HEADER DNA 01-NOV-13 2MGN TITLE SOLUTION STRUCTURE OF A G-QUADRUPLEX BOUND TO THE BISQUINOLINIUM TITLE 2 COMPOUND PHEN-DC3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP COMPND 3 *GP*GP*AP*AP*GP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS LIGAND, C-MYC PROMOTER, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.J.CHUNG,B.HEDDI,F.HAMON,M.P.TEULADE-FICHOU,A.T.PHAN REVDAT 3 02-APR-14 2MGN 1 HETATM REVDAT 2 05-FEB-14 2MGN 1 JRNL REVDAT 1 22-JAN-14 2MGN 0 JRNL AUTH W.J.CHUNG,B.HEDDI,F.HAMON,M.P.TEULADE-FICHOU,A.T.PHAN JRNL TITL SOLUTION STRUCTURE OF A G-QUADRUPLEX BOUND TO THE JRNL TITL 2 BISQUINOLINIUM COMPOUND PHEN-DC3. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 999 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 24356977 JRNL DOI 10.1002/ANIE.201308063 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, X-PLOR_NIH REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EXTRACTED DISTANCES FROM STRUCTURE OF REMARK 3 FREE DNA (PDB ENTRY 2A5P) WERE USED DURING CALCULATION REMARK 4 REMARK 4 2MGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-13. REMARK 100 THE RCSB ID CODE IS RCSB103593. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 90; 45 REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : 0.2-2.0 MM DNA, 0.2-2.0 MM PQ3, REMARK 210 90% H2O/10% D2O; 1.0 MM DNA, 1.0 REMARK 210 MM [U-100% 13C]-CH3 PQ3, 100% REMARK 210 D2O; 0.2-2.0 MM DNA, 0.2-2.0 MM REMARK 210 PQ3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 2D 13C-FILTERED REMARK 210 HSQC-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, SPARKY, TOPSPIN, X-PLOR_ REMARK 210 NIH REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: 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 3 DG A 23 C5' DG A 23 C4' 0.044 REMARK 500 5 DG A 23 C5' DG A 23 C4' 0.044 REMARK 500 6 DG A 23 C5' DG A 23 C4' 0.045 REMARK 500 10 DT A 10 C6 DT A 10 N1 -0.045 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 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 9 DA A 22 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 10 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES 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 PQ3 A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19594 RELATED DB: BMRB DBREF 2MGN A 1 24 PDB 2MGN 2MGN 1 24 SEQRES 1 A 24 DT DG DA DG DG DG DT DG DG DT DG DA DG SEQRES 2 A 24 DG DG DT DG DG DG DG DA DA DG DG HET PQ3 A 25 68 HETNAM PQ3 N2,N9-BIS(1-METHYLQUINOLIN-3-YL)-1,10-PHENANTHROLINE-2, HETNAM 2 PQ3 9-DICARBOXAMIDE HETSYN PQ3 PHEN-DC3 FORMUL 2 PQ3 C34 H26 N6 O2 SITE 1 AC1 5 DA A 3 DG A 4 DG A 8 DG A 13 SITE 2 AC1 5 DG A 17 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 MASTER 133 0 1 0 0 0 2 6 0 0 0 2 END