Calcium in PDB 6pw0: Cytochrome C Oxidase Delta 6 Mutant

All present enzymatic activity of Cytochrome C Oxidase Delta 6 Mutant:
1.9.3.1;

The structure of Cytochrome C Oxidase Delta 6 Mutant, PDB code: 6pw0 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)	42.84 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.905, 131.477, 176.601, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.8

The structure of Cytochrome C Oxidase Delta 6 Mutant 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 6 Mutant (pdb code 6pw0). 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 6 Mutant, PDB code: 6pw0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca619 b:35.5 occ:1.00 O A:GLY59 2.3 36.0 1.0 O A:ALA57 2.4 31.4 1.0 O A:GLU54 2.4 30.6 1.0 OE1 A:GLU54 2.4 33.3 1.0 OE1 A:GLN61 2.4 38.6 1.0 O A:HOH713 2.5 36.1 1.0 O A:HOH781 2.6 28.6 1.0 CD A:GLN61 3.5 34.8 1.0 C A:GLU54 3.5 33.6 1.0 C A:GLY59 3.5 35.7 1.0 CD A:GLU54 3.5 36.5 1.0 C A:ALA57 3.6 34.7 1.0 NE2 A:GLN61 3.9 32.3 1.0 CG A:GLU54 4.0 30.1 1.0 CA A:GLU54 4.0 29.6 1.0 CA A:VAL60 4.0 35.7 1.0 C A:PRO58 4.2 36.5 1.0 N A:GLN61 4.2 34.5 1.0 N A:VAL60 4.2 31.8 1.0 N A:ALA57 4.2 32.3 1.0 O A:PRO58 4.3 35.3 1.0 CA A:ALA57 4.4 37.8 1.0 N A:GLY59 4.4 38.2 1.0 O61 A:DMU605 4.5 42.6 0.8 N A:PRO58 4.5 35.8 1.0 C A:VAL60 4.6 35.5 1.0 CA A:PRO58 4.6 30.0 1.0 CA A:GLY59 4.6 29.0 1.0 OE2 A:GLU54 4.6 32.7 1.0 N A:LEU55 4.6 31.5 1.0 CB A:GLU54 4.6 30.1 1.0 CB A:ALA57 4.7 34.8 1.0 CG A:GLN61 4.8 35.1 1.0 O A:MET53 4.8 38.7 1.0 OD1 A:ASP485 4.8 31.1 1.0 CA A:LEU55 4.8 32.1 1.0 CB A:GLN61 4.9 38.6 1.0

Calcium binding site 2 out of 2 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca611 b:50.8 occ:1.00 O C:GLY59 2.3 46.5 1.0 O C:GLU54 2.3 49.6 1.0 O C:ALA57 2.4 44.9 1.0 OE1 C:GLU54 2.4 47.1 1.0 OE1 C:GLN61 2.5 56.6 1.0 O C:HOH739 2.5 52.1 1.0 O C:HOH750 2.6 45.2 1.0 C C:GLU54 3.4 48.7 1.0 C C:GLY59 3.5 42.6 1.0 CD C:GLN61 3.5 55.8 1.0 CD C:GLU54 3.5 52.7 1.0 C C:ALA57 3.6 48.6 1.0 NE2 C:GLN61 3.9 53.9 1.0 CA C:GLU54 4.0 43.5 1.0 CA C:VAL60 4.0 54.1 1.0 CG C:GLU54 4.1 49.3 1.0 C C:PRO58 4.2 50.5 1.0 N C:GLN61 4.2 57.2 1.0 O C:PRO58 4.2 51.2 1.0 N C:VAL60 4.2 45.6 1.0 N C:ALA57 4.2 48.2 1.0 CA C:ALA57 4.4 51.8 1.0 N C:GLY59 4.4 45.1 1.0 N C:LEU55 4.5 48.0 1.0 N C:PRO58 4.5 44.5 1.0 CA C:PRO58 4.6 46.7 1.0 C C:VAL60 4.6 58.5 1.0 CA C:GLY59 4.6 42.3 1.0 OE2 C:GLU54 4.6 45.9 1.0 CB C:GLU54 4.6 47.7 1.0 OD1 C:ASP485 4.7 42.8 1.0 O C:HOH702 4.7 56.6 1.0 CB C:ALA57 4.8 45.4 1.0 CG C:GLN61 4.8 58.0 1.0 CA C:LEU55 4.8 46.4 1.0 O C:MET53 4.8 49.0 1.0 CB C:GLN61 4.9 54.4 1.0 C C:LEU55 5.0 47.7 1.0 N C:MET56 5.0 49.5 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