Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17669.10 
• Atom Count: 1247 
• Residue Count: 153 
• Unique protein chains: 1

1EMY

CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET MYOGLOBIN AT 1.78 ANGSTROMS RESOLUTION. PHE 29 (B10) ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING PROPERTIES

• DOI: 10.2210/pdb1EMY/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Elephas maximus


• Deposited: 1995-02-22 Released: 1995-04-20 
• Deposition Author(s): Bisig, D.A., Piontek, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Work: 0.153 

Literature

Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties.

Bisig, D.A., Di Iorio, E.E., Diederichs, K., Winterhalter, K.H., Piontek, K.

(1995) J.Biol.Chem. 270: 20754-20762

• PubMed: 7657658 


• PubMed Abstract: 
  

The crystal structure of Asian elephant cyano-metmyoglobin which has a glutamine instead of the usual distal site histidine has been determined to high resolution. In addition to this replacement, the substitution of a conserved leucine residue in position 29(B10) at the distal side by a phenylalanine was unambiguously identified based on the available electron density. The suspicion, that there were errors in the original sequence which has caused some confusion, is thus confirmed. Comparison with other myoglobin structures in various ligated forms reveals an essentially unchanged tertiary structure in elephant myoglobin despite the two amino acid substitutions in the heme pocket. Our current structural model shows that the N epsilon 2 atom of Gln64(E7) has moved with respect to the corresponding nitrogen position of His64(E7) in the CO complex of sperm whale myoglobin. The newly assigned residue Phe29(B10) penetrates into the distal side of the heme pocket approaching the ligand within van der Waals distance and causing a much more crowded heme pocket compared to other myoglobins. Kinetic properties of Asian elephant myoglobin, wild type, and recombinant sperm whale myoglobins are discussed in relation to the structural consequences of the two amino acid substitutions H64Q and L29F.

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Related Citations: 

• 1H NMR Investigation of the Heme Cavity of Elephant (E7 Gln) met-Cyano-Myoglobin. Evidence for a B-Helix Phenylalanine Interaction with Bound Ligand
  Vyas, K.,Rajarathnam, K.,Yu, L.P.,Emerson, S.D.,La Mar, G.N.,Krishnamoorthi, R.
  (1993) J.Biol.Chem. 268: 14826
• A Double Mutant of Sperm Whale Myoglobin Mimics the Structure and Function of Elephant Myoglobin
  Zhao, X.,Vyas, K.,Nguyen, B.D.,Rajarathnam, K.,La Mar, G.N.,Li, T.,Phillips Jr., G.N.,Eich, R.F.,Olson, J.S.,Ling, J.,Bocian, D.F.
  () TO BE PUBLISHED --: --




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Organizational Affiliation: 

Laboratory of Biochemistry I, Swiss Federal Institute of Technology, CH-8092 Zürich.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MYOGLOBIN	A	153	Elephas maximus	Mutation(s): 0  Gene Names: MB
Find proteins for P02186 (Elephas maximus) Go to Gene View: MB Go to UniProtKB:  P02186

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CYN	A	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Work: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 33.510	α = 90.00
b = 58.590	β = 90.00
c = 70.440	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-02-22 
• Released Date: 1995-04-20 
• Deposition Author(s): Bisig, D.A., Piontek, K.

Revision History 

• Version 1.0: 1995-04-20
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance