HEADER DNA 26-MAR-25 9U89 TITLE STRUCTURE OF AA(GGGTT)3GGGAA G-QUADRUPLEX IN THE PRESENCE OF POTASSIUM TITLE 2 IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, FRUSTRATED SEQUENCE, PARALLEL, DNA EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR D.NEGI,R.K.R.SANNAPUREDDI,B.SATHYAMOORTHY REVDAT 1 08-APR-26 9U89 0 JRNL AUTH D.NEGI,R.K.R.SANNAPUREDDI,B.SATHYAMOORTHY JRNL TITL MOLECULAR INTERACTIONS OF A FRUSTRATED G-RICH SEQUENCE: JRNL TITL 2 ATOMISTIC INSIGHTS INTO FOLDING OF DNA G-QUADRUPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.K.REDDY SANNAPUREDDI,M.K.MOHANTY,A.K.GAUTAM, REMARK 1 AUTH 2 B.SATHYAMOORTHY REMARK 1 TITL CHARACTERIZATION OF DNA G-QUADRUPLEX TOPOLOGIES WITH NMR REMARK 1 TITL 2 CHEMICAL SHIFTS. REMARK 1 REF J PHYS CHEM LETT V. 11 10016 2020 REMARK 1 REFN ESSN 1948-7185 REMARK 1 PMID 33179931 REMARK 1 DOI 10.1021/ACS.JPCLETT.0C02969 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, AMBER, AMBER REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND REMARK 3 KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9U89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057892. 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 : 418; 418 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM DNA (5' REMARK 210 -D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP* REMARK 210 AP*A)-3'), 20 MM POTASSIUM PHOSPHATE, 50 MM POTASSIUM CHLORIDE, REMARK 210 50 UM DSS, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY; 2D 1H-15N HMQC; 2D REMARK 210 1H-13C HSQC F2 COUPLED; 2D 1H- REMARK 210 15N HMQC F2 COUPLED REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6, NMRPIPE, NMRFAM REMARK 210 -SPARKY REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 2 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 5 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 13 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 15 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 20 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DA A 21 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 21 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DA A 22 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 22 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 2 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 2 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 10 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 12 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 16 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 17 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 154 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36747 RELATED DB: BMRB REMARK 900 STRUCTURE OF AA(GGGTT)3AA G-QUADRUPLEX IN THE PRESENCE OF POTASSIUM REMARK 900 IONS DBREF 9U89 A 1 22 PDB 9U89 9U89 1 22 SEQRES 1 A 22 DA DA DG DG DG DT DT DG DG DG DT DT DG SEQRES 2 A 22 DG DG DT DT DG DG DG DA DA 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MASTER 162 0 0 0 0 0 0 6 465 1 0 2 END