2FAM

X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.

Conti, E.Moser, C.Rizzi, M.Mattevi, A.Lionetti, C.Coda, A.Ascenzi, P.Brunori, M.Bolognesi, M.

(1993) J.Mol.Biol. 233: 498-508

  • DOI: 10.1006/jmbi.1993.1527
  • Primary Citation of Related Structures:  
  • Also Cited By: 1LHT

  • PubMed Abstract: 
  • The X-ray crystal structure of the ligand-free ferric form of Aplysia limacina myoglobin (pH 6.0) has been refined at 1.7 A resolution (R = 15.1%), and its cyanide, thiocyanate and imidazole derivatives studied by difference Fourier techniques at ato ...

    The X-ray crystal structure of the ligand-free ferric form of Aplysia limacina myoglobin (pH 6.0) has been refined at 1.7 A resolution (R = 15.1%), and its cyanide, thiocyanate and imidazole derivatives studied by difference Fourier techniques at atomic resolution. The crystallographic R-factors of the three different derivatives reported are 16.1%, 16.1% and 15.6% at 1.8 A, 2.0 A and 2.0 A resolution, respectively. The present results have been analyzed in parallel with previous crystallographic studies on the molecular structures of the fluoride and azide derivatives of ferric Aplysia limacina myoglobin. Ligand binding to the distal site of the heme pocket results in different networks of hydrogen bonds involving to various degrees the bound ligand, residue Arg(66)E10, the heme propionate III, ordered water molecules and/or protein backbone atoms from the CD region. In particular, Arg(66)E10 stabilizes the bound ligand and compensates for the absence of the hydrogen bond donor residue HisE7, commonly present in oxygen-carrying globins.


    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
    • Aplysia Limacina Myoglobin: Molecular Bases for Ligand Binding
      Bolognesi, M.,Frigerio, F.,Lionetti, C.,Rizzi, M.,Ascenzi, P.,Brunori, M.
      (1991) Structure and Function of Invertebrate Oxygen Carriers --: 161
    • X-Ray Crystal Structure of the Fluoride Derivative of Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution: Stabilization of the Fluoride by Hydrogen Bonding to Arg66 (E10)
      Bolognesi, M.,Coda, A.,Frigerio, F.,Gatti, G.,Ascenzi, P.,Brunori, M.
      (1990) J.Mol.Biol. 213: 621
    • X-Ray Crystal Structure of the Ferric Sperm Whale Myoglobin: Imidazole Complex at 2.0 Angstroms Resolution
      Lionetti, C.,Guanziroli, M.G.,Frigerio, F.,Ascenzi, P.,Bolognesi, M.
      (1991) J.Mol.Biol. 217: 409
    • Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution
      Bolognesi, M.,Onesti, S.,Gatti, G.,Coda, A.,Ascenzi, P.,Brunori, M.
      (1989) J.Mol.Biol. 205: 529
    • Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study
      Bolognesi, M.,Cannillo, E.,Ascenzi, P.,Giacometti, G.M.,Merli, A.,Brunori, M.
      (1982) J.Mol.Biol. 158: 305


    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
147Aplysia limacinaMutation(s): 0 
Find proteins for P02210 (Aplysia limacina)
Go to UniProtKB:  P02210
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.980α = 90.00
b = 70.700β = 90.00
c = 32.500γ = 90.00
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