HEADER DNA 20-JAN-12 2LOA 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, BIFUNCTIONAL ZN(II) MACROCYCLIC COMPLEX, DNA, CYCLEN EXPDTA SOLUTION NMR AUTHOR J.R.MORROW,M.A.FOUNTAIN,I.A.DEL MUNDO,K.E.SITER REVDAT 3 14-JUN-23 2LOA 1 REMARK REVDAT 2 23-MAY-12 2LOA 1 JRNL REVDAT 1 14-MAR-12 2LOA 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, HYPERCHEM 6, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 HYPERCUBE, INC (HYPERCHEM), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ONE OF THE STRUCTURES FROM PDB 2LO8 WAS REMARK 3 SELECTED AND USED FOR DOCKING OF OF THE ZN(CY4Q), ONE CONFORMER REMARK 3 WAS SELECTED FROM THE THE CYANA CALCULATION ABOVE AND THE REMARK 3 ZN(CY4Q) DOCKED USING ENERGY MINIMIZATION AND DISTANCE REMARK 3 RESTRAINTS OBTAINED FROM NMR DATA. REMARK 4 REMARK 4 2LOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000102628. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 278 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' REMARK 210 -D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3'), 100% D2O; 2.0 MM DNA (5'- REMARK 210 D(*GP*CP*CP*GP*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 : SPARKY 3.14 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, DOCKING WITH ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N3 DT A 9 ZN ZN A 102 1.50 REMARK 500 REMARK 500 REMARK: NULL 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 DG A 8 O4' DG A 8 C4' -0.071 REMARK 500 DT A 9 O4' DT A 9 C4' -0.069 REMARK 500 DT A 9 C4 DT A 9 O4 -0.107 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 DG A 2 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 2 C1' - O4' - C4' ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 5 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 5 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 5 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 5 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A 7 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 8 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 8 C6 - N1 - C2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A 8 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 8 C5 - C6 - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT A 9 O4' - C4' - C3' ANGL. DEV. = -9.6 DEGREES REMARK 500 DT A 9 C5' - C4' - O4' ANGL. DEV. = 10.8 DEGREES REMARK 500 DT A 9 C1' - O4' - C4' ANGL. DEV. = 6.5 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT A 9 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT A 9 N3 - C4 - O4 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 10 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 10 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 10 C5 - C6 - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 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 DT A 9 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 9 O2 REMARK 620 2 C4Q A 101 N4' 171.4 REMARK 620 3 C4Q A 101 N3' 108.3 64.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C4Q A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LO5 RELATED DB: PDB REMARK 900 RELATED ID: 2LO8 RELATED DB: PDB REMARK 900 RELATED ID: 18199 RELATED DB: BMRB DBREF 2LOA A 2 11 PDB 2LOA 2LOA 2 11 SEQRES 1 A 10 DG DC DC DG DC DA DG DT DG DC HET C4Q A 101 50 HET ZN A 102 1 HETNAM C4Q 4-(1,4,7,10-TETRAAZACYCLODODECAN-1-YLMETHYL)QUINOLINE HETNAM ZN ZINC ION FORMUL 2 C4Q C18 H27 N5 FORMUL 3 ZN ZN 2+ LINK O2 DT A 9 ZN ZN A 102 1555 1555 1.89 LINK N4' C4Q A 101 ZN ZN A 102 1555 1555 2.64 LINK N3' C4Q A 101 ZN ZN A 102 1555 1555 2.67 SITE 1 AC1 3 DG A 8 DT A 9 ZN A 102 SITE 1 AC2 2 DT A 9 C4Q A 101 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