8VH6 | pdb_00008vh6

[F:3Au+:F] Metal-mediated DNA base pair with 2-thio-thymidine in tensegrity triangle

• PDB DOI: https://doi.org/10.2210/pdb8VH6/pdb
• NAKB: 8VH6

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


• Deposited: 2023-12-31 Released: 2025-01-15 
• Deposition Author(s): Vecchioni, S., Lu, B.
• Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.86 Å
• R-Value Free: 
  0.182 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Metal-mediated 2-thio-thymidine DNA base pairs

Vecchioni, S., Lu, B.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.41 kDa 
• Atom Count: 861 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(2SV)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*(2SV)P*AP*CP*A)-3')	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU (Subject of Investigation/LOI)	E [auth B], F [auth B], G [auth B]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.86 Å
• R-Value Free:  0.182 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.404	α = 90
b = 107.404	β = 90
c = 90.715	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: 2025-01-15 
Deposition Author(s): Vecchioni, S., Lu, B.

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Funding Organization	Location	Grant Number
Office of Naval Research (ONR)	United States	N000141912596
Department of Energy (DOE, United States)	United States	DE-SC0007991
National Science Foundation (NSF, United States)	United States	2106790
National Science Foundation (NSF, United States)	United States	CCF-2106790
National Science Foundation (NSF, United States)	United States	GCR-2317843

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release