1NZ3

K45E-K63E Variant of Horse Heart Myoglobin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Introduction and characterization of a functionally linked metal ion binding site at the exposed heme edge of myoglobin

Hunter, C.L., Maurus, R., Mauk, M.R., Lee, H., Raven, E.L., Tong, H., Nguyen, N., Smith, S., Brayer, G.D., Mauk, A.G.

(2003) Proc Natl Acad Sci U S A 100: 3647-3652

  • DOI: 10.1073/pnas.0636702100
  • Primary Citation of Related Structures:  
    1NZ2, 1NZ3, 1NZ4, 1NZ5

  • PubMed Abstract: 

    • A binding site for metal ions has been created on the surface of horse heart myoglobin (Mb) near the heme 6-propionate group by replacing K45 and K63 with glutamyl residues. One-dimensional (1)H NMR spectroscopy indicates that Mn(2+) binds in the vicinity of the heme 6-propionate as anticipated, and potentiometric titrations establish that the affinity of the new site for Mn(2+) is 1 ...

    A binding site for metal ions has been created on the surface of horse heart myoglobin (Mb) near the heme 6-propionate group by replacing K45 and K63 with glutamyl residues. One-dimensional (1)H NMR spectroscopy indicates that Mn(2+) binds in the vicinity of the heme 6-propionate as anticipated, and potentiometric titrations establish that the affinity of the new site for Mn(2+) is 1.28(4) x 10(4) M(-1) (pH 6.96, ionic strength I = 17.2 microM, 25 degrees C). In addition, these substitutions lower the reduction potential of the protein and increase the pK(a) for the water molecule coordinated to the heme iron of metmyoglobin. The peroxidase [2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid), ABTS, as substrate] and the Mn(2+)-peroxidase activity of the variant are both increased approximately 3-fold. In contrast to wild-type Mb, both the affinity for azide and the midpoint potential of the variant are significantly influenced by the addition of Mn(2+). The structure of the variant has been determined by x-ray crystallography to define the coordination environment of bound Mn(2+) and Cd(2+). Although slight differences are observed between the geometry of the binding of the two metal ions, both are hexacoordinate, and neither involves coordination by E63.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology and Protein Engineering Network of Centres of Excellence, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA153Equus caballusMutation(s): 2 
Gene Names: MB
UniProt
Find proteins for P68082 (Equus caballus)
Explore P68082 
Go to UniProtKB:  P68082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68082
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29α = 90
b = 35.8β = 90
c = 125.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations