3AYG

Crystal structure of nitric oxide reductase complex with HQNO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.

Matsumoto, Y.Tosha, T.Pisliakov, A.V.Hino, T.Sugimoto, H.Nagano, S.Sugita, Y.Shiro, Y.

(2012) Nat Struct Mol Biol 19: 238-245

  • DOI: https://doi.org/10.1038/nsmb.2213
  • Primary Citation of Related Structures:  
    3AYF, 3AYG

  • PubMed Abstract: 

    The structure of quinol-dependent nitric oxide reductase (qNOR) from G. stearothermophilus, which catalyzes the reduction of NO to produce the major ozone-depleting gas N(2)O, has been characterized at 2.5 Å resolution. The overall fold of qNOR is similar to that of cytochrome c-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are observed in qNOR, even though it harbors no heme c. In contrast to cNOR, structure-based mutagenesis and molecular dynamics simulation studies of qNOR suggest that a water channel from the cytoplasm can serve as a proton transfer pathway for the catalytic reaction. Further structural comparison of qNOR with cNOR and aerobic and microaerobic respiratory oxidases elucidates their evolutionary relationship and possible functional conversions.


  • Organizational Affiliation

    Biometal Science Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide reductase800Geobacillus stearothermophilusMutation(s): 0 
Gene Names: norZ
Membrane Entity: Yes 
UniProt
Find proteins for B3Y963 (Geobacillus stearothermophilus)
Explore B3Y963 
Go to UniProtKB:  B3Y963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y963
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BOG
Query on BOG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
HQO
Query on HQO

Download Ideal Coordinates CCD File 
K [auth A]2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
C16 H21 N O2
NZPACTGCRWDXCJ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.516α = 90
b = 149.089β = 90
c = 151.59γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data 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: 2012-01-25
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Structure summary