3SKR

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cobalt Hexammine soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299
  • R-Value Work: 0.236

Literature

Macromolecules
Sequence Display for 3SKR

Classification: RNA

Total Structure Weight: 44818.71

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (66-MER) A, B 66 synthetic dG riboswitch

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GNG
Query on GNG

A, B 2'-DEOXY-GUANOSINE
C10 H13 N5 O4
YKBGVTZYEHREMT-KVQBGUIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NCO
Query on NCO

A, B COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
A, B NON-POLYMER C10 H16 N5 O14 P3 G
CCC
Query on CCC
A, B RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299
  • R-Value Work: 0.236
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 98.53 α = 90.00
b = 35.02 β = 92.18
c = 110.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-23
  • Released Date: 2011-08-17
  • Deposition author(s): Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.

Revision History

  • Version 1_0: 2011-08-17

    Type: Initial release

  • Version 1_1: 2011-10-26

    Type: Database references