2ZKX

Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group I212121

• PDB DOI: https://doi.org/10.2210/pdb2ZKX/pdb
• Entry: 2ZKX supersedes: 2YQW

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


• Deposited: 2008-03-31 Released: 2009-03-24 
• Deposition Author(s): Yoshikawa, S., Kukimoto-Niino, M., Ito, K., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Urushitani, M., Takahashi, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 

Starting Model: experimental

Literature

Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group I212121

Yoshikawa, S., Kukimoto-Niino, M., Ito, K., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Urushitani, M., Takahashi, R., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.4 kDa 
• Atom Count: 4,213 
• Modelled Residue Count: 574 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C, D	159	Homo sapiens	Mutation(s): 1  Gene Names: SOD1 EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1	E [auth A], G [auth B], I [auth C], K [auth D]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.246 
• R-Value Work: 0.176 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.105	α = 90
b = 113.08	β = 90
c = 146.375	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Yoshikawa, S., Kukimoto-Niino, M., Ito, K., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Shirouzu, M., Urushitani, M., Takahashi, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2YQW

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-04
  Changes: Other
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description