HEADER DNA-RNA HYBRID 27-JAN-21 7NBL
TITLE SOLUTION STRUCTURE OF DNA:RNA HYBRID CONTAINING A 2'-DEOXY-2'2'-
TITLE 2 DIFLUORODEOXYCYTIDINE (GEMCITABINE) MODIFICATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3');
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 8 ORGANISM_TAXID: 32630
KEYWDS FLUORINE MODIFICATION, MODIFIED DNA, GEMCITABINE, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR C.CABRERO,N.MARTIN-PINTADO,S.MAZZINI,R.GARGALLO,R.ERITJA,A.AVINO,
AUTHOR 2 C.GONZALEZ
REVDAT 2 15-MAY-24 7NBL 1 REMARK
REVDAT 1 07-APR-21 7NBL 0
JRNL AUTH C.CABRERO,N.MARTIN-PINTADO,S.MAZZINI,R.GARGALLO,R.ERITJA,
JRNL AUTH 2 A.AVINO,C.GONZALEZ
JRNL TITL STRUCTURAL EFFECTS OF INCORPORATION OF 2 -DEOXY-2 2
JRNL TITL 2 -DIFLUORODEOXYCYTIDINE (GEMCITABINE) IN A- AND B-FORM
JRNL TITL 3 DUPLEXES.
JRNL REF CHEMISTRY 2021
JRNL REFN ISSN 0947-6539
JRNL PMID 33772916
JRNL DOI 10.1002/CHEM.202100503
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 18
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 7NBL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JAN-21.
REMARK 100 THE DEPOSITION ID IS D_1292113668.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 298
REMARK 210 PH : 7; 7
REMARK 210 IONIC STRENGTH : 125; 125
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.5 M DNA (5'
REMARK 210 -D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*
REMARK 210 UP*GP*UP*AP*G)-3'), 25 MM SODIUM PHOSPHATE, 100 MM SODIUM
REMARK 210 CHLORIDE, 0.5 % V/V DSS, 90% H2O/10% D2O; 0.5 M DNA (5'-D(*CP*TP*
REMARK 210 AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*
REMARK 210 G)-3'), 25 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 0.5 % V/
REMARK 210 V DSS, 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY;
REMARK 210 2D 1H-1H COSY
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 : TOPSPIN, NMRFAM-SPARKY, AMBER
REMARK 210 18, 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 TOTAL BURIED SURFACE AREA: 850 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3230 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL
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 HO2' A B 15 O5' G B 16 1.59
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC A 1 N3 - C4 - N4 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DC A 1 C5 - C4 - N4 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 U B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 U B 14 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 A B 15 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 A B 15 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES
REMARK 500 1 A B 15 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 A B 15 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DC A 1 N3 - C4 - N4 ANGL. DEV. = -6.3 DEGREES
REMARK 500 2 DC A 1 C5 - C4 - N4 ANGL. DEV. = 6.2 DEGREES
REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 C B 9 O5' - C5' - C4' ANGL. DEV. = -6.7 DEGREES
REMARK 500 2 C B 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 2 C B 10 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 C B 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 G B 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 U B 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 U B 12 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 U B 14 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 A B 15 C3' - C2' - C1' ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 A B 15 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 2 A B 15 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 A B 15 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DC A 1 C5 - C4 - N4 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 3 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES
REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 C B 9 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES
REMARK 500 3 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 3 G B 11 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 3 U B 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 3 A B 15 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 164 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 DC A 1 0.08 SIDE CHAIN
REMARK 500 1 DG A 7 0.06 SIDE CHAIN
REMARK 500 1 C B 9 0.06 SIDE CHAIN
REMARK 500 1 A B 15 0.07 SIDE CHAIN
REMARK 500 2 C B 10 0.07 SIDE CHAIN
REMARK 500 2 A B 15 0.07 SIDE CHAIN
REMARK 500 3 DC A 1 0.06 SIDE CHAIN
REMARK 500 3 C B 10 0.06 SIDE CHAIN
REMARK 500 3 G B 11 0.05 SIDE CHAIN
REMARK 500 3 G B 13 0.08 SIDE CHAIN
REMARK 500 3 A B 15 0.07 SIDE CHAIN
REMARK 500 4 DC A 1 0.07 SIDE CHAIN
REMARK 500 4 A B 15 0.08 SIDE CHAIN
REMARK 500 5 DC A 1 0.09 SIDE CHAIN
REMARK 500 5 C B 10 0.07 SIDE CHAIN
REMARK 500 5 G B 11 0.06 SIDE CHAIN
REMARK 500 5 A B 15 0.07 SIDE CHAIN
REMARK 500 6 G B 11 0.06 SIDE CHAIN
REMARK 500 6 A B 15 0.09 SIDE CHAIN
REMARK 500 6 G B 16 0.07 SIDE CHAIN
REMARK 500 7 DC A 1 0.07 SIDE CHAIN
REMARK 500 7 C B 9 0.06 SIDE CHAIN
REMARK 500 7 G B 11 0.06 SIDE CHAIN
REMARK 500 7 A B 15 0.07 SIDE CHAIN
REMARK 500 8 DC A 1 0.06 SIDE CHAIN
REMARK 500 8 C B 9 0.07 SIDE CHAIN
REMARK 500 8 C B 10 0.07 SIDE CHAIN
REMARK 500 8 G B 16 0.08 SIDE CHAIN
REMARK 500 9 DC A 1 0.09 SIDE CHAIN
REMARK 500 9 C B 9 0.07 SIDE CHAIN
REMARK 500 9 G B 11 0.07 SIDE CHAIN
REMARK 500 9 G B 16 0.07 SIDE CHAIN
REMARK 500 10 C B 9 0.06 SIDE CHAIN
REMARK 500 10 C B 10 0.07 SIDE CHAIN
REMARK 500 10 G B 11 0.07 SIDE CHAIN
REMARK 500 10 A B 15 0.07 SIDE CHAIN
REMARK 500 10 G B 16 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 7NBK RELATED DB: PDB
REMARK 900 STRUCTURE WITH THE SAME MODIFICATION
REMARK 900 RELATED ID: 34595 RELATED DB: BMRB
REMARK 900 SOLUTION STRUCTURE OF DNA:RNA HYBRID CONTAINING A 2'-DEOXY-2'2'-
REMARK 900 DIFLUORODEOXYCYTIDINE (GEMCITABINE) MODIFICATION
DBREF 7NBL A 1 8 PDB 7NBL 7NBL 1 8
DBREF 7NBL B 9 16 PDB 7NBL 7NBL 9 16
SEQRES 1 A 8 DC DT DA U7B DA DC DG DG
SEQRES 1 B 8 C C G U G U A G
HET U7B A 4 30
HETNAM U7B 2'-DEOXY-2'2'-DIFLUORODEOXYCYTIDINE
HETSYN U7B [(2~{R},3~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE-
HETSYN 2 U7B PYRIMIDIN-1-YL)-4,4-BIS(FLUORANYL)-3-OXIDANYL-OXOLAN-
HETSYN 3 U7B 2-YL]METHYL DIHYDROGEN PHOSPHITE
FORMUL 1 U7B C9 H12 F2 N3 O7 P
LINK O3' DA A 3 P U7B A 4 1555 1555 1.62
LINK O3' U7B A 4 P DA A 5 1555 1555 1.59
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