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

The binding sites of Cadmium atom in the Cytochrome C Oxidase Delta 16 (pdb code 6pw1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Cytochrome C Oxidase Delta 16, PDB code: 6pw1:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd307 b:40.5 occ:1.00 OE1 B:GLU280 2.4 46.1 1.0 NE2 B:HIS285 2.5 48.5 1.0 ND1 B:HIS283 2.5 44.5 1.0 OE2 B:GLU280 2.5 42.9 1.0 CD B:GLU280 2.8 43.1 1.0 CG B:HIS283 3.4 45.9 1.0 CE1 B:HIS285 3.4 46.1 1.0 CB B:HIS283 3.5 46.5 1.0 CD2 B:HIS285 3.5 50.1 1.0 CE1 B:HIS283 3.6 44.1 1.0 CG B:GLU280 4.3 38.8 1.0 ND1 B:HIS285 4.6 54.5 1.0 CD2 B:HIS283 4.6 46.0 1.0 NE2 B:HIS283 4.6 47.8 1.0 CG B:HIS285 4.7 53.1 1.0 O B:GLU280 4.8 38.8 1.0 O B:HIS283 4.8 50.3 1.0 CA B:HIS283 4.8 47.1 1.0 C4 B:HTH309 5.0 51.3 0.9

Cadmium binding site 2 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd308 b:57.1 occ:0.53 OE1 B:GLU101 2.5 47.1 1.0 OE2 B:GLU101 2.6 52.4 1.0 O B:HOH408 2.7 58.9 1.0 O B:HOH521 2.7 48.5 1.0 CD B:GLU101 2.9 51.6 1.0 ND1 B:HIS96 2.9 44.6 1.0 CB B:HIS96 3.5 46.2 1.0 CG B:HIS96 3.6 43.3 1.0 CA B:HIS96 4.0 43.2 1.0 CE1 B:HIS96 4.0 44.1 1.0 CG B:GLU101 4.3 46.0 1.0 N B:ASN97 4.4 45.0 1.0 O B:THR95 4.6 45.5 1.0 CG A:PRO315 4.8 42.1 1.0 C B:HIS96 4.8 45.8 1.0 CD2 B:HIS96 4.9 43.3 1.0 CB B:GLU101 5.0 42.9 1.0

Cadmium binding site 3 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd305 b:39.7 occ:1.00 OE2 D:GLU280 2.5 40.4 1.0 OE1 D:GLU280 2.5 41.3 1.0 NE2 D:HIS285 2.5 42.9 1.0 ND1 D:HIS283 2.5 44.2 1.0 CD D:GLU280 2.8 42.6 1.0 CG D:HIS283 3.4 48.0 1.0 CE1 D:HIS285 3.4 43.2 1.0 CD2 D:HIS285 3.5 46.3 1.0 CE1 D:HIS283 3.5 46.5 1.0 CB D:HIS283 3.5 45.9 1.0 CG D:GLU280 4.3 37.3 1.0 ND1 D:HIS285 4.6 43.7 1.0 CD2 D:HIS283 4.6 48.6 1.0 NE2 D:HIS283 4.6 49.4 1.0 CG D:HIS285 4.6 48.8 1.0 O D:GLU280 4.8 39.5 1.0 O D:HIS283 4.8 51.7 1.0 CA D:HIS283 4.9 49.0 1.0

Cadmium binding site 4 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd306 b:62.1 occ:0.66 OE2 D:GLU101 2.5 55.8 1.0 OE1 D:GLU101 2.5 61.7 1.0 O D:HOH515 2.6 54.0 1.0 O D:HOH513 2.7 64.7 1.0 CD2 D:HIS96 2.8 51.9 1.0 CD D:GLU101 2.8 59.8 1.0 CG D:HIS96 3.4 52.3 1.0 CB D:HIS96 3.4 53.1 1.0 CA D:HIS96 3.7 52.5 1.0 NE2 D:HIS96 4.0 57.5 1.0 N D:ASN97 4.3 58.3 1.0 O D:THR95 4.3 51.6 1.0 CG D:GLU101 4.3 59.6 1.0 C D:HIS96 4.6 56.2 1.0 ND1 D:HIS96 4.6 61.3 1.0 N D:HIS96 4.8 51.4 1.0 CE1 C:PHE311 4.9 47.5 1.0 CG C:PRO315 4.9 50.0 1.0 CE1 D:HIS96 4.9 57.2 1.0 CB D:GLU101 5.0 55.3 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