E. coli NrfA sulfite ocmplex

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli

Kemp, G.L.Clarke, T.A.Marritt, S.J.Lockwood, C.Poock, S.R.Hemmings, A.M.Richardson, D.J.Cheesman, M.R.Butt, J.N.

(2010) Biochem J 431: 73-80

  • DOI: https://doi.org/10.1042/BJ20100866
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NrfA is a pentahaem cytochrome present in a wide-range of γ-, δ- and ε-proteobacteria. Its nitrite and nitric oxide reductase activities have been studied extensively and contribute to respiratory nitrite ammonification and nitric oxide detoxification respectively. Sulfite is a third substrate for NrfA that may be encountered in the micro-oxic environments where nrfA is expressed. Consequently, we have performed quantitative kinetic and thermodynamic studies of the interactions between sulfite and Escherichia coli NrfA to provide a biochemical framework from which to consider their possible cellular consequences. A combination of voltammetric, spectroscopic and crystallographic analyses define dissociation constants for sulfite binding to NrfA in oxidized (~54 μM), semi-reduced (~145 μM) and reduced (~180 μM) states that are comparable with each other, and the Km (~70 μM) for sulfite reduction at pH 7. Under comparable conditions Km values of ~22 and ~300 μM describe nitrite and nitric oxide reduction respectively, whereas the affinities of nitrate and thiocyanate for NrfA fall more than 50-fold on enzyme reduction. These results are discussed in terms of the nature of sulfite co-ordination within the active site of NrfA and their implications for the cellular activity of NrfA.

  • Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-552
A, B, C, D
452Escherichia coli K-12Mutation(s): 0 
Find proteins for P0ABK9 (Escherichia coli (strain K12))
Explore P0ABK9 
Go to UniProtKB:  P0ABK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABK9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B]
C34 H34 Fe N4 O4
Query on SO3

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GA [auth C],
L [auth A],
UA [auth D],
V [auth B],
W [auth B]
O3 S
Query on EDO

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HA [auth C]
IA [auth C]
JA [auth C]
KA [auth C]
LA [auth C]
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
VA [auth D],
WA [auth D],
X [auth B],
Y [auth B]
C2 H6 O2
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
F [auth A]
NA [auth D]
O [auth B]
AA [auth C],
E [auth A],
F [auth A],
NA [auth D],
O [auth B],
OA [auth D],
P [auth B],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.52α = 90
b = 82.234β = 101.08
c = 142.172γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description