Magnesium in PDB 5xdq: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 134.45 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.307, 205.904, 177.526, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 5xdq:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution (pdb code 5xdq). 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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5xdq

Go back to Magnesium Binding Sites List in 5xdq
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:30.8
occ:1.00
NE2 A:HIS368 2.0 23.6 1.0
OE1 B:GLU198 2.2 28.2 1.0
OD2 A:ASP369 2.2 27.0 1.0
O B:HOH427 2.4 29.4 1.0
O B:HOH402 2.4 31.6 1.0
O B:HOH553 2.4 27.1 1.0
CD2 A:HIS368 3.0 25.8 1.0
CE1 A:HIS368 3.0 24.5 1.0
CD B:GLU198 3.1 26.7 1.0
CG A:ASP369 3.3 26.2 1.0
OE2 B:GLU198 3.4 26.5 1.0
O B:SER197 3.9 25.7 1.0
O A:HOH888 4.0 28.6 1.0
CB A:ASP369 4.0 27.3 1.0
ND1 A:HIS368 4.1 24.1 1.0
CG A:HIS368 4.2 25.8 1.0
OD1 B:ASP173 4.3 29.7 1.0
OD2 B:ASP173 4.3 27.8 1.0
O A:HOH820 4.3 27.3 1.0
OD1 A:ASP369 4.3 26.7 1.0
OG1 A:THR294 4.3 28.6 1.0
O B:HOH469 4.4 32.8 0.2
CG B:GLU198 4.5 25.8 1.0
O A:HOH874 4.5 27.6 1.0
O B:HOH535 4.5 31.4 0.7
O A:HOH727 4.5 28.2 1.0
O A:HOH798 4.6 28.1 1.0
CG B:ASP173 4.7 29.5 1.0
CB B:GLU198 4.7 25.4 1.0
CA A:ASP369 5.0 26.5 1.0

Magnesium binding site 2 out of 2 in 5xdq

Go back to Magnesium Binding Sites List in 5xdq
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:39.9
occ:1.00
NE2 N:HIS368 2.0 30.1 1.0
OE1 O:GLU198 2.2 37.5 1.0
OD2 N:ASP369 2.2 33.7 1.0
O O:HOH401 2.4 38.8 1.0
O O:HOH456 2.4 37.8 1.0
O O:HOH535 2.4 35.1 1.0
CD2 N:HIS368 2.9 30.6 1.0
CE1 N:HIS368 3.0 30.8 1.0
CD O:GLU198 3.1 35.2 1.0
CG N:ASP369 3.3 34.3 1.0
OE2 O:GLU198 3.4 34.8 1.0
O O:SER197 3.9 34.1 1.0
O N:HOH866 3.9 33.7 1.0
CB N:ASP369 4.0 33.8 1.0
ND1 N:HIS368 4.1 31.4 1.0
CG N:HIS368 4.1 31.2 1.0
OD1 N:ASP369 4.3 33.4 1.0
OD2 O:ASP173 4.3 35.2 1.0
O N:HOH755 4.3 32.3 1.0
OG1 N:THR294 4.3 34.0 1.0
OD1 O:ASP173 4.4 33.6 1.0
CG O:GLU198 4.4 33.0 1.0
O N:HOH707 4.5 35.1 1.0
O N:HOH872 4.5 32.3 1.0
O O:HOH514 4.6 48.9 1.0
O N:HOH861 4.6 33.6 1.0
CB O:GLU198 4.7 32.9 1.0
CG O:ASP173 4.7 34.8 1.0
CA N:ASP369 5.0 32.3 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase Crystallized at A Neutral pH Using A Fluorinated Detergent. Acta Crystallogr F Struct V. 73 416 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695851
DOI: 10.1107/S2053230X17008834
Page generated: Mon Dec 14 21:27:37 2020

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