9D6V | pdb_00009d6v

[F:Au+/Ag+:F-pH8] Heterobimetallic base pair with Ag+ and Au+ between a 2-thio-dT homopair, crystallized in the presence of Ag+, Au+ and Cu+

• PDB DOI: https://doi.org/10.2210/pdb9D6V/pdb
• NAKB: 9D6V

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


• Deposited: 2024-08-15 Released: 2025-08-20 
• Deposition Author(s): Vecchioni, S., Imstepf, L., Lu, B., Woloszyn, K., Sha, R., Ohayon, Y.P.
• Funding Organization(s): National Science Foundation (NSF, China), Department of Energy (DOE, United States), Office of Naval Research (ONR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.87 Å
• R-Value Free: 
  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Thiothymidine metal base pairs

Vecchioni, S., Imstepf, L., Lu, B., Woloszyn, K., Sha, R., Ohayon, Y.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 13.12 kDa 
• Atom Count: 860 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')	C	7	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')	D	7	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.87 Å
• R-Value Free:  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.937	α = 90
b = 105.937	β = 90
c = 92.751	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Vecchioni, S., Imstepf, L., Lu, B., Woloszyn, K., Sha, R., Ohayon, Y.P.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	GCR-2317843
Department of Energy (DOE, United States)	United States	DE-SC0007991
Office of Naval Research (ONR)	United States	N000141912596

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release