Magnesium in PDB 7xma: Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso

All present enzymatic activity of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso:
7.1.1.9;

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma was solved by Y.Nishida, K.Shinzawa-Itoh, N.Mizuno, T.Kumasaka, S.Yoshikawa, T.Tsukihara, S.Takashima, Y.Shintani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.97 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.8, 203.577, 177.859, 90, 90, 90
R / Rfree (%)	18.6 / 21.3

The structure of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso (pdb code 7xma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:13.4 occ:1.00 OE1 B:GLU198 2.1 30.1 1.0 OD2 A:ASP369 2.1 26.7 1.0 O B:HOH765 2.1 22.9 1.0 O B:HOH825 2.1 21.1 1.0 O B:HOH734 2.1 21.4 1.0 NE2 A:HIS368 2.2 29.2 1.0 CE1 A:HIS368 3.1 28.7 1.0 CD2 A:HIS368 3.2 23.6 1.0 CD B:GLU198 3.2 39.1 1.0 CG A:ASP369 3.3 23.8 1.0 O B:HOH787 3.7 41.0 0.5 OE2 B:GLU198 3.8 33.8 1.0 O B:SER197 3.8 29.2 1.0 O A:HOH903 4.0 25.8 1.0 CB A:ASP369 4.1 20.0 1.0 O A:HOH873 4.1 29.9 1.0 ND1 A:HIS368 4.2 23.7 1.0 OD1 A:ASP369 4.2 30.9 1.0 CG A:HIS368 4.2 23.9 1.0 OD2 B:ASP173 4.3 38.5 1.0 O A:HOH784 4.4 24.6 1.0 OD1 B:ASP173 4.4 27.8 1.0 CG B:GLU198 4.4 18.7 1.0 O A:HOH789 4.5 24.7 1.0 OG1 A:THR294 4.5 31.8 1.0 O A:HOH768 4.6 33.2 1.0 CB B:GLU198 4.6 33.2 1.0 CG B:ASP173 4.8 34.6 1.0 O B:HOH822 4.8 43.3 0.5 CA B:GLU198 4.9 28.6 1.0 O A:HOH815 5.0 22.0 0.7 C B:SER197 5.0 27.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:13.5 occ:1.00 OD2 N:ASP369 2.1 28.5 1.0 OE1 O:GLU198 2.1 31.4 1.0 O O:HOH741 2.1 18.6 1.0 O O:HOH738 2.1 23.8 1.0 O O:HOH802 2.1 26.9 1.0 NE2 N:HIS368 2.2 29.8 1.0 CE1 N:HIS368 3.1 32.1 1.0 CD2 N:HIS368 3.2 31.7 1.0 CD O:GLU198 3.2 50.1 1.0 CG N:ASP369 3.3 49.0 1.0 OE2 O:GLU198 3.8 36.2 1.0 O O:SER197 3.8 32.5 1.0 O N:HOH904 4.0 26.7 1.0 CB N:ASP369 4.0 22.0 1.0 ND1 N:HIS368 4.2 24.0 1.0 O N:HOH861 4.2 30.2 1.0 OD1 N:ASP369 4.2 32.9 1.0 CG N:HIS368 4.2 33.0 1.0 OD2 O:ASP173 4.3 39.0 1.0 O N:HOH758 4.4 30.6 1.0 CG O:GLU198 4.5 18.4 1.0 O N:HOH780 4.5 29.7 1.0 OG1 N:THR294 4.5 35.5 1.0 OD1 O:ASP173 4.5 33.3 1.0 O N:HOH784 4.6 27.6 1.0 CB O:GLU198 4.6 39.0 1.0 CG O:ASP173 4.8 38.8 1.0 O N:HOH809 4.8 23.8 0.7 CA O:GLU198 4.9 30.4 1.0 C O:SER197 5.0 48.8 1.0

Y.Nishida, S.Yanagisawa, R.Morita, H.Shigematsu, K.Shinzawa-Itoh, H.Yuki, S.Ogasawara, K.Shimuta, T.Iwamoto, C.Nakabayashi, W.Matsumura, H.Kato, C.Gopalasingam, T.Nagao, T.Qaqorh, Y.Takahashi, S.Yamazaki, K.Kamiya, R.Harada, N.Mizuno, H.Takahashi, Y.Akeda, M.Ohnishi, Y.Ishii, T.Kumasaka, T.Murata, K.Muramoto, T.Tosha, Y.Shiro, T.Honma, Y.Shigeta, M.Kubo, S.Takashima, Y.Shintani. Identifying Antibiotics Based on Structural Differences in the Conserved Allostery From Mitochondrial Heme-Copper Oxidases. Nat Commun V. 13 7591 2022.
ISSN: ESSN 2041-1723
PubMed: 36481732
DOI: 10.1038/S41467-022-34771-Y