1O7G

NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron

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

(2003) Science 299: 1039

  • DOI: 10.1126/science.1078020
  • Primary Citation of Related Structures:  1O7H, 1O7M, 1O7N, 1O7P, 1O7W

  • PubMed Abstract: 
  • Binding of oxygen to iron is exploited in several biological and chemical processes. Although computational and spectroscopic results have suggested side-on binding, only end-on binding of oxygen to iron has been observed in crystal structures. We ha ...

    Binding of oxygen to iron is exploited in several biological and chemical processes. Although computational and spectroscopic results have suggested side-on binding, only end-on binding of oxygen to iron has been observed in crystal structures. We have determined structures of naphthalene dioxygenase that show a molecular oxygen species bound to the mononuclear iron in a side-on fashion. In a complex with substrate and dioxygen, the dioxygen molecule is lined up for an attack on the double bond of the aromatic substrate. The structures reported here provide the basis for a reaction mechanism and for the high stereospecificity of the reaction catalyzed by naphthalene dioxygenase.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPY
Query on NPY

Download SDF File 
Download CCD File 
A
NAPHTHALENE
C10 H8
UFWIBTONFRDIAS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

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

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 139.670α = 90.00
b = 139.670β = 90.00
c = 208.109γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance