HEADER DNA 27-AUG-17 5OV2 TITLE 2'F-ANA-G MODIFIED QUADRUPLEX WITH A FLIPPED TETRAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARTIFICIAL QUADRUPLEX WITH PROPELLER, DIAGONAL, AND LATERAL COMPND 3 LOOP; COMPND 4 CHAIN: X; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, DNA, 2'F-ANA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.DICKERHOFF,K.WEISZ REVDAT 4 15-MAY-24 5OV2 1 REMARK REVDAT 3 08-MAY-19 5OV2 1 REMARK REVDAT 2 01-NOV-17 5OV2 1 JRNL REVDAT 1 18-OCT-17 5OV2 0 JRNL AUTH J.DICKERHOFF,K.WEISZ JRNL TITL NONCONVENTIONAL C-HF HYDROGEN BONDS SUPPORT A TETRAD FLIP IN JRNL TITL 2 MODIFIED G-QUADRUPLEXES. JRNL REF J PHYS CHEM LETT V. 8 5148 2017 JRNL REFN ESSN 1948-7185 JRNL PMID 28976755 JRNL DOI 10.1021/ACS.JPCLETT.7B02428 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH, AMBER, CCPNMR ANALYSIS REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR REMARK 3 -NIH), CASE, DARDEN, CHEATHAM III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLMAN (AMBER), CCPN REMARK 3 (CCPNMR ANALYSIS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OV2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006414. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.58 MM DNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.58 REMARK 210 MM DNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-13C HSQC AROMATIC; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 TOTAL BURIED SURFACE AREA: 1740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 DG X 2 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG X 2 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG X 2 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA X 4 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA X 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 4 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT X 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG X 7 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 9 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA X 9 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 9 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC X 10 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA X 11 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 11 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA X 11 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 11 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC X 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC X 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA X 13 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA X 13 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 13 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG X 15 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG X 15 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG X 16 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG X 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA X 18 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA X 18 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA X 18 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 18 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC X 19 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC X 19 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG X 21 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG X 22 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG X 2 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 2 DG X 2 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DA X 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA X 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA X 4 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DT X 5 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DG X 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DA X 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA X 9 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA X 9 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA X 9 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DC X 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC X 10 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA X 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA X 11 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 340 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DG X 7 0.06 SIDE CHAIN REMARK 500 1 DA X 9 0.08 SIDE CHAIN REMARK 500 1 DA X 11 0.14 SIDE CHAIN REMARK 500 1 DC X 12 0.08 SIDE CHAIN REMARK 500 1 DG X 16 0.07 SIDE CHAIN REMARK 500 1 DA X 18 0.09 SIDE CHAIN REMARK 500 1 DC X 19 0.06 SIDE CHAIN REMARK 500 2 DG X 8 0.07 SIDE CHAIN REMARK 500 2 DC X 10 0.08 SIDE CHAIN REMARK 500 2 DA X 11 0.06 SIDE CHAIN REMARK 500 2 DC X 12 0.11 SIDE CHAIN REMARK 500 2 DA X 13 0.06 SIDE CHAIN REMARK 500 3 DA X 9 0.06 SIDE CHAIN REMARK 500 3 DA X 11 0.14 SIDE CHAIN REMARK 500 3 DC X 12 0.09 SIDE CHAIN REMARK 500 3 DC X 19 0.07 SIDE CHAIN REMARK 500 4 DC X 12 0.08 SIDE CHAIN REMARK 500 4 DA X 13 0.07 SIDE CHAIN REMARK 500 4 DC X 19 0.06 SIDE CHAIN REMARK 500 5 DC X 10 0.08 SIDE CHAIN REMARK 500 5 DA X 11 0.07 SIDE CHAIN REMARK 500 5 DC X 12 0.13 SIDE CHAIN REMARK 500 6 DG X 7 0.06 SIDE CHAIN REMARK 500 6 DA X 9 0.06 SIDE CHAIN REMARK 500 6 DA X 11 0.05 SIDE CHAIN REMARK 500 6 DC X 12 0.13 SIDE CHAIN REMARK 500 6 DG X 21 0.06 SIDE CHAIN REMARK 500 7 DT X 5 0.06 SIDE CHAIN REMARK 500 7 DC X 10 0.08 SIDE CHAIN REMARK 500 7 DA X 11 0.13 SIDE CHAIN REMARK 500 7 DC X 12 0.13 SIDE CHAIN REMARK 500 8 DC X 10 0.07 SIDE CHAIN REMARK 500 8 DA X 11 0.07 SIDE CHAIN REMARK 500 8 DC X 12 0.10 SIDE CHAIN REMARK 500 8 DA X 13 0.06 SIDE CHAIN REMARK 500 9 DC X 12 0.12 SIDE CHAIN REMARK 500 10 DC X 10 0.07 SIDE CHAIN REMARK 500 10 DC X 12 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LOD RELATED DB: PDB REMARK 900 STRUCTURE WITHOUT MODIFICATION REMARK 900 RELATED ID: 5MCR RELATED DB: PDB REMARK 900 STRUCTURE MODIFIED WITH 2'F-RNA REMARK 900 RELATED ID: 34174 RELATED DB: BMRB REMARK 900 2'F-ANA-G MODIFIED QUADRUPLEX WITH A FLIPPED TETRAD DBREF 5OV2 X 1 22 PDB 5OV2 5OV2 1 22 SEQRES 1 X 22 GFL DG DG DA DT GFL DG DG DA DC DA DC DA SEQRES 2 X 22 DG DG DG DG DA DC GFL DG DG HET GFL X 1 31 HET GFL X 6 33 HET GFL X 20 33 HETNAM GFL 2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 GFL ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE HETSYN GFL 2'-FLUORO-2-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 GFL 3(C10 H13 F N5 O7 P) LINK O3' GFL X 1 P DG X 2 1555 1555 1.61 LINK O3' DT X 5 P GFL X 6 1555 1555 1.61 LINK O3' GFL X 6 P DG X 7 1555 1555 1.61 LINK O3' DC X 19 P GFL X 20 1555 1555 1.61 LINK O3' GFL X 20 P DG X 21 1555 1555 1.61 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 HETATM 1 O5' GFL X 1 23.490 25.134 37.916 1.00 0.00 O HETATM 2 C5' GFL X 1 24.239 25.017 39.127 1.00 0.00 C HETATM 3 C4' GFL X 1 25.709 25.441 38.964 1.00 0.00 C HETATM 4 O4' GFL X 1 26.399 24.557 38.094 1.00 0.00 O HETATM 5 C3' GFL X 1 25.879 26.874 38.432 1.00 0.00 C HETATM 6 O3' GFL X 1 26.570 27.648 39.407 1.00 0.00 O HETATM 7 C2' GFL X 1 26.667 26.697 37.129 1.00 0.00 C HETATM 8 C1' GFL X 1 27.330 25.328 37.356 1.00 0.00 C HETATM 9 N9 GFL X 1 27.687 24.578 36.129 1.00 0.00 N HETATM 10 C8 GFL X 1 26.852 24.112 35.144 1.00 0.00 C HETATM 11 N7 GFL X 1 27.443 23.418 34.211 1.00 0.00 N HETATM 12 C5 GFL X 1 28.784 23.432 34.610 1.00 0.00 C HETATM 13 C6 GFL X 1 29.950 22.862 34.003 1.00 0.00 C HETATM 14 O6 GFL X 1 30.016 22.208 32.968 1.00 0.00 O HETATM 15 N1 GFL X 1 31.113 23.092 34.709 1.00 0.00 N HETATM 16 C2 GFL X 1 31.159 23.810 35.859 1.00 0.00 C HETATM 17 N2 GFL X 1 32.321 23.982 36.425 1.00 0.00 N HETATM 18 N3 GFL X 1 30.107 24.364 36.454 1.00 0.00 N HETATM 19 C4 GFL X 1 28.942 24.141 35.780 1.00 0.00 C HETATM 20 F GFL X 1 25.762 26.718 36.072 1.00 0.00 F HETATM 21 H5'1 GFL X 1 23.786 25.652 39.892 1.00 0.00 H HETATM 22 H5'2 GFL X 1 24.213 23.985 39.482 1.00 0.00 H HETATM 23 H4' GFL X 1 26.184 25.384 39.946 1.00 0.00 H HETATM 24 H3' GFL X 1 24.903 27.314 38.217 1.00 0.00 H HETATM 25 H2' GFL X 1 27.424 27.479 37.012 1.00 0.00 H HETATM 26 H1' GFL X 1 28.225 25.478 37.964 1.00 0.00 H HETATM 27 H8 GFL X 1 25.812 24.392 35.157 1.00 0.00 H HETATM 28 HN1 GFL X 1 31.957 22.682 34.336 1.00 0.00 H HETATM 29 HN21 GFL X 1 33.172 23.641 35.995 1.00 0.00 H HETATM 30 HN22 GFL X 1 32.358 24.559 37.248 1.00 0.00 H HETATM 31 HO5' GFL X 1 22.562 24.859 38.072 1.00 0.00 H