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Zinc in PDB 3f7l: X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

Enzymatic activity of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

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

Protein crystallography data

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l 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 / 0.99
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.493, 62.493, 163.191, 90.00, 90.00, 120.00
R / Rfree (%) 11.2 / 13.8

Other elements in 3f7l:

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase 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 Alvinella Pompejana Cu,Zn Superoxide Dismutase (pdb code 3f7l). 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 Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l:

Zinc binding site 1 out of 1 in 3f7l

Go back to Zinc Binding Sites List in 3f7l
Zinc binding site 1 out of 1 in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase


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 Alvinella Pompejana Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:7.5
occ:1.00
 OD1 A:ASP81 2.0 7.3 1.0
ND1 A:HIS61 2.0 7.2 1.0
ND1 A:HIS78 2.0 7.2 1.0
ND1 A:HIS69 2.0 7.1 1.0
CG A:ASP81 2.8 7.3 1.0
CE1 A:HIS69 2.9 7.2 1.0
OD2 A:ASP81 2.9 7.9 1.0
CE1 A:HIS78 2.9 7.8 1.0
CE1 A:HIS61 3.0 8.3 1.0
CG A:HIS61 3.0 8.0 1.0
CG A:HIS78 3.1 7.3 1.0
CG A:HIS69 3.1 7.1 1.0
CB A:HIS61 3.4 8.2 1.0
CB A:HIS78 3.6 7.7 1.0
CB A:HIS69 3.7 7.4 1.0
CA A:HIS69 3.9 7.5 1.0
O A:ILE134 4.0 9.1 1.0
NE2 A:HIS78 4.1 8.1 1.0
NE2 A:HIS69 4.1 7.5 1.0
NE2 A:HIS61 4.1 9.9 1.0
CD2 A:HIS78 4.1 8.4 1.0
CD2 A:HIS61 4.2 9.7 1.0
CB A:ASP81 4.2 8.0 1.0
CD2 A:HIS69 4.2 7.5 1.0
CA A:ASP81 4.7 8.1 1.0
N A:HIS78 4.8 7.8 1.0
CA A:HIS78 4.8 7.8 1.0
N A:GLY70 4.8 7.6 1.0
CD2 A:HIS44 4.8 8.6 1.0
N A:HIS69 4.9 7.7 1.0
C A:HIS69 4.9 7.6 1.0
C A:ILE134 4.9 8.2 1.0
CA A:HIS61 4.9 8.0 1.0
N A:ASP81 4.9 7.6 1.0
CA A:THR135 5.0 8.5 1.0
O A:HOH305 5.0 12.5 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: Thu Oct 24 13:05:15 2024

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