1HMO

THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of deoxy and oxy hemerythrin at 2.0 A resolution.

Holmes, M.A.Le Trong, I.Turley, S.Sieker, L.C.Stenkamp, R.E.

(1991) J Mol Biol 218: 583-593

  • DOI: https://doi.org/10.1016/0022-2836(91)90703-9
  • Primary Citation of Related Structures:  
    1HMD, 1HMO

  • PubMed Abstract: 

    The crystallographic structure analyses of deoxy and oxy hemerythrin have been carried out at 2.0 A resolution to extend the low resolution views of the physiological forms of this oxygen-binding protein. Restrained least-squares refinement has produced molecular models giving R-values of 16.8% for deoxy (41,064 reflections from 10 A to 2.0 A) and 17.3% for oxy hemerythrin (40,413 reflections from 10.0 A to 2.0 A). The protein structure in each derivative is very similar to that of myohemerythrin and the various met forms of hemerythrin. The binuclear complex in each derivative retains an oxygen atom bridging the two iron atoms, but the bond lengths found in deoxy hemerythrin support the idea that, in that form, the bridge is protonated, i.e. the bridging group is a hydroxyl. Dioxygen binds to the pentaco-ordinate iron atom in deoxy hemerythrin in the conversion to oxy hemerythrin. The interatomic distances are consistent with the proposed mechanism where the proton from the bridging group is transferred to the bound dioxygen, stabilizing it in the peroxo oxidation state by forming a hydrogen bond between the peroxy group and the bridging oxygen atom.


  • Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMERYTHRIN
A, B, C, D
113Themiste dyscritumMutation(s): 0 
UniProt
Find proteins for P02246 (Themiste dyscrita)
Explore P02246 
Go to UniProtKB:  P02246
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02246
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
ACE
Query on ACE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.173 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.69α = 90
b = 86.69β = 90
c = 80.78γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1992-01-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance