DG A 10 O4' DG A 10 C4' -0.066 REMARK 500 5 DT A 9 O4' DT A 9 C4' -0.074 REMARK 500 6 DT A 9 O4' DT A 9 C4' -0.077 REMARK 500 6 DC A 11 O4' DC A 11 C4' -0.089 REMARK 500 7 DG A 8 O4' DG A 8 C4' -0.071 REMARK 500 7 DT A 9 O4' DT A 9 C4' -0.090 REMARK 500 7 DC A 11 O4' DC A 11 C4' -0.087 REMARK 500 8 DG A 8 O4' DG A 8 C4' -0.071 REMARK 500 8 DT A 9 O4' DT A 9 C4' -0.095 REMARK 500 8 DC A 11 O4' DC A 11 C4' -0.091 REMARK 500 9 DT A 9 O4' DT A 9 C4' -0.065 REMARK 500 10 DG A 8 O4' DG A 8 C4' -0.071 REMARK 500 10 DT A 9 O4' DT A 9 C4' -0.069 REMARK 500 11 DT A 9 O4' DT A 9 C4' -0.071 REMARK 500 12 DT A 9 O4' DT A 9 C4' -0.066 REMARK 500 13 DT A 9 O4' DT A 9 C4' -0.071 REMARK 500 14 DT A 9 O4' DT A 9 C4' -0.068 REMARK 500 15 DT A 9 O4' DT A 9 C4' -0.069 REMARK 500 16 DG A 5 O4' DG A 5 C4' -0.063 REMARK 500 16 DT A 9 O4' DT A 9 C4' -0.063 REMARK 500 17 DG A 5 O4' DG A 5 C4' -0.062 REMARK 500 17 DT A 9 O4' DT A 9 C4' -0.063 REMARK 500 18 DT A 9 O4' DT A 9 C4' -0.068 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' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 2 C1' - O4' - C4' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 5 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 5 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 5 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 5 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 7 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA A 7 C1' - O4' - C4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 8 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 8 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 8 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT A 9 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DT A 9 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT A 9 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 10 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 10 C1' - O4' - C4' ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 10 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 10 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 10 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 2 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DG A 2 C1' - O4' - C4' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DG A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 5 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DG A 5 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DG A 5 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 7 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DA A 7 C1' - O4' - C4' ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = -11.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 594 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LO5 RELATED DB: PDB REMARK 900 DNA HAIRPIN WITH THYMINE BULGE IN STEM. REMARK 900 RELATED ID: 18199 RELATED DB: BMRB DBREF 2LO8 A 2 11 PDB 2LO8 2LO8 2 11 SEQRES 1 A 10 DG DC DC DG DC DA DG DT DG DC 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 191 0 0 0 0 0 0 6 0 0 0 1 END