3EHV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3EEC, 3EFU, 3EHV

  • 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-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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA, B, C76Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1UBA52UBCEP2UBBUBC
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.357α = 90
b = 50.946β = 90
c = 93.317γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-11-13
    Changes: Data collection