1UUV

NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE BOUND IN THE ACTIVE SITE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

No Binding to Naphthalene Dioxygenase.

Karlsson, A.Parales, J.V.Parales, R.E.Gibson, D.T.Eklund, H.Ramaswamy, S.

(2005) J Biol Inorg Chem 10: 483

  • DOI: https://doi.org/10.1007/s00775-005-0657-1
  • Primary Citation of Related Structures:  
    1UUV, 1UUW

  • PubMed Abstract: 

    Nitric oxide (NO) is commonly used as an analogue for dioxygen in structural and spectroscopic studies of oxygen binding and oxygen activation. In this study, crystallographic structures of naphthalene dioxygenase (NDO) in complex with nitric oxide are reported. In the presence of the aromatic substrate indole, NO is bound end-on to the active-site mononuclear iron of NDO. The structural observations correlate well with spectroscopic measurements of NO binding to NDO in solution. However, the end-on binding of NO is in contrast to the recently reported structure of oxygen to the active-site iron of NDO that binds side-on. While NO is a good oxygen analogue with many similarities to O(2), the different binding mode of NO to the active-site iron atom leads to different mechanistic implications. Hence, caution needs to be used in extrapolating NO as an analogue to O(2) binding.


  • Organizational Affiliation

    Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, 75124 Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT449Pseudomonas putidaMutation(s): 0 
EC: 1.14.12.12
UniProt
Find proteins for P0A110 (Pseudomonas putida)
Explore P0A110 
Go to UniProtKB:  P0A110
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A110
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT194Pseudomonas putidaMutation(s): 0 
EC: 1.14.12.12
UniProt
Find proteins for P0A112 (Pseudomonas putida)
Explore P0A112 
Go to UniProtKB:  P0A112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A112
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
IND
Query on IND

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G [auth A]INDOLE
C8 H7 N
SIKJAQJRHWYJAI-UHFFFAOYSA-N
SO4
Query on SO4

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L [auth B],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

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I [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NO
Query on NO

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H [auth A]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.6α = 90
b = 139.6β = 90
c = 209.303γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-09
    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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description