Zinc in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, 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 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.3

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:39.9 occ:1.00 SG F:CYS85 2.4 39.9 1.0 SG F:CYS60 2.4 38.8 1.0 SG F:CYS62 2.4 38.6 1.0 SG F:CYS82 2.4 36.7 1.0 CB F:CYS82 3.2 38.3 1.0 CB F:CYS60 3.3 37.5 1.0 CB F:CYS85 3.4 38.9 1.0 CB F:CYS62 3.4 39.1 1.0 CA F:CYS62 3.6 41.1 1.0 N F:CYS85 3.7 40.6 1.0 CA F:CYS85 4.1 39.9 1.0 N F:CYS62 4.1 39.2 1.0 O F:CYS60 4.4 35.4 1.0 C F:CYS60 4.4 36.4 1.0 O F:HOH220 4.5 53.9 1.0 CA F:CYS60 4.5 35.7 1.0 CB F:SER84 4.5 39.9 1.0 OG1 F:THR87 4.6 52.5 1.0 CA F:CYS82 4.6 38.6 1.0 OG F:SER84 4.7 42.7 1.0 C F:SER84 4.7 40.4 1.0 C F:CYS85 4.9 40.2 1.0 C F:ILE61 4.9 39.4 1.0 CB F:ILE70 4.9 32.9 1.0 N F:GLY86 5.0 40.0 1.0 CA F:SER84 5.0 40.0 1.0 CG1 F:ILE70 5.0 31.7 1.0 C F:CYS62 5.0 42.7 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:46.2 occ:1.00 SG S:CYS85 2.4 43.6 1.0 SG S:CYS60 2.4 43.5 1.0 SG S:CYS82 2.4 43.2 1.0 SG S:CYS62 2.4 45.0 1.0 CB S:CYS82 3.2 44.0 1.0 CB S:CYS60 3.3 44.3 1.0 CB S:CYS62 3.4 47.0 1.0 CB S:CYS85 3.4 44.6 1.0 CA S:CYS62 3.6 48.5 1.0 N S:CYS85 3.7 45.5 1.0 N S:CYS62 4.1 46.3 1.0 CA S:CYS85 4.1 45.2 1.0 CB S:SER84 4.4 46.4 1.0 O S:CYS60 4.4 43.4 1.0 C S:CYS60 4.4 43.7 1.0 CA S:CYS60 4.5 44.1 1.0 CG2 S:THR87 4.5 48.9 1.0 OG S:SER84 4.6 45.8 1.0 CA S:CYS82 4.7 45.1 1.0 C S:SER84 4.7 46.2 1.0 C S:ILE61 4.9 46.3 1.0 C S:CYS85 4.9 45.9 1.0 CA S:SER84 4.9 45.9 1.0 CB S:ILE70 4.9 40.4 1.0 CG1 S:ILE70 4.9 39.9 1.0 N S:GLY86 4.9 46.9 1.0 N S:SER84 4.9 47.1 1.0

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532