3SKI

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.253

Literature

Macromolecules
Sequence Display for 3SKI

Classification: RNA

Total Structure Weight: 45396.08

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (68-MER) A 68 synthetic
RNA (68-MER) B 68 synthetic

Small Molecules
Ligands 4 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)
SIN
Query on SIN

A SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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 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: 2.3 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.253
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 34.93 α = 90.00
b = 47.79 β = 90.00
c = 228.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-22
  • 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