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Magnesium in PDB 2eil: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.379, 205.898, 178.182, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Other elements in 2eil:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Cadmium (Cd) 3 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2eil). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2eil

Go back to Magnesium Binding Sites List in 2eil
Magnesium binding site 1 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg518

b:23.6
occ:1.00
OD1 A:ASP369 2.0 20.8 1.0
OE1 B:GLU198 2.1 31.4 1.0
NE2 A:HIS368 2.2 17.3 1.0
O B:HOH2031 2.3 22.6 1.0
O B:HOH2032 2.3 23.1 1.0
O B:HOH2033 2.3 25.5 1.0
CE1 A:HIS368 3.1 18.7 1.0
CD2 A:HIS368 3.2 21.3 1.0
CG A:ASP369 3.2 23.9 1.0
CD B:GLU198 3.3 31.1 1.0
O B:SER197 3.8 24.1 1.0
OE2 B:GLU198 3.8 36.9 1.0
O A:HOH2035 3.9 19.6 1.0
CB A:ASP369 4.0 20.9 1.0
OD2 A:ASP369 4.1 27.7 1.0
ND1 A:HIS368 4.3 18.1 1.0
OD2 B:ASP173 4.3 33.2 1.0
CG A:HIS368 4.3 21.1 1.0
OD1 B:ASP173 4.4 28.2 1.0
O A:HOH2038 4.4 20.9 1.0
CG B:GLU198 4.4 23.6 1.0
O A:HOH2010 4.5 18.3 1.0
OG1 A:THR294 4.5 19.9 1.0
O A:HOH2023 4.6 19.3 1.0
CB B:GLU198 4.6 21.3 1.0
O A:HOH2020 4.6 23.6 1.0
CG B:ASP173 4.7 33.8 1.0
CA B:GLU198 4.8 22.0 1.0
O B:HOH2055 4.9 44.9 1.0
C B:SER197 5.0 25.9 1.0

Magnesium binding site 2 out of 2 in 2eil

Go back to Magnesium Binding Sites List in 2eil
Magnesium binding site 2 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1518

b:32.4
occ:1.00
OE1 O:GLU198 2.0 39.2 1.0
OD1 N:ASP369 2.1 36.9 1.0
NE2 N:HIS368 2.2 28.5 1.0
O O:HOH3031 2.3 30.9 1.0
O O:HOH3033 2.3 31.3 1.0
O O:HOH3032 2.3 28.7 1.0
CD O:GLU198 3.1 38.4 1.0
CE1 N:HIS368 3.2 25.2 1.0
CD2 N:HIS368 3.2 26.4 1.0
CG N:ASP369 3.3 35.5 1.0
OE2 O:GLU198 3.6 35.6 1.0
O O:SER197 3.8 32.8 1.0
O N:HOH3035 3.9 30.7 1.0
CB N:ASP369 4.0 34.5 1.0
OD2 O:ASP173 4.1 38.1 1.0
OD2 N:ASP369 4.2 38.0 1.0
ND1 N:HIS368 4.3 23.8 1.0
CG O:GLU198 4.3 33.2 1.0
CG N:HIS368 4.4 24.6 1.0
O N:HOH3038 4.4 26.1 1.0
O N:HOH3010 4.4 22.6 1.0
OD1 O:ASP173 4.4 34.2 1.0
CB O:GLU198 4.6 27.0 1.0
OG1 N:THR294 4.6 29.7 1.0
O N:HOH3023 4.7 22.7 1.0
O N:HOH3020 4.7 26.8 1.0
CG O:ASP173 4.7 36.7 1.0
CA O:GLU198 4.8 26.3 1.0
O O:HOH3055 4.9 58.9 1.0
C O:SER197 4.9 31.4 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Mon Dec 14 07:21:37 2020

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