HEADER DNA 30-AUG-23 8QDU TITLE FORMATION OF LEFT-HANDED HELICES BY C2'-FLUORINATED NUCLEIC ACIDS TITLE 2 UNDER PHYSIOLOGICAL SALT CONDITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(FC)P*GP*(FC)P*GP*(FC)P*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS 2'F-ANA, 2'F-RNA, Z-DNA, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.EL-KHOURY,C.CABRERO,S.MOVILLA,J.D.THORPE,M.ROMAN,M.OROZCO, AUTHOR 2 C.GONZALEZ,M.J.DAMHA REVDAT 2 31-JUL-24 8QDU 1 JRNL REVDAT 1 26-JUN-24 8QDU 0 JRNL AUTH R.EL-KHOURY,C.CABRERO,S.MOVILLA,H.KAUR,D.FRIEDLAND, JRNL AUTH 2 A.DOMINGUEZ,J.D.THORPE,M.ROMAN,M.OROZCO,C.GONZALEZ,M.J.DAMHA JRNL TITL FORMATION OF LEFT-HANDED HELICES BY C2'-FLUORINATED NUCLEIC JRNL TITL 2 ACIDS UNDER PHYSIOLOGICAL SALT CONDITIONS. JRNL REF NUCLEIC ACIDS RES. V. 52 7414 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38874502 JRNL DOI 10.1093/NAR/GKAE508 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8QDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292133067. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 M DNA (5' REMARK 210 -D(*(FC)P*GP*(FC)P*GP*(FC)P*G)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : NEO AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY, AMBER, REMARK 210 MOLMOL, 3DNA REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 4 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 4 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 8 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG B 10 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DG A 4 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DG B 8 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG B 10 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG B 10 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DG A 2 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG A 4 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES REMARK 500 4 DG A 4 N1 - C6 - O6 ANGL. DEV. = -4.6 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DG A 6 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DG B 8 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 DG B 8 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 DG B 10 N3 - C2 - N2 ANGL. DEV. = -5.1 DEGREES REMARK 500 4 DG B 10 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DG A 2 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DG A 4 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DG B 10 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 5 DG B 10 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DG A 2 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 6 DG A 4 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 6 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 6 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DG B 8 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 DG B 10 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 6 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 7 DG A 4 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 7 DG A 4 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DG B 10 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 7 DG B 10 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 8 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 8 DG A 4 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 8 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 8 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 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 A 2 0.05 SIDE CHAIN REMARK 500 2 DG A 2 0.06 SIDE CHAIN REMARK 500 2 DG B 8 0.06 SIDE CHAIN REMARK 500 3 DG A 2 0.06 SIDE CHAIN REMARK 500 3 DG B 8 0.06 SIDE CHAIN REMARK 500 4 DG A 2 0.08 SIDE CHAIN REMARK 500 4 DG A 4 0.06 SIDE CHAIN REMARK 500 4 DG B 8 0.06 SIDE CHAIN REMARK 500 4 DG B 10 0.06 SIDE CHAIN REMARK 500 5 DG A 2 0.07 SIDE CHAIN REMARK 500 5 DG B 8 0.07 SIDE CHAIN REMARK 500 6 DG A 2 0.07 SIDE CHAIN REMARK 500 6 DG B 8 0.05 SIDE CHAIN REMARK 500 6 DG B 10 0.06 SIDE CHAIN REMARK 500 7 DG A 2 0.06 SIDE CHAIN REMARK 500 7 DG B 8 0.06 SIDE CHAIN REMARK 500 8 DG A 2 0.05 SIDE CHAIN REMARK 500 8 DG B 8 0.06 SIDE CHAIN REMARK 500 9 DG A 2 0.06 SIDE CHAIN REMARK 500 9 DG B 8 0.07 SIDE CHAIN REMARK 500 10 DG A 2 0.06 SIDE CHAIN REMARK 500 10 DG B 8 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34856 RELATED DB: BMRB REMARK 900 FORMATION OF LEFT-HANDED HELICES BY C2'-FLUORINATED NUCLEIC ACIDS REMARK 900 UNDER PHYSIOLOGICAL SALT CONDITIONS DBREF 8QDU A 1 6 PDB 8QDU 8QDU 1 6 DBREF 8QDU B 7 12 PDB 8QDU 8QDU 7 12 SEQRES 1 A 6 CFL DG CFL DG CFL DG SEQRES 1 B 6 CFL DG CFL DG CFL DG HET CFL A 1 28 HET CFL A 3 30 HET CFL A 5 30 HET CFL B 7 28 HET CFL B 9 30 HET CFL B 11 30 HETNAM CFL 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 CFL ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE HETSYN CFL 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 CFL 6(C9 H13 F N3 O7 P) LINK O3' CFL A 1 P DG A 2 1555 1555 1.61 LINK O3' DG A 2 P CFL A 3 1555 1555 1.61 LINK O3' CFL A 3 P DG A 4 1555 1555 1.62 LINK O3' DG A 4 P CFL A 5 1555 1555 1.61 LINK O3' CFL A 5 P DG A 6 1555 1555 1.62 LINK O3' CFL B 7 P DG B 8 1555 1555 1.62 LINK O3' DG B 8 P CFL B 9 1555 1555 1.62 LINK O3' CFL B 9 P DG B 10 1555 1555 1.62 LINK O3' DG B 10 P CFL B 11 1555 1555 1.61 LINK O3' CFL B 11 P DG B 12 1555 1555 1.62 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' CFL A 1 32.558 31.202 4.037 1.00 0.00 O HETATM 2 C5' CFL A 1 31.912 30.186 4.797 1.00 0.00 C HETATM 3 C4' CFL A 1 30.399 30.124 4.544 1.00 0.00 C HETATM 4 O4' CFL A 1 29.788 31.345 4.944 1.00 0.00 O HETATM 5 C3' CFL A 1 30.009 29.889 3.077 1.00 0.00 C HETATM 6 O3' CFL A 1 29.212 28.706 2.955 1.00 0.00 O HETATM 7 C2' CFL A 1 29.199 31.125 2.710 1.00 0.00 C HETATM 8 C1' CFL A 1 28.675 31.545 4.083 1.00 0.00 C HETATM 9 N1 CFL A 1 28.152 32.944 4.123 1.00 0.00 N HETATM 10 C2 CFL A 1 26.962 33.235 3.447 1.00 0.00 C HETATM 11 O2 CFL A 1 26.332 32.367 2.844 1.00 0.00 O HETATM 12 N3 CFL A 1 26.464 34.495 3.442 1.00 0.00 N HETATM 13 C4 CFL A 1 27.115 35.449 4.087 1.00 0.00 C HETATM 14 N4 CFL A 1 26.559 36.637 4.085 1.00 0.00 N HETATM 15 C5 CFL A 1 28.332 35.213 4.789 1.00 0.00 C HETATM 16 C6 CFL A 1 28.817 33.945 4.792 1.00 0.00 C HETATM 17 F CFL A 1 30.041 32.092 2.184 1.00 0.00 F HETATM 18 H5'1 CFL A 1 32.070 30.373 5.862 1.00 0.00 H HETATM 19 H5'2 CFL A 1 32.346 29.212 4.550 1.00 0.00 H HETATM 20 H4' CFL A 1 29.978 29.320 5.140 1.00 0.00 H HETATM 21 H3' CFL A 1 30.895 29.841 2.441 1.00 0.00 H HETATM 22 H2' CFL A 1 28.392 30.885 2.013 1.00 0.00 H HETATM 23 H1' CFL A 1 27.874 30.847 4.342 1.00 0.00 H HETATM 24 HN41 CFL A 1 25.641 36.730 3.640 1.00 0.00 H HETATM 25 HN42 CFL A 1 26.990 37.399 4.569 1.00 0.00 H HETATM 26 H5 CFL A 1 28.854 35.987 5.326 1.00 0.00 H HETATM 27 H6 CFL A 1 29.727 33.712 5.332 1.00 0.00 H HETATM 28 HO5' CFL A 1 32.079 32.030 4.146 1.00 0.00 H