HEADER DNA 28-MAR-98 1A8W TITLE A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING TITLE 2 SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 TITLE 3 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA QUADRUPLEX CONTAINING GGGG TETRADS AND GC WATSON-CRICK COMPND 3 BASE PAIRS; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: K+ CATION STABILIZED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CATION DEPENDENT CONFORMATIONAL TRANSITIONS, K+ CATION COORDINATION KEYWDS 2 SITES, K+ CATION ENCAPSULATION WITHIN A HAIRPIN LOOP, DNA KEYWDS 3 QUADRUPLEXES TARGETED TO HIV INTEGRASE, DEOXYRIBONUCLEIC ACID, G-G- KEYWDS 4 G-C REPEAT-CONTAINING DNA QUADRUPLEXES, MONOVALENT, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR S.BOUAZIZ,A.KETTANI,D.J.PATEL REVDAT 5 22-MAY-24 1A8W 1 REMARK REVDAT 4 16-FEB-22 1A8W 1 REMARK REVDAT 3 24-FEB-09 1A8W 1 VERSN REVDAT 2 18-NOV-98 1A8W 1 COMPND REMARK TITLE JRNL REVDAT 2 2 1 KEYWDS HEADER REVDAT 1 14-OCT-98 1A8W 0 JRNL AUTH S.BOUAZIZ,A.KETTANI,D.J.PATEL JRNL TITL A K CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP JRNL TITL 2 SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C JRNL TITL 3 REPEATS. JRNL REF J.MOL.BIOL. V. 282 637 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9737927 JRNL DOI 10.1006/JMBI.1998.2031 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1A8W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170539. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5 MM NACL, 0.2 MM NA2HPO4 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : ACCEPTABLE COVALENT ENERGY, LOW REMARK 210 DISTANCE RESTRAINT VIOLATIONS, REMARK 210 FAVORABLE NON-BONDED ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED BY USING 5 NOESY MIXING TIME REMARK 210 EXPERIMENTS IN D2O (50, 100, 150, 200 AND 300 MS) AND 2 NOESY REMARK 210 MIXING TIME EXPERIMENTS IN H2O (80 AND 250 MS) 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 H3 DT A 6 O2 DT A 8 1.56 REMARK 500 H3 DT B 6 O2 DT B 8 1.56 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 DG A 1 C5' DG A 1 C4' 0.050 REMARK 500 1 DC A 4 C5' DC A 4 C4' 0.043 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.043 REMARK 500 1 DT A 7 C5 DT A 7 C7 0.044 REMARK 500 1 DG B 1 C5' DG B 1 C4' 0.050 REMARK 500 1 DT B 5 C5 DT B 5 C7 0.055 REMARK 500 1 DT B 7 C5 DT B 7 C7 0.043 REMARK 500 1 DT B 8 C5' DT B 8 C4' 0.044 REMARK 500 2 DC A 4 C5' DC A 4 C4' 0.043 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.043 REMARK 500 2 DT A 7 C5 DT A 7 C7 0.037 REMARK 500 2 DT A 8 C5' DT A 8 C4' 0.069 REMARK 500 2 DG A 9 C5' DG A 9 C4' 0.047 REMARK 500 2 DC B 4 C5' DC B 4 C4' 0.043 REMARK 500 2 DT B 5 C5 DT B 5 C7 0.037 REMARK 500 2 DT B 7 C5 DT B 7 C7 0.044 REMARK 500 2 DT B 8 C5' DT B 8 C4' 0.067 REMARK 500 2 DG B 9 C5' DG B 9 C4' 0.047 REMARK 500 3 DG A 1 C5' DG A 1 C4' 0.043 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.043 REMARK 500 3 DT A 8 C5' DT A 8 C4' 0.073 REMARK 500 3 DT A 8 C5 DT A 8 C7 0.039 REMARK 500 3 DG A 9 C5' DG A 9 C4' 0.049 REMARK 500 3 DG B 1 C5' DG B 1 C4' 0.043 REMARK 500 3 DT B 5 C5 DT B 5 C7 0.059 REMARK 500 3 DT B 7 C5 DT B 7 C7 0.043 REMARK 500 3 DT B 8 C5' DT B 8 C4' 0.074 REMARK 500 3 DT B 8 C5 DT B 8 C7 0.040 REMARK 500 3 DG B 9 C5' DG B 9 C4' 0.050 REMARK 500 4 DC A 4 C5' DC A 4 C4' 0.047 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.044 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 4 DT A 8 C5' DT A 8 C4' 0.062 REMARK 500 4 DT A 8 C5 DT A 8 C7 0.048 REMARK 500 4 DG A 9 C5' DG A 9 C4' 0.049 REMARK 500 4 DC B 4 C5' DC B 4 C4' 0.048 REMARK 500 4 DT B 5 C5 DT B 5 C7 0.041 REMARK 500 4 DT B 7 C5 DT B 7 C7 0.040 REMARK 500 4 DT B 8 C5' DT B 8 C4' 0.061 REMARK 500 4 DT B 8 C5 DT B 8 C7 0.047 REMARK 500 4 DG B 9 C5' DG B 9 C4' 0.048 REMARK 500 5 DT A 5 C5' DT A 5 C4' 0.046 REMARK 500 5 DT A 5 C5 DT A 5 C7 0.048 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.038 REMARK 500 5 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 5 DT A 8 C5' DT A 8 C4' 0.078 REMARK 500 5 DT B 5 C5' DT B 5 C4' 0.045 REMARK 500 5 DT B 5 C5 DT B 5 C7 0.049 REMARK 500 5 DT B 6 C5 DT B 6 C7 0.041 REMARK 500 5 DT B 7 C5 DT B 7 C7 0.042 REMARK 500 REMARK 500 THIS ENTRY HAS 76 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 C5' - C4' - C3' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DG A 1 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC A 4 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC A 4 C5' - C4' - C3' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DC A 4 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC A 4 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DT A 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 6 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 7 C4' - C3' - O3' ANGL. DEV. = 13.4 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 9 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 9 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 10 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 10 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DC A 12 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 12 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG B 1 C5' - C4' - C3' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DG B 1 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG B 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 4 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC B 4 C5' - C4' - C3' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC B 4 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC B 4 C3' - C2' - C1' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DT B 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 6 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 7 C4' - C3' - O3' ANGL. DEV. = 13.4 DEGREES REMARK 500 1 DT B 8 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG B 9 C5' - C4' - C3' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG B 9 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG B 10 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DG B 10 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 10 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DC B 12 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC B 12 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 1 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 2 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG A 2 C3' - C2' - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DG A 3 C5' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DG A 3 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 3 C8 - N9 - C1' ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DG A 3 C4 - N9 - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 368 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1A8W A 1 12 PDB 1A8W 1A8W 1 12 DBREF 1A8W B 1 12 PDB 1A8W 1A8W 1 12 SEQRES 1 A 12 DG DG DG DC DT DT DT DT DG DG DG DC SEQRES 1 B 12 DG DG DG DC DT DT DT DT DG DG 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 MODEL 1