9IJO | pdb_00009ijo

X-ray crystal structure of F46C myoglobin with a covalently linked 4-methyl-2,2'-bipyridine group in complex with Cu2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Rational Design of an Artificial Metalloenzyme by Constructing a Metal-Binding Site Close to the Heme Cofactor in Myoglobin.

Nie, L.S.Liu, X.C.Yu, L.Liu, A.K.Sun, L.J.Gao, S.Q.Lin, Y.W.

(2024) Inorg Chem 63: 18531-18535

  • DOI: https://doi.org/10.1021/acs.inorgchem.4c03093
  • Primary Citation Related Structures: 
    9IJO

  • PubMed Abstract: 

    In this study, we constructed a metal-binding site close to the heme cofactor in myoglobin (Mb) by covalently attaching a nonnative metal-binding ligand of bipyridine to Cys46 through the F46C mutation in the heme distal site. The X-ray structure of the designed enzyme, termed F46C-mBpy Mb, was solved in the Cu(II)-bound form, which revealed the formation of a heterodinuclear center of Cu-His-H 2 O-heme. Cu(II)-F46C-mBpy Mb exhibits not only nitrite reductase reactivity but also cascade reaction activity involving both hydrolysis and oxidation. Furthermore, F46C-mBpy Mb displays Mn-peroxidase activity by the oxidation of Mn 2+ to Mn 3+ using H 2 O 2 as an oxidant. This study shows that the construction of a nonnative metal-binding site close to the heme cofactor is a convenient approach to creating an artificial metalloenzyme with a heterodinuclear center that confers multiple functions.


  • Organizational Affiliation
    • School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.

Macromolecule Content 

  • Total Structure Weight: 18.19 kDa 
  • Atom Count: 1,463 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 1 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.989α = 90
b = 77.523β = 90
c = 39.751γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-07-02 
  • Deposition Author(s): Lin, Y.W.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Database references