Zinc in PDB 8h8s: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State:
7.1.1.9;

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State, PDB code: 8h8s was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.1, 204.7, 177.9, 90, 90, 90
R / Rfree (%)	12.4 / 15.7

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Iron	(Fe)	4 atoms
Magnesium	(Mg)	2 atoms
Copper	(Cu)	6 atoms

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State (pdb code 8h8s). 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 Calcium-Bound Fully Reduced State, PDB code: 8h8s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State


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 Calcium-Bound Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:37.9 occ:1.00 SG F:CYS62 2.3 37.1 1.0 SG F:CYS85 2.3 39.0 1.0 SG F:CYS60 2.3 37.3 1.0 SG F:CYS82 2.3 37.6 1.0 CB F:CYS82 3.2 39.9 1.0 CB F:CYS60 3.3 37.9 1.0 CB F:CYS62 3.3 38.8 1.0 CB F:CYS85 3.4 37.7 1.0 CA F:CYS62 3.6 40.5 1.0 N F:CYS85 3.7 39.5 1.0 CA F:CYS85 4.1 37.3 1.0 N F:CYS62 4.2 36.4 1.0 O F:CYS60 4.4 34.4 1.0 CA F:CYS60 4.4 36.1 1.0 C F:CYS60 4.4 36.1 1.0 OG1 F:THR87 4.5 46.7 0.5 O F:HOH206 4.5 57.5 1.0 CB F:SER84 4.6 38.8 1.0 CA F:CYS82 4.6 35.9 1.0 C F:SER84 4.7 37.1 1.0 CB F:THR87 4.8 38.8 0.5 OG F:SER84 4.8 45.1 1.0 C F:CYS85 4.9 40.3 1.0 C F:ILE61 4.9 37.2 1.0 CG1 F:ILE70 5.0 38.1 1.0 C F:CYS62 5.0 37.8 1.0 N F:GLY86 5.0 39.5 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State


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 Calcium-Bound Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:39.4 occ:1.00 SG S:CYS62 2.3 39.1 1.0 SG S:CYS85 2.3 39.7 1.0 SG S:CYS82 2.4 38.9 1.0 SG S:CYS60 2.4 37.3 1.0 CB S:CYS82 3.1 37.9 1.0 CB S:CYS60 3.2 40.1 1.0 CB S:CYS62 3.4 41.3 1.0 CB S:CYS85 3.4 41.5 1.0 CA S:CYS62 3.7 42.0 1.0 N S:CYS85 3.8 39.0 1.0 CA S:CYS85 4.2 40.6 1.0 N S:CYS62 4.2 38.0 1.0 CG2 S:THR87 4.4 42.9 0.5 CA S:CYS60 4.4 37.4 1.0 C S:CYS60 4.4 34.9 1.0 O S:CYS60 4.5 34.8 1.0 CB S:SER84 4.5 43.2 1.0 O S:HOH211 4.5 60.0 1.0 CA S:CYS82 4.6 39.5 1.0 OG S:SER84 4.7 44.9 1.0 OG1 S:THR87 4.7 39.5 0.5 C S:SER84 4.7 37.4 1.0 CB S:THR87 4.8 38.6 0.5 C S:CYS85 4.9 40.2 1.0 CG1 S:ILE70 4.9 37.2 1.0 C S:ILE61 4.9 36.6 1.0 N S:GLY86 5.0 41.3 1.0 CB S:ILE70 5.0 35.1 1.0 CA S:SER84 5.0 39.0 1.0 N S:SER84 5.0 40.1 1.0 C S:CYS62 5.0 40.0 1.0

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956