8ASM | pdb_00008asm

Cobalt(II) bound to a non-canonical quadruplex

• PDB DOI: https://doi.org/10.2210/pdb8ASM/pdb
• NAKB: 8ASM

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


• Deposited: 2022-08-19 Released: 2023-08-30 
• Deposition Author(s): Lambert, M.C., Hall, J.P.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.192 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Identifying metal-DNA binding sites, what is the best method to get transition metals into a crystal system?

Lambert, M.C., Hall, J.P., Brazier, J.A., Cardin, C.J.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.99 kDa 
• Atom Count: 362 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')	A, B	7	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	D [auth A], E [auth A], G [auth B], H [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)	C [auth A], F [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.192 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.898	α = 90
b = 58.659	β = 90
c = 45.567	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Lambert, M.C., Hall, J.P.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary