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

The binding sites of Cadmium atom in the Cytochrome C Oxidase Delta 6 Mutant (pdb code 6pw0). 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 6 Mutant, PDB code: 6pw0:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd309 b:49.5 occ:1.00 OE1 B:GLU280 2.5 45.2 1.0 OE2 B:GLU280 2.5 49.7 1.0 NE2 B:HIS285 2.5 55.5 1.0 ND1 B:HIS283 2.6 47.0 1.0 CD B:GLU280 2.8 51.0 1.0 CD2 B:HIS285 3.4 59.5 1.0 CG B:HIS283 3.5 52.9 1.0 CE1 B:HIS285 3.5 57.0 1.0 CB B:HIS283 3.6 45.0 1.0 CE1 B:HIS283 3.6 55.7 1.0 CG B:GLU280 4.4 43.8 1.0 CG B:HIS285 4.6 58.7 1.0 ND1 B:HIS285 4.6 60.1 1.0 CD2 B:HIS283 4.6 60.6 1.0 NE2 B:HIS283 4.7 61.2 1.0 O B:GLU280 4.8 47.4 1.0 C4 B:HTH306 4.8 60.6 1.0 CA B:HIS283 5.0 60.2 1.0

Cadmium binding site 2 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd310 b:69.9 occ:0.64 OE1 B:GLU101 2.5 57.4 1.0 O B:HOH489 2.6 70.0 1.0 OE2 B:GLU101 2.6 82.5 1.0 O B:HOH523 2.7 62.0 1.0 CD B:GLU101 2.9 71.3 1.0 ND1 B:HIS96 2.9 54.6 1.0 CB B:HIS96 3.7 48.8 1.0 CG B:HIS96 3.7 57.4 1.0 CE1 B:HIS96 4.0 65.5 1.0 CA B:HIS96 4.0 54.4 1.0 CG B:GLU101 4.4 54.9 1.0 N B:ASN97 4.4 59.0 1.0 OG B:SER98 4.6 80.8 1.0 O B:THR95 4.6 56.9 1.0 CG A:PRO315 4.8 55.8 1.0 C B:HIS96 4.8 55.7 1.0 CD2 B:HIS96 4.9 50.9 1.0

Cadmium binding site 3 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd307 b:49.8 occ:1.00 OE1 D:GLU280 2.4 37.3 1.0 OE2 D:GLU280 2.6 46.8 1.0 NE2 D:HIS285 2.6 57.9 1.0 ND1 D:HIS283 2.6 51.3 1.0 CD D:GLU280 2.8 51.6 1.0 CG D:HIS283 3.5 58.6 1.0 CD2 D:HIS285 3.5 60.5 1.0 CE1 D:HIS285 3.6 51.5 1.0 CE1 D:HIS283 3.6 67.8 1.0 CB D:HIS283 3.6 51.0 1.0 CG D:GLU280 4.4 46.6 1.0 CD2 D:HIS283 4.6 67.9 1.0 CG D:HIS285 4.7 63.9 1.0 NE2 D:HIS283 4.7 65.2 1.0 ND1 D:HIS285 4.7 61.6 1.0 O D:GLU280 4.9 50.8 1.0 CA D:HIS283 4.9 60.7 1.0 O D:HIS283 5.0 64.1 1.0

Cadmium binding site 4 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd308 b:84.5 occ:0.65 OE1 D:GLU101 2.6 93.5 1.0 OE2 D:GLU101 2.7 84.6 1.0 O D:HOH448 2.8 95.9 1.0 CD D:GLU101 2.8 86.5 1.0 O D:HOH491 2.9 78.6 1.0 CD2 D:HIS96 2.9 76.8 1.0 CG D:HIS96 3.6 76.7 1.0 CB D:HIS96 3.8 74.7 1.0 NE2 D:HIS96 3.9 85.6 1.0 CA D:HIS96 4.1 69.8 1.0 CG D:GLU101 4.1 78.0 1.0 O D:THR95 4.5 72.2 1.0 N D:ASN97 4.6 84.2 1.0 ND1 D:HIS96 4.7 75.7 1.0 CG C:PRO315 4.7 69.6 1.0 CE1 D:HIS96 4.8 84.6 1.0 CB D:GLU101 4.9 73.4 1.0 C D:HIS96 4.9 77.1 1.0 CA C:GLY312 5.0 57.6 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