1GJN

Hydrogen Peroxide Derived Myoglobin Compound II at pH 5.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An Iron Hydroxide Moiety in the 1.35 A Resolution Structure of Hydrogen Peroxide Derived Myoglobin Compound II at Ph 5.2

Hersleth, H.-P.Dalhus, B.Gorbitz, C.H.Andersson, K.K.

(2002) J.Biol.Inorg.Chem. 7: 299

  • DOI: 10.1007/s007750100296
  • Also Cited By: 2V1E, 2V1F, 2V1G, 2VLX, 2VLY, 2VLZ, 2VM0

  • PubMed Abstract: 
  • The biological conversions of O(2) and peroxides to water as well as certain incorporations of oxygen atoms into small organic molecules can be catalyzed by metal ions in different clusters or cofactors. The catalytic cycle of these reactions passes ...

    The biological conversions of O(2) and peroxides to water as well as certain incorporations of oxygen atoms into small organic molecules can be catalyzed by metal ions in different clusters or cofactors. The catalytic cycle of these reactions passes through similar metal-based complexes in which one oxygen- or peroxide-derived oxygen atom is coordinated to an oxidized form of the catalytic metal center. In haem-based peroxidases or oxygenases the ferryl (Fe(IV)O) form is important in compound I and compound II, which are two and one oxidation equivalents higher than the ferric (Fe(III)) form, respectively. In this study we report the 1.35 A structure of a compound II model protein, obtained by reacting hydrogen peroxide with ferric myoglobin at pH 5.2. The molecular geometry is virtually unchanged compared to the ferric form, indicating that these reactive intermediates do not undergo large structural changes. It is further suggested that at low pH the dominating compound II resonance form is a hydroxyl radical ferric iron rather than an oxo-ferryl form, based on the short hydrogen bonding to the distal histidine (2.70 A) and the Fe...O distance. The 1.92 A Fe...O distance is in agreement with an EXAFS study of compound II in horseradish peroxidase.


    Related Citations: 
    • A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket
      Maurus, R.,Overall, C.M.,Bogumil, R.,Luo, Y.,Mauk, A.G.,Smith, M.,Brayer, G.D.
      (1997) Biochim.Biophys.Acta 1341: 1
    • Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
      Sherwood, C.,Mauk, A.G.,Brayer, G.D.
      (1987) J.Mol.Biol. 193: 227


    Organizational Affiliation

    Department of Chemistry, University of Oslo, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Equus caballusGene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OH
Query on OH

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Download CCD File 
A
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.862α = 90.00
b = 28.650β = 105.93
c = 35.352γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance