Magnesium 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:

Cadmium	(Cd)	4 atoms
Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms
Copper	(Cu)	6 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg618 b:15.9 occ:1.00 OD2 A:ASP412 1.7 37.5 1.0 O B:HOH431 2.0 27.8 1.0 OE1 B:GLU254 2.0 29.5 1.0 O A:HOH772 2.0 26.1 1.0 O A:HOH721 2.0 26.5 1.0 NE2 A:HIS411 2.2 24.5 1.0 CG A:ASP412 3.0 29.2 1.0 CE1 A:HIS411 3.1 25.1 1.0 CD B:GLU254 3.2 29.2 1.0 CD2 A:HIS411 3.2 26.0 1.0 OD1 A:ASP412 3.7 35.5 1.0 OE2 B:GLU254 3.7 29.0 1.0 O B:SER253 3.9 26.1 1.0 O A:HOH707 3.9 27.4 1.0 CB A:ASP412 4.1 24.8 1.0 OD2 B:ASP229 4.1 30.9 1.0 O A:HOH734 4.2 28.2 1.0 ND1 A:HIS411 4.2 25.1 1.0 CG A:HIS411 4.3 25.6 1.0 OD1 B:ASP229 4.3 29.3 1.0 CG B:GLU254 4.3 25.5 1.0 O A:HOH783 4.4 28.2 1.0 O A:HOH704 4.5 27.3 1.0 OG1 A:THR337 4.6 28.7 1.0 CB B:GLU254 4.6 27.7 1.0 O B:HOH455 4.6 34.7 1.0 O A:HOH821 4.6 27.0 1.0 CG B:ASP229 4.6 30.9 1.0 CA B:GLU254 4.8 28.4 1.0 CE2 A:TYR175 4.9 28.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg607 b:19.1 occ:1.00 OD2 C:ASP412 1.8 40.6 1.0 O D:HOH428 2.0 31.3 1.0 OE1 D:GLU254 2.0 33.4 1.0 O D:HOH473 2.1 29.4 1.0 O C:HOH716 2.1 27.1 1.0 NE2 C:HIS411 2.1 27.3 1.0 CG C:ASP412 2.9 35.2 1.0 CE1 C:HIS411 3.0 28.0 1.0 CD D:GLU254 3.2 33.8 1.0 CD2 C:HIS411 3.2 27.3 1.0 OD1 C:ASP412 3.5 38.6 1.0 OE2 D:GLU254 3.7 34.5 1.0 O C:HOH706 3.9 30.6 1.0 O D:SER253 4.0 29.5 1.0 OD2 D:ASP229 4.1 36.3 1.0 O C:HOH722 4.2 35.6 1.0 ND1 C:HIS411 4.2 28.9 1.0 CB C:ASP412 4.2 27.4 1.0 OD1 D:ASP229 4.3 30.5 1.0 CG C:HIS411 4.3 27.6 1.0 CG D:GLU254 4.3 30.6 1.0 O D:HOH417 4.4 35.6 1.0 O D:HOH402 4.5 42.7 1.0 O C:HOH749 4.5 31.3 1.0 OG1 C:THR337 4.5 28.7 1.0 CB D:GLU254 4.6 28.5 1.0 O C:HOH704 4.6 31.1 1.0 CG D:ASP229 4.6 34.8 1.0 O C:HOH775 4.6 30.6 1.0 CE2 C:TYR175 4.8 31.5 1.0 CA D:GLU254 4.8 32.0 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