HEADER DNA 24-JUL-99 1C34 TITLE SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE CAVEAT 1C34 SEVEN RIBOSE CARBONS HAVE INCORRECT CHIRALITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THROMBIN BINDING APTAMER INTERMIDIATE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS APTAMER, THROMBIN BINDING, POTASSIUM, METAL BINDING SITES, KEYWDS 2 QUADRUPLEX, INTERMEDIATE, DNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR P.H.BOLTON,V.M.MARATHIAS,K.WANG REVDAT 6 22-MAY-24 1C34 1 REMARK REVDAT 5 16-FEB-22 1C34 1 REMARK REVDAT 4 24-FEB-09 1C34 1 VERSN REVDAT 3 16-MAY-00 1C34 1 CAVEAT JRNL EXPDTA REVDAT 2 29-DEC-99 1C34 1 JRNL REVDAT 1 18-AUG-99 1C34 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 MANGANESE REMARK 1 TITL 2 BINDING SITES OF DNA QUADRUPLEXES IN SOLUTION BY EPR AND NMR REMARK 1 TITL 3 IN THE PRESENCE AND 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 : VNMR 6.1B, FELIX 970, X-PLOR 3.1 REMARK 3 AUTHORS : VARIAN (VNMR), MSI (FELIX), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C34 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 DEPOSITION ID IS D_1000009397. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 278 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, 1.4 MM KCL, 20 MM REMARK 210 TRISD11 PH=7.0; 140 MM NACL, 1.4 REMARK 210 MM KCL, 20 MM TRISD11 PH=7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; PE-COSY; ROESY; BASD REMARK 210 -TOCSY 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 3.1 REMARK 210 METHOD USED : STRUCTURE REFINEMENT OF THE DNA REMARK 210 WAS PREFORMED USING COMPLETE REMARK 210 RELAXATION MATRIX, RESTRAINED REMARK 210 MOLECULAR DYNAMICS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : 80 TO 100PS STRUCTURES FROM REMARK 210 DYNAMICS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE IS THE INTERMEDIATE FORM OF THE 15MER REMARK 210 QUADRUPLEX WITH ONLY 1 POTASSSIUM PER DNA MOLECULE. 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 OP1 DG A 11 H3 DT A 12 1.37 REMARK 500 H1 DG A 10 O6 DG A 15 1.43 REMARK 500 O6 DG A 1 H1 DG A 15 1.48 REMARK 500 H22 DG A 8 O4 DT A 9 1.52 REMARK 500 H1 DG A 1 O6 DG A 6 1.54 REMARK 500 H3 DT A 7 N3 DG A 11 1.57 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 1 DT A 3 C6 DT A 3 N1 -0.043 REMARK 500 1 DG A 5 C5' DG A 5 C4' 0.042 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.040 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.055 REMARK 500 3 DG A 1 C5' DG A 1 C4' 0.044 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.040 REMARK 500 4 DT A 3 N3 DT A 3 C4 -0.067 REMARK 500 4 DT A 3 C4 DT A 3 C5 -0.057 REMARK 500 4 DT A 3 C6 DT A 3 N1 -0.069 REMARK 500 4 DT A 3 C2 DT A 3 O2 -0.057 REMARK 500 4 DT A 4 C5 DT A 4 C7 0.044 REMARK 500 4 DT A 9 N1 DT A 9 C2 0.052 REMARK 500 4 DT A 13 C5 DT A 13 C7 0.044 REMARK 500 5 DT A 3 C4 DT A 3 C5 -0.077 REMARK 500 5 DG A 15 C2' DG A 15 C1' 0.072 REMARK 500 6 DT A 4 C5 DT A 4 C7 0.050 REMARK 500 6 DT A 9 C5 DT A 9 C7 0.042 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.040 REMARK 500 6 DT A 13 C5 DT A 13 C7 0.046 REMARK 500 6 DG A 15 C2' DG A 15 C1' 0.065 REMARK 500 7 DG A 2 O3' DT A 3 P -0.101 REMARK 500 7 DT A 3 C5 DT A 3 C7 0.047 REMARK 500 7 DT A 4 C5 DT A 4 C7 0.043 REMARK 500 7 DT A 9 C5 DT A 9 C7 0.047 REMARK 500 7 DT A 12 C3' DT A 12 C2' 0.073 REMARK 500 7 DT A 13 C5 DT A 13 C7 0.040 REMARK 500 8 DT A 3 C5 DT A 3 C7 0.037 REMARK 500 8 DT A 13 C5 DT A 13 C7 0.043 REMARK 500 8 DG A 15 C2' DG A 15 C1' 0.061 REMARK 500 9 DT A 4 C5 DT A 4 C7 0.036 REMARK 500 9 DT A 12 C3' DT A 12 C2' 0.079 REMARK 500 10 DT A 3 N3 DT A 3 C4 -0.051 REMARK 500 10 DT A 3 C4 DT A 3 C5 -0.064 REMARK 500 10 DT A 3 C6 DT A 3 N1 -0.048 REMARK 500 10 DT A 13 C5 DT A 13 C7 0.039 REMARK 500 11 DG A 1 C5' DG A 1 C4' 0.046 REMARK 500 11 DG A 2 C5' DG A 2 C4' 0.046 REMARK 500 11 DT A 7 C5 DT A 7 C7 0.044 REMARK 500 11 DT A 13 C5 DT A 13 C7 0.039 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. = -5.5 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 2 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT A 3 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 3 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 4 P - O5' - C5' ANGL. DEV. = 11.3 DEGREES REMARK 500 1 DT A 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 4 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 5 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DT A 7 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DT A 9 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 9 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 11 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 11 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 12 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 12 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 13 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 13 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DG A 14 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DG A 14 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG A 15 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DG A 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DG A 2 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 471 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1C34 A 1 15 PDB 1C34 1C34 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 MODEL 1