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Magnesium in PDB 5b3s: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s was solved by J.Baba, A.Shimada, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.491, 203.303, 177.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.4

Other elements in 5b3s:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) 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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) (pdb code 5b3s). 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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K), PDB code: 5b3s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5b3s

Go back to Magnesium Binding Sites List in 5b3s
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:26.2
occ:1.00
 NE2 A:HIS368 2.0 20.3 1.0
OD2 A:ASP369 2.1 23.0 1.0
OE1 B:GLU198 2.1 25.8 1.0
O B:HOH459 2.2 24.3 1.0
O B:HOH563 2.3 22.4 1.0
O B:HOH410 2.3 26.6 1.0
CE1 A:HIS368 3.1 21.1 1.0
CD2 A:HIS368 3.1 22.7 1.0
CD B:GLU198 3.1 24.8 1.0
CG A:ASP369 3.3 23.7 1.0
OE2 B:GLU198 3.4 27.1 1.0
O B:SER197 3.9 21.9 1.0
CB A:ASP369 4.0 23.8 1.0
O A:HOH902 4.0 23.5 1.0
OD1 A:ASP369 4.2 23.1 1.0
CG A:HIS368 4.2 20.3 1.0
ND1 A:HIS368 4.3 20.6 1.0
OD2 B:ASP173 4.3 23.8 1.0
OD1 B:ASP173 4.3 26.1 1.0
O A:HOH798 4.3 25.7 1.0
OG1 A:THR294 4.4 23.4 1.0
O B:HOH452 4.4 23.0 0.4
CG B:GLU198 4.4 24.7 1.0
O A:HOH728 4.5 24.6 1.0
O A:HOH893 4.5 23.7 1.0
O A:HOH862 4.6 25.8 1.0
O B:HOH560 4.6 21.9 0.4
CB B:GLU198 4.7 20.5 1.0
CG B:ASP173 4.7 23.0 1.0
CA B:GLU198 4.9 20.9 1.0
CA A:ASP369 5.0 24.1 1.0

Magnesium binding site 2 out of 2 in 5b3s

Go back to Magnesium Binding Sites List in 5b3s
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K)


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 Carbon Monoxide-Bound Mixed- Valence State at 1.68 Angstrom Resolution (50 K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:29.4
occ:1.00
 NE2 N:HIS368 2.0 21.9 1.0
OE1 O:GLU198 2.1 31.1 1.0
OD2 N:ASP369 2.1 25.4 1.0
O O:HOH466 2.2 26.4 1.0
O O:HOH406 2.3 31.3 1.0
O O:HOH550 2.3 26.0 1.0
CD2 N:HIS368 3.1 25.3 1.0
CE1 N:HIS368 3.1 23.7 1.0
CD O:GLU198 3.2 30.6 1.0
CG N:ASP369 3.3 25.4 1.0
OE2 O:GLU198 3.6 31.8 1.0
O O:SER197 3.9 27.4 1.0
CB N:ASP369 3.9 24.7 1.0
O N:HOH824 4.0 26.3 1.0
OD2 O:ASP173 4.2 28.9 1.0
CG N:HIS368 4.2 23.2 1.0
ND1 N:HIS368 4.3 23.4 1.0
OD1 N:ASP369 4.3 25.7 1.0
O N:HOH800 4.3 25.2 1.0
OD1 O:ASP173 4.4 28.8 1.0
OG1 N:THR294 4.4 26.7 1.0
O O:HOH457 4.4 23.6 0.4
O N:HOH712 4.4 26.8 1.0
CG O:GLU198 4.5 25.0 1.0
O N:HOH902 4.5 24.2 1.0
O N:HOH844 4.6 26.0 1.0
CB O:GLU198 4.6 24.8 1.0
O O:HOH539 4.6 27.3 0.4
CG O:ASP173 4.7 28.4 1.0
CA O:GLU198 4.9 24.3 1.0
O N:HOH802 4.9 27.3 0.7
CA N:ASP369 5.0 25.2 1.0

Reference:

A.Shimada, J.Baba, E.Yamashita, K.Shinzawa-Ito, S.Yoshikawa, T.Tsukihara. Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Mixed-Valence State at 1.68 Angstrom Resolution (50 K) To Be Published.
Page generated: Mon Dec 14 20:02:07 2020

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