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Magnesium in PDB 3abm: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 3abm:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset) 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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) (pdb code 3abm). 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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3abm

Go back to Magnesium Binding Sites List in 3abm
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg518

b:27.1
occ:1.00
NE2 A:HIS368 2.1 25.8 1.0
OD1 A:ASP369 2.1 25.9 1.0
O B:HOH2031 2.1 27.3 1.0
OE1 B:GLU198 2.1 33.4 1.0
O B:HOH2033 2.1 22.5 1.0
O A:HOH2032 2.1 28.9 1.0
CD2 A:HIS368 3.0 31.5 1.0
CE1 A:HIS368 3.1 27.0 1.0
CD B:GLU198 3.2 34.1 1.0
CG A:ASP369 3.2 28.4 1.0
OE2 B:GLU198 3.6 33.9 1.0
O B:SER197 3.8 26.0 1.0
CB A:ASP369 3.9 28.0 1.0
O A:HOH2035 3.9 25.7 1.0
OD1 B:ASP173 4.1 29.4 1.0
CG A:HIS368 4.2 28.1 1.0
ND1 A:HIS368 4.2 25.3 1.0
OD2 A:ASP369 4.2 27.2 1.0
O A:HOH2038 4.3 25.0 1.0
OD2 B:ASP173 4.4 33.4 1.0
OG1 A:THR294 4.4 27.1 1.0
O A:HOH2023 4.5 27.1 1.0
O A:HOH2010 4.5 25.0 1.0
CG B:GLU198 4.5 22.6 1.0
CG B:ASP173 4.7 33.7 1.0
CB B:GLU198 4.7 24.9 1.0
O A:HOH2020 4.7 28.3 1.0
CA A:ASP369 5.0 27.7 1.0

Magnesium binding site 2 out of 2 in 3abm

Go back to Magnesium Binding Sites List in 3abm
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1518

b:34.2
occ:1.00
O O:HOH3031 2.0 34.5 1.0
NE2 N:HIS368 2.1 28.4 1.0
OD1 N:ASP369 2.1 34.6 1.0
OE1 O:GLU198 2.1 37.8 1.0
O N:HOH3032 2.2 33.8 1.0
O O:HOH3033 2.2 32.2 1.0
CE1 N:HIS368 3.0 31.5 1.0
CD2 N:HIS368 3.1 35.9 1.0
CD O:GLU198 3.2 36.8 1.0
CG N:ASP369 3.3 35.9 1.0
OE2 O:GLU198 3.6 41.9 1.0
O O:SER197 3.8 33.7 1.0
O N:HOH3035 3.9 34.1 1.0
CB N:ASP369 4.0 36.8 1.0
ND1 N:HIS368 4.2 31.3 1.0
CG N:HIS368 4.2 27.9 1.0
OD2 N:ASP369 4.3 33.9 1.0
OD1 O:ASP173 4.3 37.7 1.0
OD2 O:ASP173 4.4 42.1 1.0
O N:HOH3038 4.4 31.7 1.0
CG O:GLU198 4.5 32.6 1.0
OG1 N:THR294 4.5 34.4 1.0
O N:HOH3010 4.5 29.5 1.0
O N:HOH3023 4.6 32.8 1.0
CB O:GLU198 4.6 27.8 1.0
O N:HOH3020 4.7 34.7 1.0
CG O:ASP173 4.8 37.7 1.0
CA N:ASP369 4.9 34.5 1.0
C O:SER197 4.9 32.5 1.0
CA O:GLU198 4.9 31.0 1.0
N N:ASP369 5.0 35.1 1.0
O N:HOH3054 5.0 45.8 1.0

Reference:

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106
Page generated: Mon Dec 14 07:52:53 2020

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