Magnesium in PDB 6juw: Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw was solved by A.Shimada, K.Muramoto, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.217, 204.650, 177.397, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.8

Other elements in 6juw:

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution (pdb code 6juw). 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 Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6juw

Go back to Magnesium Binding Sites List in 6juw
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:29.2
occ:1.00
OE1 B:GLU198 2.1 35.2 1.0
OD2 A:ASP369 2.1 30.0 1.0
O B:HOH471 2.1 27.5 1.0
O B:HOH422 2.1 27.3 1.0
NE2 A:HIS368 2.2 27.4 1.0
O A:HOH891 2.2 26.7 1.0
CD B:GLU198 3.1 31.0 1.0
CD2 A:HIS368 3.1 28.0 1.0
CE1 A:HIS368 3.2 27.9 1.0
CG A:ASP369 3.2 32.0 1.0
OE2 B:GLU198 3.5 33.5 1.0
O B:SER197 3.8 25.3 1.0
CB A:ASP369 3.9 26.4 1.0
O A:HOH874 4.0 27.4 1.0
OD1 A:ASP369 4.2 30.5 1.0
CG A:HIS368 4.3 25.7 1.0
ND1 A:HIS368 4.3 26.7 1.0
O A:HOH810 4.3 27.3 1.0
OD2 B:ASP173 4.3 31.1 1.0
OD1 B:ASP173 4.3 30.0 1.0
OG1 A:THR294 4.4 30.4 1.0
CG B:GLU198 4.4 25.0 1.0
O B:HOH512 4.4 65.5 1.0
O A:HOH716 4.5 26.2 1.0
CB B:GLU198 4.5 26.5 1.0
O A:HOH821 4.5 26.9 1.0
O A:HOH832 4.6 26.0 1.0
CG B:ASP173 4.7 32.5 1.0
CA B:GLU198 4.8 29.6 1.0
O A:HOH830 5.0 41.9 1.0
C B:SER197 5.0 27.3 1.0
CA A:ASP369 5.0 26.0 1.0

Magnesium binding site 2 out of 2 in 6juw

Go back to Magnesium Binding Sites List in 6juw
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 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 Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:31.8
occ:1.00
OD2 N:ASP369 2.0 30.6 1.0
OE1 O:GLU198 2.1 36.2 1.0
O O:HOH426 2.1 34.5 1.0
O O:HOH462 2.1 30.6 1.0
NE2 N:HIS368 2.2 32.2 1.0
O O:HOH518 2.2 30.9 1.0
CD2 N:HIS368 3.1 30.5 1.0
CE1 N:HIS368 3.2 30.0 1.0
CD O:GLU198 3.2 37.1 1.0
CG N:ASP369 3.2 52.3 1.0
OE2 O:GLU198 3.7 36.0 1.0
O O:SER197 3.9 30.7 1.0
CB N:ASP369 4.0 27.1 1.0
O N:HOH886 4.0 30.8 1.0
OD1 N:ASP369 4.1 30.4 1.0
CG N:HIS368 4.3 28.2 1.0
ND1 N:HIS368 4.3 27.3 1.0
O N:HOH807 4.3 29.2 1.0
OD2 O:ASP173 4.3 34.6 1.0
OD1 O:ASP173 4.3 31.2 1.0
O N:HOH710 4.4 29.4 1.0
OG1 N:THR294 4.4 32.0 1.0
CG O:GLU198 4.4 30.8 1.0
CB O:GLU198 4.5 25.7 1.0
O N:HOH868 4.6 28.0 1.0
O N:HOH845 4.6 31.0 1.0
CG O:ASP173 4.7 36.1 1.0
CA O:GLU198 4.8 30.8 1.0
O N:HOH795 4.8 40.9 1.0
C O:SER197 5.0 35.5 1.0
CA N:ASP369 5.0 28.6 1.0

Reference:

A.Shimada, Y.Etoh, R.Kitoh-Fujisawa, A.Sasaki, K.Shinzawa-Itoh, T.Hiromoto, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structures of Catalytic Intermediates of Cytochromecoxidase Provide Insights Into Its O2-Activation and Unidirectional Proton-Pump Mechanisms. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32165497
DOI: 10.1074/JBC.RA119.009596
Page generated: Mon Dec 14 23:03:26 2020

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