Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.51 kDa 
• Atom Count: 1026 
• Residue Count: 48 
• Unique nucleic acid chains: 2

429D

CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS

• DOI: 10.2210/pdb429D/pdb
• NDB: UR0001

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-09-29 Released: 1999-03-01 
• Deposition Author(s): Wedekind, J.E., McKay, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 

Literature

Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis.

Wedekind, J.E., McKay, D.B.

(1999) Nat Struct Biol 6: 261-268

• PubMed: 10074945 
• DOI: 10.1038/6700
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two independent molecules per asymmetric unit. Both molecules feature an internal loop in which a bulged purine base stack twists away from the helical stem. This kinks the backbone, rendering the phosphodiester bond susceptible to cleavage. The independent molecules have different conformations: one leadzyme copy coordinates Mg2+, whereas the other binds only Ba2+ or Pb2+. In the active site of the latter molecule, a single Ba2+ ion coordinates the 2'-OH nucleophile, and appears to mimic the binding of catalytic lead. These observations allow a bond cleavage reaction to be modeled, which reveals the minimal structural features necessary for catalysis by this small ribozyme.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, California 94305-5126, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism
RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')	A, C	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')	B, D	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.4	α = 90
b = 60.4	β = 90
c = 133.1	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-09-29 
• Released Date: 1999-03-01 
Deposition Author(s): Wedekind, J.E., McKay, D.B.

Revision History 

• Version 1.0: 1999-03-01
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance