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Zinc in PDB 3f7k: X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Enzymatic activity of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

All present enzymatic activity of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex, PDB code: 3f7k was solved by D.S.Shin, M.Didonato, D.P.Barondeau, E.D.Getzoff, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.35
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.563, 62.563, 163.745, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 17.6

Other elements in 3f7k:

The structure of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex (pdb code 3f7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex, PDB code: 3f7k:

Zinc binding site 1 out of 1 in 3f7k

Go back to Zinc Binding Sites List in 3f7k
Zinc binding site 1 out of 1 in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:10.9
occ:1.00
 OD1 A:ASP81 2.0 11.2 1.0
ND1 A:HIS78 2.0 10.8 1.0
ND1 A:HIS61 2.0 11.7 1.0
ND1 A:HIS69 2.0 10.7 1.0
CG A:ASP81 2.7 11.3 1.0
CE1 A:HIS69 2.9 11.6 1.0
CE1 A:HIS78 2.9 11.1 1.0
OD2 A:ASP81 2.9 12.4 1.0
CE1 A:HIS61 2.9 12.9 1.0
CG A:HIS78 3.1 10.5 1.0
CG A:HIS61 3.1 13.2 1.0
CG A:HIS69 3.1 10.7 1.0
CB A:HIS61 3.4 12.4 1.0
CB A:HIS78 3.6 11.3 1.0
CB A:HIS69 3.7 11.7 1.0
CA A:HIS69 3.9 11.8 1.0
O A:ILE134 4.0 13.5 1.0
NE2 A:HIS78 4.1 12.5 1.0
NE2 A:HIS69 4.1 11.0 1.0
NE2 A:HIS61 4.1 13.0 1.0
CD2 A:HIS78 4.1 13.0 1.0
CD2 A:HIS61 4.2 13.7 1.0
CB A:ASP81 4.2 11.7 1.0
CD2 A:HIS69 4.2 11.9 1.0
CA A:ASP81 4.7 11.1 1.0
N A:HIS78 4.8 11.6 1.0
CD2 A:HIS44 4.8 12.4 1.0
CA A:HIS78 4.8 10.9 1.0
N A:GLY70 4.8 12.8 1.0
N A:HIS69 4.9 11.8 1.0
C A:HIS69 4.9 12.5 1.0
C A:ILE134 4.9 12.3 1.0
CA A:HIS61 4.9 11.0 1.0
N A:ASP81 5.0 11.3 1.0

Reference:

D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, J.A.Tainer. Superoxide Dismutase From the Eukaryotic Thermophile Alvinella Pompejana: Structures, Stability, Mechanism, and Insights Into Amyotrophic Lateral Sclerosis. J.Mol.Biol. V. 385 1534 2009.
ISSN: ISSN 0022-2836
PubMed: 19063897
DOI: 10.1016/J.JMB.2008.11.031
Page generated: Wed Dec 16 04:17:57 2020

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