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Magnesium in PDB 5iy5: Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

Enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

All present enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5 was solved by S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.290, 183.872, 148.929, 90.00, 102.12, 90.00
R / Rfree (%) 16.7 / 20.7

Other elements in 5iy5:

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution (pdb code 5iy5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5iy5

Go back to Magnesium Binding Sites List in 5iy5
Magnesium binding site 1 out of 2 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:36.6
occ:1.00
NE2 A:HIS368 2.0 27.0 1.0
OD2 A:ASP369 2.1 28.1 1.0
OE1 B:GLU198 2.1 41.4 1.0
O B:HOH434 2.2 29.0 1.0
O B:HOH531 2.3 33.0 1.0
O B:HOH436 2.3 34.8 1.0
CD2 A:HIS368 2.9 26.2 1.0
CE1 A:HIS368 3.1 23.8 1.0
CD B:GLU198 3.2 33.0 1.0
CG A:ASP369 3.3 30.4 1.0
OE2 B:GLU198 3.5 38.8 1.0
O A:HOH821 3.9 31.3 1.0
O B:SER197 4.0 27.3 1.0
CB A:ASP369 4.0 27.4 1.0
CG A:HIS368 4.1 29.6 1.0
ND1 A:HIS368 4.2 25.4 1.0
OD1 A:ASP369 4.2 31.8 1.0
OD1 B:ASP173 4.2 30.0 1.0
O A:HOH817 4.3 29.4 1.0
OG1 A:THR294 4.4 28.6 1.0
OD2 B:ASP173 4.4 33.3 1.0
O A:HOH706 4.4 32.5 1.0
CG B:GLU198 4.5 29.5 1.0
O A:HOH827 4.6 27.6 1.0
CB B:GLU198 4.6 26.3 1.0
O A:HOH847 4.6 31.9 1.0
O B:HOH547 4.7 55.2 1.0
CG B:ASP173 4.7 34.0 1.0
O A:HOH816 4.9 36.0 1.0
CA A:ASP369 5.0 27.9 1.0

Magnesium binding site 2 out of 2 in 5iy5

Go back to Magnesium Binding Sites List in 5iy5
Magnesium binding site 2 out of 2 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg603

b:42.8
occ:1.00
NE2 N:HIS368 2.0 36.9 1.0
OE1 O:GLU198 2.1 41.0 1.0
OD2 N:ASP369 2.2 38.4 1.0
O O:HOH512 2.3 39.7 1.0
O O:HOH445 2.3 40.6 1.0
O O:HOH414 2.4 38.6 1.0
CD2 N:HIS368 2.9 34.1 1.0
CE1 N:HIS368 3.0 34.5 1.0
CG N:ASP369 3.3 40.7 1.0
CD O:GLU198 3.3 39.1 1.0
OE2 O:GLU198 3.8 40.8 1.0
CB N:ASP369 3.8 41.8 1.0
O N:HOH811 3.9 42.4 1.0
O O:SER197 3.9 36.1 1.0
CG N:HIS368 4.1 34.1 1.0
ND1 N:HIS368 4.1 35.8 1.0
O N:HOH819 4.2 38.1 1.0
OD1 O:ASP173 4.3 37.0 1.0
OD1 N:ASP369 4.3 46.4 1.0
OD2 O:ASP173 4.3 40.1 1.0
O N:HOH864 4.4 36.6 1.0
O N:HOH713 4.4 41.3 1.0
OG1 N:THR294 4.5 38.0 1.0
CG O:GLU198 4.5 35.2 1.0
O N:HOH851 4.5 37.7 1.0
O O:HOH511 4.7 69.7 1.0
CB O:GLU198 4.7 36.0 1.0
CG O:ASP173 4.7 39.7 1.0
O N:HOH789 4.9 48.0 1.0
CA N:ASP369 5.0 39.9 1.0

Reference:

S.Shimada, K.Shinzawa-Itoh, J.Baba, S.Aoe, A.Shimada, E.Yamashita, J.Kang, M.Tateno, S.Yoshikawa, T.Tsukihara. Complex Structure of Cytochrome C-Cytochrome C Oxidase Reveals A Novel Protein-Protein Interaction Mode Embo J. V. 36 291 2017.
ISSN: ESSN 1460-2075
PubMed: 27979921
DOI: 10.15252/EMBJ.201695021
Page generated: Mon Dec 14 20:31:40 2020

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