8F5C | pdb_00008f5c

Mirror-image DNA containing 2'-OMe-L-dC modification

• PDB DOI: https://doi.org/10.2210/pdb8F5C/pdb
• NAKB: 8F5C

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


• Deposited: 2022-11-13 Released: 2023-09-20 
• Deposition Author(s): Zhang, W., Dantsu, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.204 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Synthesis and Structural Characterization of 2'-Deoxy-2'-Methoxy-L-Cytidine Nucleic Acids

Dantsu, Y., Zhang, W.

(2023) ChemistrySelect 

• DOI: https://doi.org/10.1002/slct.202301966

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.51 kDa 
• Atom Count: 218 
• 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))-R(P*(XE6))-D(P*(0DG)P*(0DT)P*(0DA)P*(0DC)P*(0DG)P*(0DC))-3')	A	8	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.204 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.9	α = 90
b = 41.9	β = 90
c = 23.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Zhang, W., Dantsu, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Derived calculations, Experimental preparation
• Version 1.2: 2026-03-04
  Changes: Derived calculations, Refinement description, Structure summary