Zinc in PDB 5b1a: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.938, 204.400, 177.896, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.2

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 5b1a). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 5b1a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:26.1 occ:1.00 SG F:CYS62 2.3 25.8 1.0 SG F:CYS85 2.3 26.4 1.0 SG F:CYS82 2.4 24.4 1.0 SG F:CYS60 2.4 25.6 1.0 CB F:CYS82 3.1 26.0 1.0 CB F:CYS60 3.3 25.6 1.0 CB F:CYS85 3.4 25.4 1.0 CB F:CYS62 3.4 26.2 1.0 CA F:CYS62 3.6 27.8 1.0 N F:CYS85 3.7 26.1 1.0 CA F:CYS85 4.1 27.8 1.0 N F:CYS62 4.2 25.2 1.0 O F:CYS60 4.4 24.1 1.0 CB F:SER84 4.4 29.4 1.0 CA F:CYS60 4.5 25.6 1.0 C F:CYS60 4.5 24.3 1.0 OG1 F:THR87 4.5 30.8 0.5 O F:HOH223 4.6 39.4 1.0 OG1 F:THR87 4.6 30.2 0.5 CA F:CYS82 4.6 26.6 1.0 C F:SER84 4.7 27.8 1.0 OG F:SER84 4.8 33.4 1.0 C F:CYS85 4.9 27.1 1.0 C F:ILE61 4.9 28.8 1.0 N F:GLY86 4.9 25.6 1.0 C F:CYS62 4.9 28.0 1.0 CB F:ILE70 5.0 21.2 1.0 CG1 F:ILE70 5.0 22.3 1.0 CA F:SER84 5.0 28.0 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 1.5 Angstrom Resolution


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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:26.7 occ:1.00 SG S:CYS82 2.3 25.9 1.0 SG S:CYS62 2.3 27.0 1.0 SG S:CYS60 2.3 26.5 1.0 SG S:CYS85 2.4 26.9 1.0 CB S:CYS82 3.1 27.8 1.0 CB S:CYS60 3.3 24.3 1.0 CB S:CYS62 3.3 26.0 1.0 CB S:CYS85 3.4 26.1 1.0 CA S:CYS62 3.7 27.1 1.0 N S:CYS85 3.7 28.5 1.0 CA S:CYS85 4.1 28.6 1.0 N S:CYS62 4.3 25.8 1.0 CG2 S:THR87 4.3 22.7 0.5 CB S:SER84 4.4 30.0 1.0 O S:CYS60 4.4 23.3 1.0 C S:CYS60 4.5 24.4 1.0 CA S:CYS60 4.5 24.3 1.0 CG2 S:THR87 4.6 28.7 0.5 O S:HOH225 4.6 41.9 1.0 CA S:CYS82 4.6 26.9 1.0 C S:SER84 4.7 27.1 1.0 OG S:SER84 4.7 35.6 1.0 C S:CYS85 4.9 29.3 1.0 N S:SER84 4.9 29.3 1.0 C S:ILE61 4.9 27.8 1.0 CB S:ILE70 4.9 21.2 1.0 C S:CYS62 5.0 31.9 1.0 N S:GLY86 5.0 26.9 1.0 CA S:SER84 5.0 28.8 1.0 CG1 S:ILE70 5.0 24.4 1.0

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770