2G9C

Modified pyrimidines Specifically bind the purine riboswitch

• PDB DOI: https://doi.org/10.2210/pdb2G9C/pdb
• NAKB: 2G9C

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-03-06 Released: 2006-11-21 
• Deposition Author(s): Gilbert, S.D., Mediatore, S.J., Batey, R.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.231 

Literature

Modified pyrimidines specifically bind the purine riboswitch.

Gilbert, S.D., Mediatore, S.J., Batey, R.T.

(2006) J Am Chem Soc 128: 14214-14215

• PubMed: 17076468 
• DOI: https://doi.org/10.1021/ja063645t
• Primary Citation of Related Structures:  
  2G9C


• PubMed Abstract: 
  

  The purine riboswitch is a genetic regulatory element found in the 5'-untranslated regions of Gram-positive bacteria that regulates expression of the mRNA specifically in response to either guanine or adenine. We report that the adenine-responsive RNA element is also capable of specifically recognizing pyrimidine compounds bearing modifications at the 6- or 5,6-positions in a fashion similar to that of purine compounds. Using isothermal titration calorimetry and X-ray crystallography, the binding of these compounds is characterized.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.63 kDa 
• Atom Count: 1,872 
• Modelled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
guanine riboswitch	A	67	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
3AY	O [auth A]	PYRIMIDINE-2,4,6-TRIAMINE C4 H7 N5 JTTIOYHBNXDJOD-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
3AY	PDBBind:  2G9C	Kd: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.99	α = 90
b = 35.1	β = 90.43
c = 41.8	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BOS	data collection
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Gilbert, S.D., Mediatore, S.J., Batey, R.T.

Revision History  

• Version 1.0: 2006-11-21
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations