Native human manganese superoxide dismutase

Experimental Data Snapshot

  • Resolution: 1.82 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase.

Azadmanesh, J.Trickel, S.R.Borgstahl, G.E.O.

(2017) J Struct Biol 199: 68-75

  • DOI: https://doi.org/10.1016/j.jsb.2017.04.011
  • Primary Citation of Related Structures:  
    5T30, 5VF9

  • PubMed Abstract: 

    Superoxide dismutases (SODs) are enzymes that play a key role in protecting cells from toxic oxygen metabolites by disproportionation of two molecules of superoxide into molecular oxygen and hydrogen peroxide via cyclic reduction and oxidation at the active site metal. The azide anion is a potent competitive inhibitor that binds directly to the metal and is used as a substrate analog to superoxide in studies of SOD. The crystal structure of human MnSOD-azide complex was solved and shows the putative binding position of superoxide, providing a model for binding to the active site. Azide is bound end-on at the sixth coordinate position of the manganese ion. Tetrameric electrostatic surfaces were calculated incorporating accurate partial charges for the active site in three states, including a state with superoxide coordinated to the metal using the position of azide as a model. These show facilitation of the anionic ligand to the active site pit via a 'valley' of positively-charged surface patches. Surrounding ridges of negative charge help guide the superoxide anion. Within the active site pit, Arg173 and Glu162 further guide and align superoxide for efficient catalysis. Superoxide coordination at the sixth position causes the electrostatic surface of the active site pit to become nearly neutral. A model for electrostatic-mediated diffusion, and efficient binding of superoxide for catalysis is presented.

  • Organizational Affiliation

    The Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA; Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Mn], mitochondrial
A, B
199Homo sapiensMutation(s): 0 
Gene Names: SOD2
UniProt & NIH Common Fund Data Resources
Find proteins for P04179 (Homo sapiens)
Explore P04179 
Go to UniProtKB:  P04179
PHAROS:  P04179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04179
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.82 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.24α = 90
b = 78.24β = 90
c = 238.47γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Aeronautic Space Administration (NASA, United States)United States44-0307-1021-201

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-02-01
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2023-10-04
    Changes: Data collection
  • Version 1.5: 2023-10-25
    Changes: Refinement description