2NOK

Crystal Structure of an RNA domain from Hepatitis C virus.

• PDB DOI: https://doi.org/10.2210/pdb2NOK/pdb
• NAKB: 2NOK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-10-25 Released: 2007-02-13 
• Deposition Author(s): Dibrov, S.M., Johnston-Cos, H., Weng, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.302 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 

Literature

Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution.

Dibrov, S.M., Johnston-Cox, H., Weng, Y.H., Hermann, T.

(2007) Angew Chem Int Ed Engl 46: 226-229

• PubMed: 17131443 
• DOI: https://doi.org/10.1002/anie.200603807
• Primary Citation of Related Structures:  
  2NOK

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.57 kDa 
• Atom Count: 1,869 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'	A, C	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*CP*GP*UP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*CP*GP*G)-3'	B, D	20	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	F [auth A], G [auth A], M [auth C], N [auth C], O [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.302 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.098	α = 90
b = 65.351	β = 90
c = 92.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Dibrov, S.M., Johnston-Cos, H., Weng, Y.H.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations