Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17848.48 
• Atom Count: 1250 
• Residue Count: 153 
• Unique protein chains: 1

2EVP

The Structures of Thiolate- and Carboxylate-Ligated Ferric H93G Myoglobin: Models for Cytochrome P450 and for Oxyanion-Bound Heme Proteins

• DOI: 10.2210/pdb2EVP/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter catodon
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2005-10-31 Released: 2006-03-28 
• Deposition Author(s): Qin, J., Perera, R., Lovelace, L.L., Dawson, J.H., Lebioda, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 

Literature

Structures of Thiolate- and Carboxylate-Ligated Ferric H93G Myoglobin: Models for Cytochrome P450 and for Oxyanion-Bound Heme Proteins(,).

Qin, J., Perera, R., Lovelace, L.L., Dawson, J.H., Lebioda, L.

(2006) Biochemistry 45: 3170-3177

• PubMed: 16519512 
• DOI: 10.1021/bi052171s
• Primary Citation of Related Structures:  
  2EVK


• PubMed Abstract: 
  

Crystal structures of the ferric H93G myoglobin (Mb) cavity mutant containing either an anionic proximal thiolate sulfur donor or a carboxylate oxygen donor ligand are reported at 1.7 and 1.4 A resolution, respectively. The crystal structure and magnetic circular dichroism spectra of the H93G Mb beta-mercaptoethanol (BME) thiolate adduct reveal a high-spin, five-coordinate complex. Furthermore, the bound BME appears to have an intramolecular hydrogen bond involving the alcohol proton and the ligated thiolate sulfur, mimicking one of the three proximal N-H...S hydrogen bonds in cytochrome P450. The Fe is displaced from the porphyrin plane by 0.5 A and forms a 2.41 A Fe-S bond. The Fe(3+)-S-C angle is 111 degrees , indicative of a covalent Fe-S bond with sp(3)-hybridized sulfur. Therefore, the H93G Mb.BME complex provides an excellent protein-derived structural model for high-spin ferric P450. In particular, the Fe-S bond in high-spin ferric P450-CAM has essentially the same geometry despite the constraints imposed by covalent linkage of the cysteine to the protein backbone. This suggests that evolution led to the geometric optimization of the proximal Fe-S(cysteinate) bond in P450. The crystal structure and spectral properties of the H93G Mb acetate adduct reveal a high-spin, six-coordinate complex with proximal acetate and distal water axial ligands. The distal His-64 forms a hydrogen bond with the bound water. The Fe-acetate bonding geometry is inconsistent with an electron pair along the Fe-O bond as the Fe-O-C angle is 152 degrees and the Fe is far from the plane of the acetate. Thus, the Fe-O bonding is ionic. The H93G Mb cavity mutant has already been shown to be a versatile model system for the study of ligand binding to heme proteins; this investigation affords the first structural evidence that nonimidazole exogenous ligands bind in the proximal ligation site.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Myoglobin	A	153	Physeter catodon	Mutation(s): 1  Gene Names: MB
Find proteins for P02185 (Physeter catodon) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 39.670	α = 90.00
b = 47.770	β = 90.00
c = 77.430	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
CNS	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-31 
• Released Date: 2006-03-28 
• Deposition Author(s): Qin, J., Perera, R., Lovelace, L.L., Dawson, J.H., Lebioda, L.

Revision History 

• Version 1.0: 2006-03-28
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance