1SNR

Nitric oxide bound to Cu nitrite reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Side-on copper-nitrosyl coordination by nitrite reductase.

Tocheva, E.I.Rosell, F.I.Mauk, A.G.Murphy, M.E.

(2004) Science 304: 867-870

  • DOI: 10.1126/science.1095109
  • Primary Citation of Related Structures:  
    1SJM, 1SNR

  • PubMed Abstract: 
  • A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an ...

    A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper-containing nitrite reductaseABC341Alcaligenes faecalisMutation(s): 0 
Gene Names: nirKnir
EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis)
Explore P38501 
Go to UniProtKB:  P38501
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CU1
Query on CU1

Download Ideal Coordinates CCD File 
A, B, C
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NO
Query on NO

Download Ideal Coordinates CCD File 
A, B, C
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.726α = 90
b = 102.595β = 90
c = 145.652γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-04-30
    Changes: Data collection, Database references