7EDV | pdb_00007edv

DNA duplex containing C-G-Au-C base triple

• PDB DOI: https://doi.org/10.2210/pdb7EDV/pdb
• NAKB: 7EDV

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


• Deposited: 2021-03-17 Released: 2022-03-23 
• Deposition Author(s): Kondo, J., Iwase, E.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold

Kosugi, K., Sugawara, A., Iwase, E., Park, H., Fujiwara, S., Kanazawa, H., Ono, A., Kondo, J.

(2025) Chembiochem 26

• DOI: https://doi.org/10.1002/cbic.202500565

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.82 kDa 
• Atom Count: 278 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*CP*CP*CP*CP*GP*GP*TP*CP*C)-3')	A	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU (Subject of Investigation/LOI)	B [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.595	α = 90
b = 38.595	β = 90
c = 46.688	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Kondo, J., Iwase, E.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2025-11-26
  Changes: Database references, Structure summary