Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme

Experimental Data Snapshot

  • Resolution: 2.61 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.161 

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This is version 1.5 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2QPP


Comparison of Apo- and Heme-bound Crystal Structures of a Truncated Human Heme Oxygenase-2.

Bianchetti, C.M.Yi, L.Ragsdale, S.W.Phillips Jr., G.N.

(2007) J Biol Chem 282: 37624-37631

  • DOI: https://doi.org/10.1074/jbc.M707396200
  • Primary Citation of Related Structures:  
    2Q32, 2QPP, 2RGZ

  • PubMed Abstract: 

    Heme oxygenase (HO) catalyzes the first step in the heme degradation pathway. The crystal structures of apo- and heme-bound truncated human HO-2 reveal a primarily alpha-helical architecture similar to that of human HO-1 and other known HOs. Proper orientation of heme in HO-2 is required for the regioselective oxidation of the alpha-mesocarbon. This is accomplished by interactions within the heme binding pocket, which is made up of two helices. The iron coordinating residue, His(45), resides on the proximal helix. The distal helix contains highly conserved glycine residues that allow the helix to flex and interact with the bound heme. Tyr(154), Lys(199), and Arg(203) orient the heme through direct interactions with the heme propionates. The rearrangements of side chains in heme-bound HO-2 compared with apoHO-2 further elucidate HO-2 heme interactions.

  • Organizational Affiliation

    Graduate Program in Biophysics, Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme oxygenase 2
A, B
264Homo sapiensMutation(s): 1 
Gene Names: HMOX2HO2
UniProt & NIH Common Fund Data Resources
Find proteins for P30519 (Homo sapiens)
Explore P30519 
Go to UniProtKB:  P30519
PHAROS:  P30519
GTEx:  ENSG00000103415 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30519
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.61 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.977α = 90
b = 85.094β = 90
c = 97.846γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Other
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description