Calcium in PDB 6pw1: Cytochrome C Oxidase Delta 16

All present enzymatic activity of Cytochrome C Oxidase Delta 16:
1.9.3.1;

The structure of Cytochrome C Oxidase Delta 16, PDB code: 6pw1 was solved by J.Liu, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.96 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.315, 130.000, 177.539, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The structure of Cytochrome C Oxidase Delta 16 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Cadmium	(Cd)	4 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms

The binding sites of Calcium atom in the Cytochrome C Oxidase Delta 16 (pdb code 6pw1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cytochrome C Oxidase Delta 16, PDB code: 6pw1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca619 b:28.0 occ:1.00 O A:GLU54 2.3 26.1 1.0 OE1 A:GLU54 2.3 25.3 1.0 O A:GLY59 2.3 29.3 1.0 O A:ALA57 2.3 27.4 1.0 OE1 A:GLN61 2.5 29.8 1.0 O A:HOH727 2.6 24.8 1.0 O A:HOH785 2.6 25.6 1.0 C A:GLU54 3.4 28.4 1.0 CD A:GLU54 3.4 28.0 1.0 CD A:GLN61 3.5 34.2 1.0 C A:ALA57 3.6 26.9 1.0 C A:GLY59 3.6 28.4 1.0 NE2 A:GLN61 3.9 29.3 1.0 CA A:GLU54 4.0 26.8 1.0 CG A:GLU54 4.0 26.8 1.0 CA A:VAL60 4.1 29.1 1.0 N A:ALA57 4.2 27.7 1.0 N A:GLN61 4.2 32.5 1.0 C A:PRO58 4.2 31.3 1.0 N A:VAL60 4.3 26.8 1.0 O A:PRO58 4.3 29.8 1.0 O A:HOH701 4.3 48.2 1.0 CA A:ALA57 4.4 30.5 1.0 N A:GLY59 4.5 28.4 1.0 OE2 A:GLU54 4.5 28.2 1.0 N A:PRO58 4.5 28.2 1.0 N A:LEU55 4.5 26.3 1.0 CA A:PRO58 4.6 28.0 1.0 CB A:GLU54 4.6 26.2 1.0 CA A:GLY59 4.6 28.4 1.0 C A:VAL60 4.6 33.2 1.0 O A:MET53 4.7 29.4 1.0 CB A:ALA57 4.7 29.7 1.0 CA A:LEU55 4.8 27.4 1.0 CG A:GLN61 4.8 30.7 1.0 OD1 A:ASP485 4.9 29.3 1.0 CB A:GLN61 4.9 33.0 1.0 C A:LEU55 5.0 28.6 1.0 N A:MET56 5.0 28.1 1.0

Calcium binding site 2 out of 2 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca608 b:34.0 occ:1.00 O C:GLY59 2.3 37.0 1.0 OE1 C:GLU54 2.3 33.6 1.0 O C:ALA57 2.3 34.1 1.0 O C:GLU54 2.4 34.4 1.0 O C:HOH769 2.5 32.4 1.0 OE1 C:GLN61 2.6 37.5 1.0 O C:HOH734 2.7 35.4 1.0 CD C:GLU54 3.5 36.0 1.0 C C:GLU54 3.5 36.8 1.0 C C:GLY59 3.5 33.4 1.0 C C:ALA57 3.6 32.7 1.0 CD C:GLN61 3.6 43.2 1.0 CA C:GLU54 4.0 32.6 1.0 CA C:VAL60 4.0 34.5 1.0 CG C:GLU54 4.0 33.1 1.0 NE2 C:GLN61 4.0 34.8 1.0 N C:GLN61 4.1 39.8 1.0 N C:ALA57 4.2 32.1 1.0 N C:VAL60 4.2 34.6 1.0 C C:PRO58 4.3 39.1 1.0 CA C:ALA57 4.3 36.9 1.0 O C:PRO58 4.4 36.9 1.0 N C:GLY59 4.5 34.3 1.0 OE2 C:GLU54 4.5 34.4 1.0 C C:VAL60 4.5 40.4 1.0 N C:PRO58 4.5 32.9 1.0 N C:LEU55 4.6 34.1 1.0 CA C:GLY59 4.6 33.8 1.0 CA C:PRO58 4.6 35.5 1.0 CB C:GLU54 4.6 34.0 1.0 CB C:ALA57 4.7 32.9 1.0 O C:MET53 4.8 33.0 1.0 OD1 C:ASP485 4.8 32.5 1.0 CA C:LEU55 4.8 33.6 1.0 CG C:GLN61 4.9 38.4 1.0 O C:HOH799 4.9 40.2 1.0 C C:LEU55 5.0 36.3 1.0 CB C:GLN61 5.0 39.0 1.0 N C:MET56 5.0 34.4 1.0

J.Berg, J.Liu, E.Svahn, S.Ferguson-Miller, P.Brzezinski. Structural Changes at the Surface of Cytochrome C Oxidase Alter the Proton-Pumping Stoichiometry. Biochim Biophys Acta 48116 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 31733183
DOI: 10.1016/J.BBABIO.2019.148116