Pseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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This is version 1.4 of the entry. See complete history


Cyanide Binding to Cd(1) Nitrite Reductase from Pseudomonas Aeruginosa: Role of the Active-Site His369 in Ligand Stabilization.

Sun, W.Arese, M.Brunori, M.Nurizzo, D.Brown, K.Cambillau, C.Tegoni, M.Cutruzzola, F.

(2002) Biochem Biophys Res Commun 291: 1

  • DOI: https://doi.org/10.1006/bbrc.2002.6391
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cyanide binding to fully reduced Pseudomonas aeruginosa cd(1) nitrite reductase (Pa cd(1) NiR) has been investigated for the wild-type enzyme and a site-directed mutant in which the active-site His369 was replaced by Ala. This mutation reduces the affinity toward cyanide (by approximately 13-fold) and especially decreases the rate of binding of cyanide to the reduced d(1) heme (by approximately 100-fold). The crystal structure of wild-type reduced Pa cd(1) NiR saturated with cyanide was determined to a resolution of 2.7 A. Cyanide binds to the iron of the d(1) heme, with an Fe-C-N angle of 168 degrees for both subunits of the dimer and only His369 is within hydrogen bonding distance of the nitrogen atom of the ligand. These results suggest that in Pa cd(1) NiR the invariant distal residue His369 plays a dominant role in controlling the binding of anionic ligands and allow the discussion of the mechanism of cyanide binding to the wild-type enzyme.

  • Organizational Affiliation

    Dipartimento di Scienze Biochimiche A. Rossi Fanelli and Centro di Biologia Molecolare del CNR, Università di Roma La Sapienza, Rome, Italy.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
543Pseudomonas aeruginosaMutation(s): 0 
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P24474 
Go to UniProtKB:  P24474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24474
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.4α = 90
b = 88.6β = 90
c = 113.4γ = 90
Software Package:
Software NamePurpose
DENZOdata 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: 2002-08-01
    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: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description