7KW4 | pdb_00007kw4

L-DNA containing 2'-fluoro modification

• PDB DOI: https://doi.org/10.2210/pdb7KW4/pdb
• NAKB: 7KW4

• Classification: DNA
• Organism(s): synthetic construct
• Expression System: synthetic construct
• Mutation(s): No 


• Deposited: 2020-11-29 Released: 2021-09-01 
• Deposition Author(s): Zhang, W., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Synthesis and Structural Characterization of 2'-Deoxy-2'-fluoro-l-uridine Nucleic Acids.

Dantsu, Y., Zhang, Y., Zhang, W.

(2021) Org Lett 23: 5007-5011

• PubMed: 34142829 
• DOI: https://doi.org/10.1021/acs.orglett.1c01498
• Primary Citation Related Structures: 
  7KW4


• PubMed Abstract: 
  

  Despite the development of artificial l-RNA/DNA as therapeutic molecules, the in-depth investigation on their chemical modifications is still limited. Here, we synthesize a chemically derivatized 2'-deoxy-2'-fluoro-l-uridine building block and incorporate it into oligonucleotides. Our thermo-denaturization and enzymatic digestion experiments reveal their superior stability. Furthermore, one crystal structure of l-type fluoro-DNA is determined to characterize its handedness. Our results reveal the increase of l-helix stability by fluoro-modification and provide the foundation for its future functional application.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 2.44 kDa 
• Atom Count: 216 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(0DG)P*(0FU)P*(0DG)P*(0DT)P*(0DA)P*(0DC)P*(0DA)P*(0DC))-3')	A	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.33	α = 90
b = 32.33	β = 90
c = 75.58	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Zhang, W., Zhang, Y.

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description