2FAL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.151 

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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:  
    2FAM, 2FAL

  • 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 atomic resolution ...

    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: 
    • 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: 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
    • 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 Recognit 4: 1
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOGLOBINA147Aplysia limacinaMutation(s): 0 
UniProt
Find proteins for P02210 (Aplysia limacina)
Explore P02210 
Go to UniProtKB:  P02210
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
B [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.98α = 90
b = 70.7β = 90
c = 32.5γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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