9NR0 | pdb_00009nr0

Finding the exit route of hydrogen peroxide from the manganese superoxide dismutase (MnSOD) active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.214 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NR0

This is version 1.1 of the entry. See complete history

Literature

High-resolution X-ray structure of Gln143Asn manganese superoxide dismutase captures multiple hydrogen peroxide-binding sites.

Dasgupta, M.Slobodnik, K.Cone, E.A.Azadmanesh, J.Kroll, T.Borgstahl, G.E.O.

(2025) Acta Crystallogr F Struct Biol Commun 81: 467-477

  • DOI: https://doi.org/10.1107/S2053230X25009045
  • Primary Citation Related Structures: 
    9NR0, 9NSJ

  • PubMed Abstract: 

    Human mitochondrial manganese superoxide dismutase (MnSOD) converts superoxide into hydrogen peroxide and molecular oxygen, serving as a key defence against oxidative damage. Despite extensive studies, the full structural characterization of H 2 O 2 -binding sites in MnSOD remains largely unexplored. Previous H 2 O 2 -soaked MnSOD structures have identified two distinct H 2 O 2 -binding sites: one directly ligated to the catalytic manganese (LIG position) and another at the active-site gateway (PEO position) between the second-shell residues Tyr34 and His30. In this study, a kinetically impaired Gln143Asn MnSOD variant is used to trap and explore additional H 2 O 2 -binding sites beyond the second-shell solvent gate. In the wild-type enzyme, Gln143 mediates proton transfers with the manganese-bound solvent (WAT1) to drive redox cycling of the metal, which is necessary for effective superoxide dismutation. Substitution with Asn stalls catalysis because the increased distance from WAT1 disrupts critical proton-coupled electron-transfer (PCET) events, and the redox cycling of the active-site metal is impaired. This, in turn, stalls the electrostatic cycling of positive charge on the enzyme surface and enhances the likelihood of trapping transient H 2 O 2 -bound states in this variant. The results reveal several H 2 O 2 molecules leading up to the active site, in addition to the canonical LIG and PEO positions.


  • Organizational Affiliation
    • Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE 68198, USA.

Macromolecule Content 

  • Total Structure Weight: 45.97 kDa 
  • Atom Count: 4,186 
  • Modeled Residue Count: 397 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Mn], mitochondrial
A, B
199Homo sapiensMutation(s): 1 
Gene Names: SOD2
EC: 1.15.1.1
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
D [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A],
L [auth B],
M [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.203α = 90
b = 78.203β = 90
c = 237.208γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references