Macromolecule Content

• Total Structure Weight: 15.90 kDa 
• Atom Count: 1113 
• Residue Count: 153 
• Unique protein chains: 1

1KMG

The Solution Structure Of Monomeric Copper-free Superoxide Dismutase

• DOI: 10.2210/pdb1KMG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-12-15 Released: 2002-10-02 
• Deposition Author(s): Banci, L., Bertini, I., Cantini, F., D'Onofrio, M., Viezzoli, M.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 35 
• Selection Criteria: target function 

Literature

Structure and dynamics of copper-free SOD: The protein before binding copper.

Banci, L., Bertini, I., Cantini, F., D'Onofrio, M., Viezzoli, M.S.

(2002) Protein Sci 11: 2479-2492

• PubMed: 12237469 
• DOI: 10.1110/ps.0210802
• Primary Citation of Related Structures:  
  1KMG


• PubMed Abstract: 
  

The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.

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Organizational Affiliation: 

The Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide Dismutase	A	153	Homo sapiens	Mutation(s): 5  Gene Names: SOD1 EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
NIH Common Fund Data Resources
PHAROS:  P00441 GTEx:  ENSG00000142168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 400 
• Conformers Submitted: 35 
• Selection Criteria: target function 
• OLDERADO: 1KMG Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-15 
• Released Date: 2002-10-02 
Deposition Author(s): Banci, L., Bertini, I., Cantini, F., D'Onofrio, M., Viezzoli, M.S.

Revision History 

• Version 1.0: 2002-10-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance