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Sodium in PDB 7vuw: Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.92 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.076, 204.481, 177.68, 90, 90, 90
R / Rfree (%) 15.4 / 17.5

Other elements in 7vuw:

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K also contains other interesting chemical elements:

Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K (pdb code 7vuw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K, PDB code: 7vuw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7vuw

Go back to Sodium Binding Sites List in 7vuw
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:23.2
occ:1.00
O A:HOH869 2.2 23.3 1.0
O A:GLY45 2.3 27.3 1.0
OE1 A:GLU40 2.3 25.2 1.0
O A:SER441 2.4 23.5 1.0
O A:GLU40 2.4 22.4 1.0
CD A:GLU40 3.2 25.9 1.0
O A:HOH730 3.4 32.9 1.0
C A:GLU40 3.4 23.2 1.0
CG A:GLU40 3.5 22.4 1.0
C A:GLY45 3.5 27.1 1.0
C A:SER441 3.6 24.7 1.0
O A:GLN43 4.0 24.9 1.0
CA A:ASP442 4.0 22.3 1.0
CB A:ASP442 4.0 22.3 1.0
CA A:THR46 4.1 25.7 1.0
OD2 A:ASP442 4.2 26.9 1.0
CG A:ASP442 4.2 24.6 1.0
N A:THR46 4.2 27.1 1.0
CA A:GLU40 4.2 23.5 1.0
N A:ASP442 4.2 21.7 1.0
N A:LEU41 4.3 23.1 1.0
N A:LEU47 4.4 26.5 1.0
CA A:LEU41 4.4 22.4 1.0
OE2 A:GLU40 4.4 27.1 1.0
N A:GLY45 4.4 25.2 1.0
CB A:GLU40 4.5 21.2 1.0
CA A:GLY45 4.6 27.4 1.0
CD2 A:LEU41 4.7 23.5 1.0
C A:THR46 4.7 28.2 1.0
CA A:SER441 4.7 23.5 1.0
OD1 A:ASP442 4.9 25.2 1.0
CB A:SER441 5.0 21.6 1.0

Sodium binding site 2 out of 2 in 7vuw

Go back to Sodium Binding Sites List in 7vuw
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Cyanide-Bound Fully Oxidized State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:29.4
occ:1.00
O N:HOH873 2.2 28.7 1.0
O N:SER441 2.3 28.1 1.0
O N:GLY45 2.3 31.9 1.0
OE1 N:GLU40 2.3 31.6 1.0
O N:GLU40 2.4 33.0 1.0
CD N:GLU40 3.3 37.5 1.0
C N:GLU40 3.4 32.0 1.0
O N:HOH768 3.5 38.6 1.0
C N:GLY45 3.5 34.4 1.0
C N:SER441 3.5 29.9 1.0
CG N:GLU40 3.5 31.7 1.0
CA N:ASP442 4.0 28.4 1.0
O N:GLN43 4.0 32.0 1.0
CB N:ASP442 4.0 30.7 1.0
OD2 N:ASP442 4.1 32.1 1.0
CA N:THR46 4.1 32.7 1.0
CG N:ASP442 4.2 31.5 1.0
N N:ASP442 4.2 30.3 1.0
N N:THR46 4.2 35.4 1.0
N N:LEU41 4.2 29.2 1.0
CA N:GLU40 4.2 27.9 1.0
CA N:LEU41 4.3 31.9 1.0
CB N:GLU40 4.4 27.9 1.0
OE2 N:GLU40 4.4 32.6 1.0
N N:LEU47 4.5 36.2 1.0
N N:GLY45 4.5 31.2 1.0
CD2 N:LEU41 4.5 28.6 1.0
CA N:GLY45 4.6 33.4 1.0
CA N:SER441 4.6 28.1 1.0
C N:THR46 4.7 36.6 1.0
OD1 N:ASP442 4.9 32.9 1.0
CB N:SER441 5.0 31.7 1.0

Reference:

A.Shimada, T.Tsukihara. Bovine Cytochrome C Oxidese in Cn-Bound Fully Oxidized State at 50 K To Be Published.
Page generated: Fri Apr 7 16:52:46 2023

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