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Magnesium in PDB 3aso: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso was solved by M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, 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) 15.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.874, 204.106, 177.874, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.5

Other elements in 3aso:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength (pdb code 3aso). 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 Measured at 0.9 Angstrom Wavelength, PDB code: 3aso:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3aso

Go back to Magnesium Binding Sites List in 3aso
Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg518

b:21.1
occ:1.00
NE2 A:HIS368 2.1 14.8 1.0
OD1 A:ASP369 2.1 20.2 1.0
OE1 B:GLU198 2.1 25.1 1.0
O B:HOH2268 2.3 19.7 1.0
O A:HOH2267 2.3 19.5 1.0
O B:HOH2266 2.3 22.0 1.0
CE1 A:HIS368 3.0 15.4 1.0
CD2 A:HIS368 3.1 12.2 1.0
CD B:GLU198 3.2 18.9 1.0
CG A:ASP369 3.3 19.6 1.0
OE2 B:GLU198 3.6 23.7 1.0
O B:SER197 3.8 18.0 1.0
O A:HOH2278 4.0 17.3 1.0
CB A:ASP369 4.0 19.1 1.0
ND1 A:HIS368 4.1 13.9 1.0
OD1 B:ASP173 4.2 20.2 1.0
CG A:HIS368 4.2 16.0 1.0
OD2 A:ASP369 4.2 19.7 1.0
O A:HOH2297 4.3 18.1 1.0
OD2 B:ASP173 4.3 23.0 1.0
O A:HOH2219 4.4 17.6 1.0
O A:HOH2116 4.4 16.6 1.0
OG1 A:THR294 4.4 19.2 1.0
CG B:GLU198 4.5 15.9 1.0
O A:HOH2209 4.6 25.3 1.0
CG B:ASP173 4.7 21.6 1.0
CB B:GLU198 4.7 17.9 1.0
C B:SER197 5.0 18.4 1.0
O A:HOH2475 5.0 30.7 1.0
CA B:GLU198 5.0 17.6 1.0
CA A:ASP369 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in 3aso

Go back to Magnesium Binding Sites List in 3aso
Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg518

b:23.6
occ:1.00
NE2 N:HIS368 2.0 18.8 1.0
OD1 N:ASP369 2.1 19.4 1.0
OE1 O:GLU198 2.1 28.2 1.0
O O:HOH3268 2.3 20.6 1.0
O O:HOH3266 2.3 23.1 1.0
O O:HOH3267 2.3 22.5 1.0
CD2 N:HIS368 2.9 18.0 1.0
CE1 N:HIS368 3.0 16.5 1.0
CD O:GLU198 3.2 23.8 1.0
CG N:ASP369 3.3 21.7 1.0
OE2 O:GLU198 3.6 24.8 1.0
O N:HOH3278 3.8 24.3 1.0
O O:SER197 3.9 22.3 1.0
CB N:ASP369 3.9 20.9 1.0
CG N:HIS368 4.1 20.0 1.0
ND1 N:HIS368 4.1 16.3 1.0
OD2 N:ASP369 4.2 22.2 1.0
OD2 O:ASP173 4.3 25.2 1.0
O N:HOH3297 4.3 16.4 1.0
O N:HOH3116 4.4 23.3 1.0
OD1 O:ASP173 4.4 21.0 1.0
OG1 N:THR294 4.4 19.1 1.0
CG O:GLU198 4.5 20.7 1.0
O N:HOH3219 4.5 18.1 1.0
O N:HOH3209 4.6 24.8 1.0
CB O:GLU198 4.7 20.9 1.0
CG O:ASP173 4.7 21.0 1.0
O N:HOH3475 4.9 26.1 1.0
CA N:ASP369 4.9 22.1 1.0
CA O:GLU198 5.0 21.5 1.0

Reference:

M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa. Distinguishing Between Cl- and O2(2-) As the Bridging Element Between FE3+ and CU2+ in Resting-Oxidized Cytochrome C Oxidase Acta Crystallogr.,Sect.D V. 67 742 2011.
ISSN: ISSN 0907-4449
PubMed: 21795816
DOI: 10.1107/S0907444911022803
Page generated: Mon Dec 14 07:54:09 2020

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