2E7E

Bent-binding of cyanide to the heme iron in rat heme oxygenase-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternative cyanide-binding modes to the haem iron in haem oxygenase

Sugishima, M.Oda, K.Ogura, T.Sakamoto, H.Noguchi, M.Fukuyama, K.

(2007) Acta Crystallogr.,Sect.F 63: 471-474

  • DOI: 10.1107/S174430910702475X

  • PubMed Abstract: 
  • Cyanide is a well known potent inhibitor of haem proteins, including haem oxygenase (HO). Generally, cyanide coordinates to the ferric haem iron with a linear binding geometry; the Fe-C-N angle ranges from 160 to 180 degrees . The Fe-C-N angle observ ...

    Cyanide is a well known potent inhibitor of haem proteins, including haem oxygenase (HO). Generally, cyanide coordinates to the ferric haem iron with a linear binding geometry; the Fe-C-N angle ranges from 160 to 180 degrees . The Fe-C-N angle observed in the crystal structure of haem-HO bound to cyanide prepared at alkaline pH was 166 degrees . Here, it is reported that cyanide can bind to the haem iron in HO in a bent mode when the ternary complex is prepared at neutral pH; a crystal structure showed that the Fe-C-N angle was bent by 47 degrees . Unlike the ternary complex prepared at alkaline pH, in which the haem group, including the proximal ligand and the distal helix, was displaced upon cyanide binding, the positions of the haem group and the distal helix in the complex prepared at neutral pH were nearly identical to those in haem-HO. Cyanide that was bound to haem-HO with a bent geometry was readily photodissociated, whereas that bound with a linear geometry was not photodissociated. Thus, alternative cyanide-binding modes with linear and bent geometries exist in the crystalline state of haem-HO.


    Organizational Affiliation

    Department of Medical Biochemistry, Kurume University School of Medicine, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme oxygenase 1
A
267Rattus norvegicusMutation(s): 0 
Gene Names: Hmox1
EC: 1.14.14.18
Find proteins for P06762 (Rattus norvegicus)
Go to UniProtKB:  P06762
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
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: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.400α = 90.00
b = 65.400β = 90.00
c = 121.000γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance