HEADER DNA 24-JUL-99 1C32 TITLE SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS TITLE 2 INTERMIDIATE CAVEAT 1C32 SIX RIBOSE CARBONS HAVE INCORRECT CHIRALITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THROMBIN BINDING QUADRUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS APTAMER, QUADRUPLEX, DNA, METAL BINDING DNA, POTASSIUM, KEYWDS 2 THROMBIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR P.H.BOLTON,V.M.MARATHIAS,K.WANG REVDAT 4 24-FEB-09 1C32 1 VERSN REVDAT 3 16-MAY-00 1C32 1 CAVEAT JRNL CRYST1 EXPDTA REVDAT 2 29-DEC-99 1C32 1 JRNL REVDAT 1 18-AUG-99 1C32 0 JRNL AUTH V.M.MARATHIAS,P.H.BOLTON JRNL TITL STRUCTURES OF THE POTASSIUM-SATURATED, 2:1, AND JRNL TITL 2 INTERMEDIATE, 1:1, FORMS OF A QUADRUPLEX DNA. JRNL REF NUCLEIC ACIDS RES. V. 28 1969 2000 JRNL REFN ISSN 0305-1048 JRNL PMID 10756199 JRNL DOI 10.1093/NAR/28.9.1969 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.H.BOLTON,V.M.MARATHIAS,K.WANG REMARK 1 TITL DETERMINATION OF THE NUMBER AND LOCATION OF THE REMARK 1 TITL 2 MANGANESE BINDING SITES OF DNA QUADRUPLEXES IN REMARK 1 TITL 3 SOLUTION BY EPR AND NMR IN THE PRESENCE AND REMARK 1 TITL 4 ABSENCE OF THROMBIN REMARK 1 REF J.MOL.BIOL. V. 260 378 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1996.0408 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 970, X-PLOR 3.1 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 303 NOE VOLUME CONSTRAINTS FROM THE REMARK 3 100 MS AND 498 NOE FROM THE 250 MS NOESY DATA WERE USED. IN REMARK 3 ADDITION 10 NOE CONSTRAINTS INVOLVING THE IMINO PROTONS OF REMARK 3 RESIDUES G1, G5, G6, G8, G10, G14, AND G15 WERE USED AS REMARK 3 DISTANCE CONSTRAINTS. FOUR HYDROGEN BONDS WERE USED FOR EACH REMARK 3 GUANINE INVOLVED IN A QUARTET. EXPERIMENTAL COUPLING CONSTANTS REMARK 3 WERE USED TO GENERATE 45 DIHEDRAL CONSTRAINTS, 15 FROM BASHD- REMARK 3 TOCSY EXPERIMENTS (H3*-31P), AND 30 FROM PE-COSY DATA (H1*-C1* REMARK 3 - C2*-1H2* AND H1*-C1*-C2*-2H2*). ADDITIONAL CONSTRAINTS WERE REMARK 3 USED TO KEEP THE PURINE RINGS PLANAR. THE STARTING STRUCTURE REMARK 3 USED WAS THE STRUCTURE OBTAINED IN A PREVIOUS REFINEMENT. THE REMARK 3 NON-BONDED INTERACTION CUT-OFF WAS SET TO 11.5 A, USING X-PLOR REMARK 3 PROTOCOLS. THE ACTIVE DISTANCE OF THE SWITCHING FUNCTIONS WAS REMARK 3 7.5 TO 10.5 A. THE DISTANCE CUT-OFF FOR THE HYDROGEN BONDING REMARK 3 INTERACTIONS WAS 7.5 A. THE SWITCHING FUNCTION FOR HYDROGEN REMARK 3 BONDING INTERACTIONS WAS ACTIVE FROM 4.0 TO 6.5 A. THE ENERGY REMARK 3 OF THE STARTING STRUCTURE WAS MINIMIZED IN 200 STEPS OF REMARK 3 POWELL'S CONJUGATE GRADIENT MINIMIZATION. THE RELAXATION REMARK 3 MATRIX REFINEMENTS WERE CARRIED OUT IN VACUUM AT 300K WITH A REMARK 3 RELATIVE WEIGHTING OF ALL THE EXPERIMENTAL CONSTRAINTS (NOE, REMARK 3 DISTANCE AND DIHEDRAL) OF 60 KCAL/MOL. SUBSEQUENTLY, A 100 PS REMARK 3 RELAXATION MATRIX TRAJECTORY WAS CONDUCTED WITH STRUCTURES REMARK 3 SAVED EVERY 2 PS. THE TRAJECTORIES STABILIZED AFTER 30 PS. REMARK 3 UPON COMPLETION OF THE SIMULATION AN ADDITIONAL 200 STEP REMARK 3 CONJUGATE GRADIENT MINIMIZATION WAS CONDUCTED TO PRODUCE THE REMARK 3 FINAL STRUCTURES. THE ROOT MEAN SQUARE DEVIATION {OF WHAT?} REMARK 3 WAS CALCULATED TO BE 0.14. THE NOE CROSS-PEAK VOLUMES OF THE REMARK 3 STRUCTURES OBTAINED BETWEEN 80-100 PS AT INTERVALS OF 2 PS REMARK 3 WERE BACKCALCULATED USING THE FELIX 970 SOFTWARE PACKAGE (MSI REMARK 3 INC.) PARAMETERS USED IN THE BACKCALCULATION PROTOCOL ARE AS REMARK 3 FOLLOWS: A CORRELATION TIME OF 5.0 NS, A Z-LEAKAGE RATE OF 3.0 REMARK 3 S-1 AND A DISTANCE CUT OFF OF 7.5 A. NOE SPECTRA OF THESE 10 REMARK 3 STRUCTURES WERE THEN BACKCALCULATED AND AVERAGED. 40 NOE REMARK 3 INTENSITIES FROM THE EXPERIMENTAL NOESY SPECTRA WERE USED TO REMARK 3 NORMALIZE THE BACKCALCULATED TO THE THEORETICAL NOES. THE REMARK 3 NORMALIZATION AND AVERAGING PROCESSES WERE CONDUCTED ON A IN REMARK 3 HOUSE PROGRAM. THE RMS, R AND Q VALUES OF THE AVERAGED REMARK 3 STRUCTURE THAT ARE 0.28, 0.68 AND 0.30. REMARK 4 REMARK 4 1C32 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009395. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 15; 5 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 140 MM NACL; 140 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 140 MM NACL, 5 MM KCL, 20 MM REMARK 210 TRISD11, PH=7.0 BUFFER; 140 MM REMARK 210 NACL, 5 MM KCL, 20 MM TRISD11, REMARK 210 PH=7.0 BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, PE-COSY, ROESY, REMARK 210 BASD-TOCSY, WATERGATED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1B, FELIX 970, X-PLOR REMARK 210 3.1 REMARK 210 METHOD USED : STRUCTURE REFINEMENT OF THE REMARK 210 DNA WAS PERFORMED USING REMARK 210 COMPLETE RELAXATION MATRIX, REMARK 210 RESTRAINED MOLECULAR DYNAMICS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 80-88 AND 91-100 PS REMARK 210 STRUCTURES FORM TRAJECTORY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THIS FILE CONTAINS THE COORDINATES OF 10 STRUCTURES REMARK 210 FROM 80-88 AND 91-100 PS. 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 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 4 C5 DT A 4 C7 0.048 REMARK 500 1 DG A 5 C2' DG A 5 C1' 0.088 REMARK 500 1 DG A 8 C4' DG A 8 C3' 0.064 REMARK 500 1 DG A 8 C2' DG A 8 C1' 0.063 REMARK 500 1 DG A 10 C5' DG A 10 C4' 0.042 REMARK 500 1 DT A 12 C5' DT A 12 C4' 0.053 REMARK 500 1 DT A 12 C2' DT A 12 C1' 0.065 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.054 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.047 REMARK 500 2 DG A 8 C5' DG A 8 C4' 0.042 REMARK 500 2 DG A 8 C2' DG A 8 C1' 0.062 REMARK 500 2 DG A 10 C5' DG A 10 C4' 0.043 REMARK 500 2 DG A 11 C6 DG A 11 N1 -0.049 REMARK 500 2 DT A 12 C5 DT A 12 C7 0.037 REMARK 500 2 DT A 13 C5 DT A 13 C7 0.041 REMARK 500 3 DT A 3 C4 DT A 3 C5 -0.065 REMARK 500 3 DT A 4 C5' DT A 4 C4' 0.046 REMARK 500 3 DG A 10 C5' DG A 10 C4' 0.043 REMARK 500 3 DT A 12 C5' DT A 12 C4' 0.048 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.036 REMARK 500 4 DG A 5 C2' DG A 5 C1' 0.063 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 4 DG A 8 C2' DG A 8 C1' 0.082 REMARK 500 4 DT A 9 C5' DT A 9 C4' 0.044 REMARK 500 4 DG A 10 C5' DG A 10 C4' 0.048 REMARK 500 4 DT A 12 C5 DT A 12 C7 0.044 REMARK 500 4 DT A 13 C5 DT A 13 C7 0.046 REMARK 500 5 DG A 2 C5' DG A 2 C4' 0.067 REMARK 500 5 DT A 3 C5 DT A 3 C7 0.049 REMARK 500 5 DT A 4 C5 DT A 4 C7 0.048 REMARK 500 5 DG A 5 P DG A 5 OP1 -0.128 REMARK 500 5 DG A 5 P DG A 5 OP2 -0.123 REMARK 500 5 DG A 5 P DG A 5 O5' -0.079 REMARK 500 5 DG A 5 C6 DG A 5 N1 -0.044 REMARK 500 5 DG A 8 C5' DG A 8 C4' 0.053 REMARK 500 5 DG A 8 C2' DG A 8 C1' 0.069 REMARK 500 5 DT A 9 P DT A 9 O5' 0.072 REMARK 500 5 DT A 12 C5 DT A 12 C7 0.041 REMARK 500 5 DT A 13 C5 DT A 13 C7 0.052 REMARK 500 5 DG A 14 C3' DG A 14 C2' 0.075 REMARK 500 6 DG A 5 C2 DG A 5 N2 -0.061 REMARK 500 6 DT A 7 C5 DT A 7 C7 0.072 REMARK 500 6 DT A 12 C2' DT A 12 C1' 0.061 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.049 REMARK 500 6 DT A 13 C5 DT A 13 C7 0.037 REMARK 500 7 DG A 2 C5' DG A 2 C4' 0.043 REMARK 500 7 DT A 4 C5 DT A 4 C7 0.042 REMARK 500 7 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 7 DT A 7 N1 DT A 7 C2 -0.059 REMARK 500 7 DT A 7 N3 DT A 7 C4 -0.054 REMARK 500 REMARK 500 THIS ENTRY HAS 77 BOND DEVIATIONS. 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 1 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG A 1 O4' - C1' - C2' ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 1 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 14.8 DEGREES REMARK 500 1 DT A 3 C4' - C3' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT A 3 O4' - C1' - C2' ANGL. DEV. = -10.9 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 14.2 DEGREES REMARK 500 1 DT A 4 C1' - O4' - C4' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 4 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 5 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 7 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 8 C1' - O4' - C4' ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 8 C3' - C2' - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -8.9 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 7 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DT A 9 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 9 C4 - C5 - C6 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 10 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -11.3 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DT A 9 C3' - O3' - P ANGL. DEV. = 11.8 DEGREES REMARK 500 1 DG A 11 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT A 12 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 12 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 13 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 602 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QDF RELATED DB: PDB REMARK 900 OLDER STRUCTURE DETERMINATION DBREF 1C32 A 1 15 PDB 1C32 1C32 1 15 SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG 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 245 0 0 0 0 0 0 6 0 0 0 2 END