5MBA

BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution.

Mattevi, A.Gatti, G.Coda, A.Rizzi, M.Ascenzi, P.Brunori, M.Bolognesi, M.

(1991) J.Mol.Recog. 4: 1-6

  • DOI: 10.1002/jmr.300040102

  • PubMed Abstract: 
  • The binding mode of azide to the ferric form of Aplysia limacina myoglobin has been studied by X-ray crystallography. The three-dimensional structure of the complex has been refined at 1.9 A resolution to a crystallographic R-factor of 13.9%, includi ...

    The binding mode of azide to the ferric form of Aplysia limacina myoglobin has been studied by X-ray crystallography. The three-dimensional structure of the complex has been refined at 1.9 A resolution to a crystallographic R-factor of 13.9%, including 126 ordered solvent molecules. Azide binds to the heme iron, at the sixth co-ordination position, and is oriented towards the outer part of the distal site crevice. This orientation is stabilized by an ionic interaction with the side-chain of Arg66 (E10) which, from an outer orientation in the 'aquo-met' ligand-free myoglobin, folds back towards the distal site in the presence of the anionic ligand. In the absence of a hydrogen bond donor residue at the distal E7 position in Aplysia limacina myoglobin, a different polar residue, Arg66 at the E10 topological position, has been selected by molecular evolution in order to grant ligand stabilization.


    Related Citations: 
    • Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution
      Bolognesi, M.,Coda, A.,Gatti, G.,Ascenzi, P.,Brunori, M.
      (1985) J.Mol.Biol. 183: 113
    • The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution
      Ungaretti, L.,Bolognesi, M.,Cannillo, E.,Oberti, R.,Rossi, G.
      (1978) Acta Crystallogr.,Sect.B 34: 3658
    • The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina
      Tentori, L.,Vivaldi, G.,Carta, S.,Marinucci, M.,Massa, A.,Antonini, E.,Brunori, M.
      (1973) Int.J.Pept.Protein Res. 5: 187
    • 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
    • The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution
      Bolognesi, M.,Cannillo, E.,Oberti, R.,Rossi, G.,Ungaretti, L.
      (1978) Acta Crystallogr.,Sect.A (Supplement) 34: 62
    • Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina
      Blundell, T.L.,Brunori, M.,Curti, B.,Bolognesi, M.,Coda, A.,Fumagalli, M.,Ungaretti, L.
      (1975) J.Mol.Biol. 97: 665
    • 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
    • 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


    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
AZI
Query on AZI

Download SDF File 
Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-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
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: 1.9 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: 1992-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance