Calcium 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:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Calcium Binding Sites:

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 6pw0

Go back to Calcium Binding Sites List in 6pw0
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 6pw0

Go back to Calcium Binding Sites List in 6pw0
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

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: Sat Dec 12 07:26:22 2020

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