2RGZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.161 

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This is version 1.4 of the entry. See complete history. 

Re-refinement Note

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


Literature

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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme oxygenase 2A, B264Homo sapiensMutation(s): 1 
Gene Names: HMOX2, HO2
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30519 (Homo sapiens)
Explore P30519 
Go to UniProtKB:  P30519
PHAROS:  P30519
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30519
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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