1BJE

H64T VARIANT OF MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and spectroscopic studies of azide complexes of horse heart myoglobin and the His-64-->Thr variant.

Maurus, R.Bogumil, R.Nguyen, N.T.Mauk, A.G.Brayer, G.

(1998) Biochem.J. 332: 67-74

  • Primary Citation of Related Structures:  1AZI

  • PubMed Abstract: 
  • The high-resolution X-ray crystallographic structures of horse heart azidometmyoglobin complexes of the wild-type protein and the His-64-->Thr variant have been determined to 2.0 and 1.8 A respectively. Azide binds to wild-type metmyoglobin in a bent ...

    The high-resolution X-ray crystallographic structures of horse heart azidometmyoglobin complexes of the wild-type protein and the His-64-->Thr variant have been determined to 2.0 and 1.8 A respectively. Azide binds to wild-type metmyoglobin in a bent configuration with an Fe-N-1-N-3 angle of 119 degrees and is oriented into the distal crevice in the direction of Ile-107. The proximity of the His-64 NE2 atom to the N-1 atom of the bound azide indicates stabilization of the ligand by the His-64 side chain through hydrogen bonding. In addition, structural characterization of wild-type horse heart azidometmyoglobin establishes that the only structural change induced by ligand binding is a small movement of the Leu-29 side chain away from the azide ligand. EPR and Fourier transform infrared spectroscopy were used to characterize the myoglobin azide complexes further. EPR spectroscopy revealed that, in contrast with wild-type azidometmyoglobin, two slightly different low-spin species are formed by azide bound to the His-64-->Thr variant both in solution and in a polycrystalline sample. One of these low-spin species has a greater relative intensity, with g values very similar to those of the azide complex of the wild-type protein. These EPR results together with structural information on this variant indicate the presence of two distinct conformations of bound azide, with one form predominating. The major conformation is comparable to that formed by wild-type myoglobin in which azide is oriented into the distal crevice. In the minor conformation the azide is oriented towards the exterior of the protein.


    Related Citations: 
    • Three-Dimensional Structure of Cyanomet-Sulfmyoglobin C
      Evans, S.V.,Sishta, B.P.,Mauk, A.G.,Brayer, G.D.
      (1994) Proc.Natl.Acad.Sci.USA 91: 4723
    • A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket
      Maurus, R.,Overall, C.M.,Bogumil, R.,Luo, Y.,Mauk, A.G.,Smith, M.,Brayer, G.D.
      (1997) Biochim.Biophys.Acta 1341: 1
    • High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin
      Evans, S.V.,Brayer, G.D.
      (1990) J.Mol.Biol. 213: 885
    • Expression in Escherichia Coli of a Synthetic Gene Coding for Horse Heart Myoglobin
      Guillemette, J.G.,Matsushima-Hibiya, Y.,Atkinson, T.,Smith, M.
      (1991) Protein Eng. 4: 585
    • Horse Heart Metmyoglobin. A 2.8-A Resolution Three-Dimensional Structure Determination
      Evans, S.V.,Brayer, G.D.
      (1988) J.Biol.Chem. 263: 4263
    • Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
      Sherwood, C.,Mauk, A.G.,Brayer, G.D.
      (1987) J.Mol.Biol. 193: 227
    • Structural Characterization of Heme Ligation in the His64-->Tyr Variant of Myoglobin
      Maurus, R.,Bogumil, R.,Luo, Y.,Tang, H.L.,Smith, M.,Mauk, A.G.,Brayer, G.D.
      (1994) J.Biol.Chem. 269: 12606
    • Ftir Analysis of the Interaction of Azide with Horse Heart Myoglobin Variants
      Bogumil, R.,Hunter, C.L.,Maurus, R.,Tang, H.L.,Lee, H.,Lloyd, E.,Brayer, G.D.,Smith, M.,Mauk, A.G.
      (1994) Biochemistry 33: 7600


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Equus caballusGene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.019α = 90.00
b = 28.812β = 106.95
c = 35.840γ = 90.00
Software Package:
Software NamePurpose
OSCILLdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance