359D

INHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-SPECIFIC BINDING OF TB(III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.

Feig, A.L.Scott, W.G.Uhlenbeck, O.C.

(1998) Science 279: 81-84


  • PubMed Abstract: 
  • Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribo ...

    Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribozyme, approximately 10 angstroms from the cleavage site. Synthetic modifications near this binding site yielded an RNA substrate that was resistant to Tb(III) binding and capable of being cleaved, even in the presence of up to 20 micromolar Tb(III). It is suggested that the magnesium(II) ion thought to bind at this site may act as a switch, affecting the conformational changes required to achieve the transition state.


    Related Citations: 
    • Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme
      Scott, W.G.,Murray, J.B.,Arnold, J.R.P.,Stoddard, B.L.,Klug, A.
      (1996) Science 274: 2065


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA HAMMERHEAD RIBOZYMEA16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA HAMMERHEAD RIBOZYMEB25N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download SDF File 
Download CCD File 
A, B
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.256 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.540α = 90.00
b = 65.540β = 90.00
c = 138.080γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
CCP4data scaling
X-PLORrefinement
X-PLORphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance