1O7M

NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN

• PDB DOI: https://doi.org/10.2210/pdb1O7M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-11-11 Released: 2003-02-20 
• Deposition Author(s): Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.187 
• R-Value Work: 0.178 

Starting Model: experimental

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

• PubMed: 12586937 
• DOI: https://doi.org/10.1126/science.1078020
• Primary Citation of Related Structures:  
  1O7G, 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 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.

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Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, 75124 Uppsala, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 73.56 kDa 
• Atom Count: 5,694 
• Modelled Residue Count: 641 
• Deposited Residue Count: 643 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT	A	449	Pseudomonas putida	Mutation(s): 0  EC: 1.14.12.12
UniProt
Find proteins for P0A110 (Pseudomonas putida) Explore P0A110  Go to UniProtKB:  P0A110

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT	B	194	Pseudomonas putida	Mutation(s): 0  EC: 1.14.12.12
UniProt
Find proteins for P0A112 (Pseudomonas putida) Explore P0A112  Go to UniProtKB:  P0A112

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	H [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
SO4	G [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	I [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
OXY	F [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.187 
• R-Value Work: 0.178 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.277	α = 90
b = 140.277	β = 90
c = 208.754	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-20 
Deposition Author(s): Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

Revision History  

• Version 1.0: 2003-02-20
  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: 2017-07-05
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description