5MBA | pdb_00005mba

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

• PDB DOI: https://doi.org/10.2210/pdb5MBA/pdb
• Entry: 5MBA supersedes: 2MBA

• Classification: OXYGEN STORAGE
• Organism(s): Aplysia limacina
• Mutation(s): No 


• Deposited: 1991-01-14 Released: 1992-07-15 
• Deposition Author(s): Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P., Brunori, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 
  0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

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 Recognit 4: 1-6

• PubMed: 1931125 
• DOI: https://doi.org/10.1002/jmr.300040102
• Primary Citation of Related Structures:  
  5MBA


• 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%, 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.

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Organizational Affiliation: 
• Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.01 kDa 
• Atom Count: 1,258 
• Modeled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	147	Aplysia limacina	Mutation(s): 0
UniProt
Find proteins for P02210 (Aplysia limacina) Explore P02210  Go to UniProtKB:  P02210

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
AZI	B [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work:  0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.98	α = 90
b = 70.7	β = 90
c = 32.5	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-07-15 
Deposition Author(s): Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P., Brunori, M.
• This entry supersedes: 2MBA

Revision History  

• Version 1.0: 1992-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Structure summary