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Zinc 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
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5b3s

Go back to Zinc Binding Sites List in 5b3s
Zinc 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 Zinc with other atoms in the Zn 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
F:Zn101

b:29.9
occ:1.00
 SG F:CYS62 2.3 30.3 1.0
SG F:CYS60 2.3 28.9 1.0
SG F:CYS82 2.4 28.3 1.0
SG F:CYS85 2.4 30.5 1.0
CB F:CYS82 3.2 27.2 1.0
CB F:CYS60 3.3 28.9 1.0
CB F:CYS62 3.3 31.5 1.0
CB F:CYS85 3.5 27.1 1.0
CA F:CYS62 3.6 29.5 1.0
N F:CYS85 3.7 30.5 1.0
N F:CYS62 4.2 30.1 1.0
CA F:CYS85 4.2 30.0 1.0
O F:CYS60 4.4 26.8 1.0
C F:CYS60 4.4 28.0 1.0
CA F:CYS60 4.4 25.6 1.0
O F:HOH239 4.5 48.5 1.0
CB F:SER84 4.6 29.5 1.0
CA F:CYS82 4.6 28.8 1.0
C F:SER84 4.7 31.1 1.0
OG F:SER84 4.7 34.9 1.0
CG2 F:THR87 4.8 31.6 1.0
C F:ILE61 4.9 29.9 1.0
C F:CYS85 4.9 32.3 1.0
CG1 F:ILE70 4.9 24.0 1.0
C F:CYS62 4.9 33.5 1.0
CB F:ILE70 5.0 22.3 1.0
N F:SER84 5.0 29.1 1.0
N F:GLY86 5.0 28.5 1.0
CA F:SER84 5.0 28.2 1.0

Zinc binding site 2 out of 2 in 5b3s

Go back to Zinc Binding Sites List in 5b3s
Zinc 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 Zinc with other atoms in the Zn 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
S:Zn101

b:29.4
occ:1.00
 SG S:CYS60 2.3 26.6 1.0
SG S:CYS62 2.3 29.6 1.0
SG S:CYS85 2.3 29.2 1.0
SG S:CYS82 2.4 28.2 1.0
CB S:CYS82 3.2 27.4 1.0
CB S:CYS60 3.3 28.9 1.0
CB S:CYS62 3.3 28.1 1.0
CB S:CYS85 3.5 26.6 1.0
CA S:CYS62 3.6 28.3 1.0
N S:CYS85 3.8 30.1 1.0
N S:CYS62 4.2 28.6 1.0
CA S:CYS85 4.2 33.1 1.0
C S:CYS60 4.4 26.0 1.0
O S:CYS60 4.4 24.7 1.0
CA S:CYS60 4.4 27.2 1.0
O S:HOH235 4.5 43.4 1.0
CB S:SER84 4.5 33.5 1.0
CA S:CYS82 4.6 28.6 1.0
OG1 S:THR87 4.7 48.8 1.0
C S:SER84 4.7 29.9 1.0
OG S:SER84 4.8 36.5 1.0
CG2 S:THR87 4.8 35.2 1.0
C S:ILE61 4.9 28.8 1.0
C S:CYS85 4.9 30.9 1.0
C S:CYS62 5.0 32.3 1.0
N S:SER84 5.0 31.3 1.0
CB S:ILE70 5.0 21.2 1.0
CA S:SER84 5.0 30.9 1.0
N S:GLY86 5.0 28.9 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: Thu Aug 21 00:54:30 2025

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