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 1.4 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase
A, B, C
341Alcaligenes faecalisMutation(s): 0 
Gene Names: NIRKNIR
EC: 1.7.2.1
UniProt
Find proteins for P38501 (Alcaligenes faecalis)
Explore P38501 
Go to UniProtKB:  P38501
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38501
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CU
Query on CU

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
Q [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CU1
Query on CU1

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
P [auth C]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
T [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NO
Query on NO

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B],
U [auth C]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations