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

Enzymatic activity of Cytochrome C Oxidase Delta 6 Mutant

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

Protein crystallography data

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

Other elements in 6pw0:

The structure of Cytochrome C Oxidase Delta 6 Mutant also contains other interesting chemical elements:

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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6pw0

Go back to Magnesium Binding Sites List in 6pw0
Magnesium binding site 1 out of 2 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg618

b:19.2
occ:1.00
O A:HOH714 1.7 34.1 1.0
OD2 A:ASP412 1.9 51.6 1.0
OE1 B:GLU254 1.9 39.0 1.0
O B:HOH468 2.0 40.3 1.0
NE2 A:HIS411 2.2 29.3 1.0
O A:HOH716 2.2 31.5 1.0
CE1 A:HIS411 3.0 33.2 1.0
CG A:ASP412 3.0 42.4 1.0
CD B:GLU254 3.1 44.5 1.0
CD2 A:HIS411 3.2 33.0 1.0
OD1 A:ASP412 3.6 36.9 1.0
OE2 B:GLU254 3.7 41.7 1.0
O B:SER253 3.9 37.1 1.0
O A:HOH794 4.0 37.9 1.0
OD1 B:ASP229 4.1 48.2 1.0
ND1 A:HIS411 4.2 27.0 1.0
CB A:ASP412 4.3 32.4 1.0
O A:HOH717 4.3 38.1 1.0
CG B:GLU254 4.3 32.3 1.0
CG A:HIS411 4.3 34.4 1.0
OD2 B:ASP229 4.4 36.2 1.0
O B:HOH462 4.4 40.5 1.0
O A:HOH782 4.5 35.1 1.0
CB B:GLU254 4.6 29.1 1.0
O A:HOH807 4.6 32.2 1.0
OG1 A:THR337 4.7 37.3 1.0
CG B:ASP229 4.7 37.4 1.0
O A:HOH712 4.7 33.8 1.0
CA B:GLU254 4.8 33.0 1.0
CE2 A:TYR175 4.9 34.9 1.0

Magnesium binding site 2 out of 2 in 6pw0

Go back to Magnesium Binding Sites List in 6pw0
Magnesium binding site 2 out of 2 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg610

b:24.0
occ:1.00
O C:HOH708 1.8 40.2 1.0
OD2 C:ASP412 1.8 51.6 1.0
OE1 D:GLU254 1.9 49.4 1.0
O D:HOH446 2.0 44.8 1.0
NE2 C:HIS411 2.2 38.5 1.0
O D:HOH423 2.5 40.9 1.0
CE1 C:HIS411 2.9 35.7 1.0
CG C:ASP412 2.9 52.4 1.0
CD D:GLU254 3.1 50.1 1.0
CD2 C:HIS411 3.3 39.6 1.0
OD1 C:ASP412 3.5 53.0 1.0
OE2 D:GLU254 3.7 50.0 1.0
O C:HOH760 3.9 43.1 1.0
O D:SER253 4.0 43.5 1.0
ND1 C:HIS411 4.0 37.5 1.0
CB C:ASP412 4.2 37.1 1.0
O C:HOH715 4.2 41.6 1.0
CG D:GLU254 4.3 43.5 1.0
CG C:HIS411 4.3 40.5 1.0
OD1 D:ASP229 4.4 52.1 1.0
O C:HOH762 4.4 44.5 1.0
OD2 D:ASP229 4.4 46.5 1.0
O D:HOH462 4.5 48.6 1.0
O C:HOH716 4.6 42.8 1.0
CB D:GLU254 4.6 38.5 1.0
O C:HOH754 4.7 37.3 1.0
OG1 C:THR337 4.7 40.5 1.0
CA D:GLU254 4.8 39.4 1.0
CG D:ASP229 4.8 46.4 1.0
CE2 C:TYR175 4.8 46.6 1.0

Reference:

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
Page generated: Mon Dec 14 23:51:00 2020

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