1FCS

CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution.

Rizzi, M.Bolognesi, M.Coda, A.Cutruzzola, F.Allocatelli, C.T.Brancaccio, A.Brunori, M.

(1993) FEBS Lett. 320: 13-16


  • PubMed Abstract: 
  • The three-dimensional structure of sperm whale myoglobin His64(E7)-->Val,Thr67(E10)-->Arg double mutant has been studied by X-ray crystallography at 1.6 A resolution, and refined to a crystallographic R-factor of 0.197. The Arg67(E10) side chain is e ...

    The three-dimensional structure of sperm whale myoglobin His64(E7)-->Val,Thr67(E10)-->Arg double mutant has been studied by X-ray crystallography at 1.6 A resolution, and refined to a crystallographic R-factor of 0.197. The Arg67(E10) side chain is extended in the direction of the ligand binding site, and its NH1 atom is at a distance of 3.11 A from the NH1 atom of Arg45(CD3), which is also pointing towards the distal site. Both are kept in this position by hydrogen bonding and electrostatic interactions with a solvent sulfate ion, located amongst the two, on the protein surface. No liganded water molecule is present at the sixth coordination position of the Fe(III) heme.


    Related Citations: 
    • Binding Mode of Azide to Ferric Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.9 Angstroms Resolution
      Mattevi, A.,Gatti, G.,Coda, A.,Rizzi, M.,Ascenzi, P.,Brunori, M.,Bolognesi, M.
      (1991) J.Mol.Recog. 4: 1
    • Control and Recognition of Anionic Ligands in Myoglobin
      Cutruzzola, F.,Allocatelli, C.T.,Ascenzi, P.,Bolognesi, M.,Sligar, S.G.,Brunori, M.
      (1991) FEBS Lett. 282: 281


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 2 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
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: 1.6 Å
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 91.300α = 90.00
b = 91.300β = 90.00
c = 45.860γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance