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Magnesium in PDB 5b1b: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.606, 204.140, 177.653, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 5b1b:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution (pdb code 5b1b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5b1b

Go back to Magnesium Binding Sites List in 5b1b
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:19.5
occ:1.00
OD2 A:ASP369 2.0 20.1 1.0
OE1 B:GLU198 2.1 18.9 1.0
O B:HOH467 2.2 20.3 1.0
NE2 A:HIS368 2.2 17.4 1.0
O B:HOH432 2.2 21.1 1.0
O B:HOH540 2.2 19.4 1.0
CE1 A:HIS368 3.1 17.3 1.0
CD2 A:HIS368 3.2 19.2 1.0
CG A:ASP369 3.3 19.1 1.0
CD B:GLU198 3.3 22.6 1.0
O B:SER197 3.9 18.5 1.0
O A:HOH909 4.0 19.9 1.0
CB A:ASP369 4.0 18.6 1.0
OE2 B:GLU198 4.1 21.5 1.0
O A:HOH708 4.1 20.1 1.0
OD1 A:ASP369 4.2 21.0 1.0
O B:HOH464 4.2 20.2 0.9
O A:HOH780 4.3 19.8 1.0
CG A:HIS368 4.3 17.4 1.0
ND1 A:HIS368 4.3 17.7 1.0
OD2 B:ASP173 4.3 20.7 1.0
CG B:GLU198 4.3 19.6 1.0
OD1 B:ASP173 4.4 19.4 1.0
CB B:GLU198 4.5 19.4 1.0
O B:HOH412 4.5 20.4 0.7
O A:HOH806 4.5 19.4 1.0
OG1 A:THR294 4.5 20.4 1.0
CA B:GLU198 4.6 18.2 1.0
O A:HOH827 4.7 19.8 1.0
CG B:ASP173 4.8 19.1 1.0
C B:SER197 5.0 19.2 1.0

Magnesium binding site 2 out of 2 in 5b1b

Go back to Magnesium Binding Sites List in 5b1b
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:24.3
occ:1.00
OD2 N:ASP369 2.0 24.0 1.0
OE1 O:GLU198 2.1 23.6 1.0
NE2 N:HIS368 2.1 21.4 1.0
O O:HOH436 2.2 25.1 1.0
O O:HOH540 2.2 22.5 1.0
O O:HOH448 2.2 24.9 1.0
CD2 N:HIS368 3.1 22.5 1.0
CE1 N:HIS368 3.2 22.0 1.0
CG N:ASP369 3.2 24.5 1.0
CD O:GLU198 3.4 24.0 1.0
O O:SER197 3.9 23.5 1.0
CB N:ASP369 3.9 23.4 1.0
O N:HOH896 4.0 23.8 1.0
OE2 O:GLU198 4.1 25.5 1.0
O N:HOH704 4.1 23.3 1.0
OD1 N:ASP369 4.2 24.4 1.0
O O:HOH459 4.2 23.8 0.9
CG N:HIS368 4.3 21.2 1.0
O N:HOH791 4.3 21.8 1.0
ND1 N:HIS368 4.3 21.7 1.0
OD2 O:ASP173 4.3 23.1 1.0
CG O:GLU198 4.4 23.0 1.0
CB O:GLU198 4.4 22.2 1.0
OD1 O:ASP173 4.5 23.8 1.0
O N:HOH818 4.5 22.6 1.0
OG1 N:THR294 4.5 24.1 1.0
O O:HOH425 4.6 26.1 0.7
CA O:GLU198 4.6 23.6 1.0
O N:HOH865 4.6 22.3 1.0
CG O:ASP173 4.8 22.6 1.0
C O:SER197 5.0 24.3 1.0

Reference:

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770
Page generated: Mon Dec 14 20:01:55 2020

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