Calcium in PDB 8h8r: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

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

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r 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 (°)	182.8, 205.7, 177.9, 90, 90, 90
R / Rfree (%)	12.2 / 15.3

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

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

The binding sites of Calcium atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State (pdb code 8h8r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:33.7 occ:1.00 O A:GLN43 2.3 32.9 1.0 OE1 A:GLU40 2.3 35.8 1.0 O A:GLY45 2.3 37.6 1.0 O A:GLU40 2.3 32.9 1.0 O A:HOH775 2.5 33.8 1.0 O A:HOH819 2.5 41.8 1.0 O A:HOH796 2.5 40.7 1.0 C A:GLU40 3.5 32.4 1.0 CD A:GLU40 3.5 37.4 1.0 C A:GLN43 3.5 35.8 1.0 C A:GLY45 3.5 34.1 1.0 CA A:GLU40 4.0 30.5 1.0 N A:LEU47 4.0 45.1 1.0 CG A:GLU40 4.1 36.0 1.0 N A:GLY45 4.1 35.1 1.0 C A:PRO44 4.1 34.3 1.0 N A:GLN43 4.3 33.0 1.0 CB A:LEU47 4.3 48.5 1.0 N A:THR46 4.3 34.5 1.0 CA A:GLN43 4.4 34.3 1.0 CA A:THR46 4.4 41.1 1.0 O A:PRO44 4.4 34.0 1.0 CA A:GLY45 4.4 35.9 1.0 N A:PRO44 4.4 35.0 1.0 C A:THR46 4.4 41.7 1.0 CA A:PRO44 4.4 33.8 1.0 O A:SER441 4.5 32.8 1.0 OE2 A:GLU40 4.5 40.6 1.0 N A:LEU41 4.5 30.5 1.0 CB A:GLU40 4.7 32.4 1.0 CB A:GLN43 4.7 41.4 1.0 O A:ALA39 4.8 33.6 1.0 CA A:LEU41 4.8 31.2 1.0 OD1 A:ASP442 4.8 35.4 1.0 CA A:LEU47 4.8 47.2 1.0 C A:LEU41 5.0 31.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca607 b:45.6 occ:1.00 O N:GLU40 2.3 43.4 1.0 O N:GLN43 2.3 45.7 1.0 O N:GLY45 2.3 52.1 1.0 OE1 N:GLU40 2.3 47.1 1.0 O N:HOH2894 2.4 44.5 1.0 O N:HOH2947 2.4 57.9 1.0 O N:HOH2915 2.5 48.5 1.0 C N:GLU40 3.4 41.2 1.0 C N:GLY45 3.5 46.1 1.0 CD N:GLU40 3.5 48.1 1.0 C N:GLN43 3.5 43.8 1.0 CA N:GLU40 4.0 42.5 1.0 N N:LEU47 4.0 58.3 1.0 C N:PRO44 4.1 47.0 1.0 CG N:GLU40 4.1 48.4 1.0 N N:GLY45 4.2 44.0 1.0 N N:THR46 4.3 44.5 1.0 N N:GLN43 4.3 41.4 1.0 O N:PRO44 4.3 48.3 1.0 CA N:THR46 4.4 54.0 1.0 CB N:LEU47 4.4 60.1 1.0 CA N:GLY45 4.4 50.4 1.0 N N:PRO44 4.4 48.2 1.0 CA N:PRO44 4.5 48.2 1.0 C N:THR46 4.5 54.4 1.0 CA N:GLN43 4.5 44.5 1.0 O N:SER441 4.5 42.8 1.0 N N:LEU41 4.5 40.0 1.0 OE2 N:GLU40 4.6 48.2 1.0 O N:ALA39 4.7 43.1 1.0 CB N:GLU40 4.7 44.0 1.0 CG N:GLN43 4.8 72.8 1.0 OD1 N:ASP442 4.8 46.5 1.0 CA N:LEU41 4.8 41.0 1.0 CA N:LEU47 4.9 63.3 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