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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1007/s00775-005-0657-1
  • Primary Citation of Related Structures:  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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
A
449Pseudomonas putidaGene Names: ndoB (nahA3, nahAC, ndoC2)
EC: 1.14.12.12
Find proteins for P0A110 (Pseudomonas putida)
Go to UniProtKB:  P0A110
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
B
194Pseudomonas putidaGene Names: ndoC (nahAD)
EC: 1.14.12.12
Find proteins for P0A112 (Pseudomonas putida)
Go to UniProtKB:  P0A112
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

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Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
IND
Query on IND

Download SDF File 
Download CCD File 
A
INDOLE
C8 H7 N
SIKJAQJRHWYJAI-UHFFFAOYSA-N
 Ligand Interaction
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 = 139.600α = 90.00
b = 139.600β = 90.00
c = 209.303γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance