1HMD

THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

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

  • Primary Citation of Related Structures:  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 produ ...

    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.


    Related Citations: 
    • Structure of the Binuclear Iron Complex in Metazidohaemerythrin from Themiste Dyscritum at 2.2 Angstroms Resolution
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.,Sanders-Loehr, J.
      (1981) Nature 291: 263
    • Structure of the Iron Complex in Methemerythrin
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.
      (1976) Proc.Natl.Acad.Sci.USA 73: 349
    • Binuclear Iron Complexes in Methemerythrin and Azidomethemerythrin at 2.0-Angstroms Resolution
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.
      (1984) J.Am.Chem.Soc. 106: 618
    • Adjustment of Restraints in the Refinement of Methemerythrin and Azidomethemerythrin at 2.0 Angstroms Resolution.
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.
      (1983) Acta Crystallogr.,Sect.B 39: 697
    • Crystallographic Studies of Azide, Thiocyanate and Perchlorate Complexes of Methemerythrin
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.
      (1978) J.Mol.Biol. 126: 457
    • Active Site Structures of Deoxyhemerythrin and Oxyhemerythrin
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.,Mccallum, J.D.,Sanders-Loehr, J.
      (1985) Proc.Natl.Acad.Sci.USA 82: 713
    • An X-Ray Crystallographic Study of Hemerythrin
      Loehr, J.S.,Meyerhoff, K.N.,Sieker, L.C.,Jensen, L.H.
      (1975) J.Mol.Biol. 91: 521
    • Structure of Methemerythrin at 5 Angstroms Resolution
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.,Loehr, J.S.
      (1976) J.Mol.Biol. 100: 23
    • Structure of Methemerythrin at 2.8-Angstroms Resolution. Computer Graphics Fit of an Averaged Electron Density Map
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.,Mcqueenjunior, J.E.
      (1978) Biochemistry 17: 2499
    • Amino Acid Sequence of Hemerythrin from Themiste Dyscritum.
      Stenkamp, R.E.,Lammers, P.J.,Brimhall, B.,Hermodson, M.A.
      (1978) J.Biol.Chem. 253: 5726
    • Restrained Least-Squares Refinement of Themiste Dyscritum Methydroxohemerythrin at 2.0 Angstroms Resolution
      Stenkamp, R.E.,Sieker, L.C.,Jensen, L.H.
      (1982) Acta Crystallogr.,Sect.B 38: 784


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMERYTHRIN
A, B, C, D
113Themiste dyscritaN/A
Find proteins for P02246 (Themiste dyscrita)
Go to UniProtKB:  P02246
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B, C, D
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
ACE
Query on ACE

Download SDF File 
Download CCD File 
A, B, C, D
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 86.840α = 90.00
b = 86.840β = 90.00
c = 80.820γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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