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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 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 po ...

    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.


    Related Citations: 
    • 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 --: --
    • 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


    Organizational Affiliation

    Laboratory of Biochemistry I, Swiss Federal Institute of Technology, CH-8092 Z├╝rich.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Elephas maximusGene Names: MB
Find proteins for P02186 (Elephas maximus)
Go to Gene View: MB
Go to UniProtKB:  P02186
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-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: 1.78 Å
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.510α = 90.00
b = 58.590β = 90.00
c = 70.440γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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