Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.99 kDa 
• Atom Count: 1219 
• Modelled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

2FAL

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

• DOI: 10.2210/pdb2FAL/pdb

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


• Deposited: 1993-06-14 Released: 1993-10-31 
• Deposition Author(s): Conti, E., Moser, C., Rizzi, M., Mattevi, A., Lionetti, C., Coda, A., Ascenzi, P., Brunori, M., Bolognesi, M.

---

Experimental Data Snapshot

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

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

• PubMed: 8411158 
• 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 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

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 (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	B [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

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 = 52.98	α = 90
b = 70.7	β = 90
c = 32.5	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 1993-06-14 
• Released Date: 1993-10-31 
Deposition Author(s): Conti, E., Moser, C., Rizzi, M., Mattevi, A., Lionetti, C., Coda, A., Ascenzi, P., Brunori, M., Bolognesi, M.

Revision History  

• 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