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Sodium 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
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Crystal Structure of An Alvinella Pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex, PDB code: 3f7k:

Sodium binding site 1 out of 1 in 3f7k

Go back to Sodium Binding Sites List in 3f7k
Sodium 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 Sodium with other atoms in the Na 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:Na204

b:14.2
occ:0.28
OD1 A:ASP90 1.4 22.6 1.0
O A:HOH392 2.2 25.2 0.7
CG A:ASP90 2.4 21.8 1.0
CA A:GLY88 3.0 14.0 1.0
N A:ASP90 3.2 16.5 1.0
OD2 A:ASP90 3.2 22.5 1.0
C A:GLY88 3.3 14.6 1.0
N A:GLY88 3.3 14.6 1.0
O A:LYS92 3.3 15.4 1.0
CB A:ASP90 3.4 20.8 1.0
N A:LYS92 3.4 13.8 1.0
CA A:ASP90 3.5 17.5 1.0
O A:GLY88 3.6 15.0 1.0
N A:GLY91 3.7 14.0 1.0
N A:GLU89 3.7 16.5 1.0
C A:ASP90 3.7 16.0 1.0
CA A:LYS92 4.0 13.9 1.0
O A:HOH371 4.0 23.7 1.0
CB A:LYS92 4.1 15.8 1.0
C A:LYS92 4.1 13.2 1.0
C A:GLU89 4.3 16.7 1.0
C A:GLY91 4.5 14.5 1.0
O A:ASP90 4.6 16.9 1.0
C A:ALA87 4.6 14.0 1.0
CA A:GLU89 4.6 17.5 1.0
CA A:GLY91 4.7 13.8 1.0
CG A:LYS92 4.7 15.8 1.0
O A:HOH328 5.0 19.0 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: Tue Dec 15 06:10:27 2020

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