Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after full x-ray-induced reduction

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 

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This is version 1.3 of the entry. See complete history


Crystal structure of nickel-containing superoxide dismutase reveals another type of active site

Wuerges, J.Lee, J.-W.Yim, Y.-I.Yim, H.-S.Kang, S.-O.Djinovic Carugo, K.

(2004) Proc Natl Acad Sci U S A 101: 8569-8574

  • DOI: https://doi.org/10.1073/pnas.0308514101
  • Primary Citation of Related Structures:  
    1Q0D, 1Q0F, 1Q0G, 1Q0K, 1Q0M

  • PubMed Abstract: 

    Superoxide dismutases (SODs, EC are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.

  • Organizational Affiliation

    International School for Advanced Studies, Via Beirut 2-4, I-34014 Trieste, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Ni]
A, B, C, D, E
A, B, C, D, E, F
117Streptomyces seoulensisMutation(s): 0 
Find proteins for P80734 (Streptomyces seoulensis)
Explore P80734 
Go to UniProtKB:  P80734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80734
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
M [auth C]
P [auth D]
H [auth A],
J [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth D],
T [auth E],
V [auth F]
O4 S
Query on ACY

Download Ideal Coordinates CCD File 
N [auth C],
R [auth D],
W [auth F]
C2 H4 O2
Query on NI

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
O [auth D]
S [auth E]
G [auth A],
I [auth B],
K [auth C],
O [auth D],
S [auth E],
U [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.532α = 90
b = 119.428β = 90
c = 121.176γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations