Cytochrome cd1 Nitrite Reductase, reoxidised enzyme

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 

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This is version 1.5 of the entry. See complete history


Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase.

Sjogren, T.Hajdu, J.

(2001) J Biol Chem 276: 13072-13076

  • DOI: https://doi.org/10.1074/jbc.M011312200
  • Primary Citation of Related Structures:  
    1HJ3, 1HJ4, 1HJ5

  • PubMed Abstract: 

    Reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. Cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water. The latter is a cytochrome oxidase reaction. Here we describe the structure of an active dioxygen species in the enzyme captured by cryo-trapping. The productive binding mode of dioxygen in the active site is very similar to that of nitrite and suggests that the catalytic mechanisms of oxygen reduction and nitrite reduction are closely related. This finding has implications to the understanding of the evolution of oxygen-reducing enzymes. Comparison of the dioxygen complex to complexes of cytochrome cd(1) with stable diatomic ligands shows that nitric oxide and cyanide bind in a similar bent conformation to the iron as dioxygen whereas carbon monoxide forms a linear complex. The significance of these differences is discussed.

  • Organizational Affiliation

    Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, S-751 23 Uppsala, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrite reductase
A, B
567Paracoccus pantotrophusMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P72181 (Paracoccus pantotrophus)
Explore P72181 
Go to UniProtKB:  P72181
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72181
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DHE

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
C34 H32 Fe N4 O10
Query on HEC

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C [auth A],
J [auth B]
C34 H34 Fe N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.821α = 90
b = 60.968β = 112.24
c = 100.326γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description