3EFU

X-ray structure of human ubiquitin-Hg(II) adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural probing of Zn(ii), Cd(ii) and Hg(ii) binding to human ubiquitin.

Falini, G.Fermani, S.Tosi, G.Arnesano, F.Natile, G.

(2008) Chem.Commun.(Camb.) 45: 5960-5962

  • DOI: 10.1039/b813463d
  • Primary Citation of Related Structures:  
  • Also Cited By: 4K7W, 4K7U, 4K7S

  • PubMed Abstract: 
  • A structural investigation performed on adducts of human ubiquitin with group-12 metal ions reveals common preferential anchoring sites, the most populated one being His68; at higher metal ion concentration a second and a third site, close to the N-t ...

    A structural investigation performed on adducts of human ubiquitin with group-12 metal ions reveals common preferential anchoring sites, the most populated one being His68; at higher metal ion concentration a second and a third site, close to the N-terminus of the protein, become populated and promote a polymorphic transition from orthorhombic to cubic form; Glu16 and Glu18, involved in the latter metal binding, undergo a remarkable displacement from their position in native ubiquitin; the aggregate stereochemistry appears to be driven by the clustering of deshielded backbone hydrogen-bond patches, and metal ions foster this process.


    Organizational Affiliation

    Dipartimento di Chimica, G. Ciamician, Università di Bologna, via Selmi 2, 40126, Bologna, Italy. giuseppe.falini@unibo.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 28.024α = 90.00
b = 42.828β = 90.00
c = 50.374γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance