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Sodium in PDB 5b3s: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s was solved by J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.491, 203.303, 177.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.4

Other elements in 5b3s:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) (pdb code 5b3s). 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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5b3s

Go back to Sodium Binding Sites List in 5b3s
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:26.9
occ:1.00
 O A:SER441 2.3 26.7 1.0
OE1 A:GLU40 2.3 26.9 1.0
O A:GLY45 2.3 29.6 1.0
O A:HOH836 2.3 28.5 1.0
O A:GLU40 2.3 26.5 1.0
CD A:GLU40 3.2 28.6 1.0
C A:GLU40 3.4 24.2 1.0
O A:HOH762 3.4 36.6 1.0
CG A:GLU40 3.5 27.1 1.0
C A:SER441 3.5 25.9 1.0
C A:GLY45 3.5 28.5 1.0
CB A:ASP442 3.9 24.4 1.0
CA A:ASP442 4.0 26.8 1.0
O A:GLN43 4.0 28.8 1.0
CA A:THR46 4.0 27.5 1.0
OD1 A:ASP442 4.2 28.8 1.0
CG A:ASP442 4.2 28.2 1.0
CA A:GLU40 4.2 25.1 1.0
N A:ASP442 4.2 26.1 1.0
N A:THR46 4.2 31.3 1.0
N A:LEU41 4.3 24.9 1.0
N A:LEU47 4.3 29.4 1.0
CA A:LEU41 4.4 25.4 1.0
OE2 A:GLU40 4.4 30.8 1.0
CB A:GLU40 4.4 26.1 1.0
N A:GLY45 4.4 29.4 1.0
C A:THR46 4.6 30.1 1.0
CA A:GLY45 4.6 29.6 1.0
CA A:SER441 4.7 26.1 1.0
CD2 A:LEU41 4.7 26.6 1.0
OD2 A:ASP442 4.9 29.3 1.0
CB A:SER441 5.0 26.6 1.0

Sodium binding site 2 out of 2 in 5b3s

Go back to Sodium Binding Sites List in 5b3s
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:31.7
occ:1.00
 O N:SER441 2.3 30.4 1.0
OE1 N:GLU40 2.3 32.1 1.0
O N:GLY45 2.3 32.8 1.0
O N:GLU40 2.3 29.8 1.0
O N:HOH870 2.3 30.4 1.0
CD N:GLU40 3.2 35.3 1.0
C N:GLU40 3.3 28.2 1.0
O N:HOH804 3.4 37.6 1.0
C N:SER441 3.5 29.0 1.0
CG N:GLU40 3.5 30.7 1.0
C N:GLY45 3.5 36.3 1.0
CA N:ASP442 4.0 28.3 1.0
O N:GLN43 4.0 34.1 1.0
CA N:THR46 4.1 35.3 1.0
CB N:ASP442 4.1 30.8 1.0
OD1 N:ASP442 4.2 32.1 1.0
CG N:ASP442 4.2 33.0 1.0
CA N:GLU40 4.2 30.1 1.0
N N:ASP442 4.2 29.7 1.0
N N:LEU41 4.2 30.7 1.0
N N:THR46 4.3 33.5 1.0
CA N:LEU41 4.4 32.0 1.0
N N:LEU47 4.4 39.2 1.0
OE2 N:GLU40 4.4 33.8 1.0
CB N:GLU40 4.4 29.4 1.0
N N:GLY45 4.5 34.0 1.0
CA N:SER441 4.6 28.5 1.0
CA N:GLY45 4.6 32.7 1.0
C N:THR46 4.7 37.5 1.0
CD2 N:LEU41 4.7 29.9 1.0
OD2 N:ASP442 4.9 32.9 1.0
CB N:SER441 4.9 31.7 1.0

Reference:

A.Shimada, J.Baba, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara. Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed-Valence State at 1.68 Angstrom Resolution (50 K) To Be Published.
Page generated: Sun Aug 17 23:02:57 2025

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