Sodium 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
Magnesium	(Mg)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bovine Heart Cytochrome C Oxidase, Apo Structure with Dmso, PDB code: 7xma:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na605 b:15.2 occ:1.00 O A:GLU40 2.3 27.1 1.0 O A:GLY45 2.3 29.9 1.0 O A:SER441 2.3 25.2 1.0 OE2 A:GLU40 2.3 35.9 1.0 O A:HOH863 2.5 26.6 1.0 CD A:GLU40 3.2 28.6 1.0 C A:GLU40 3.3 39.9 1.0 CG A:GLU40 3.4 40.6 1.0 O A:HOH757 3.5 49.4 1.0 C A:GLY45 3.5 32.3 1.0 C A:SER441 3.5 34.8 1.0 CA A:THR46 4.0 51.9 1.0 CA A:ASP442 4.1 25.4 1.0 O A:GLN43 4.1 31.0 1.0 CA A:GLU40 4.1 22.9 1.0 CB A:ASP442 4.2 24.4 1.0 N A:THR46 4.2 33.4 1.0 N A:LEU41 4.2 25.8 1.0 OD1 A:ASP442 4.2 34.7 1.0 N A:ASP442 4.2 22.0 1.0 CB A:GLU40 4.3 28.4 1.0 CG A:ASP442 4.3 33.3 1.0 CA A:LEU41 4.3 26.5 1.0 OE1 A:GLU40 4.4 36.3 1.0 N A:LEU47 4.5 33.2 1.0 N A:GLY45 4.5 31.4 1.0 CD2 A:LEU41 4.5 24.2 1.0 CA A:SER441 4.6 37.2 1.0 CA A:GLY45 4.6 27.3 1.0 C A:THR46 4.7 54.6 1.0 CB A:SER441 4.9 32.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na605 b:17.6 occ:1.00 OE2 N:GLU40 2.3 34.0 1.0 O N:GLY45 2.3 31.6 1.0 O N:GLU40 2.3 29.4 1.0 O N:SER441 2.3 35.1 1.0 O N:HOH890 2.5 29.8 1.0 CD N:GLU40 3.2 44.5 1.0 C N:GLU40 3.4 41.4 1.0 CG N:GLU40 3.4 50.0 1.0 O N:HOH744 3.4 50.6 1.0 C N:GLY45 3.5 36.2 1.0 C N:SER441 3.5 31.6 1.0 CA N:THR46 4.1 38.8 1.0 CA N:ASP442 4.1 30.7 1.0 O N:GLN43 4.1 31.5 1.0 CA N:GLU40 4.1 40.5 1.0 CB N:ASP442 4.2 34.5 1.0 N N:THR46 4.2 32.1 1.0 N N:ASP442 4.3 26.9 1.0 N N:LEU41 4.3 26.8 1.0 OD1 N:ASP442 4.3 33.0 1.0 CB N:GLU40 4.3 29.5 1.0 CG N:ASP442 4.4 44.6 1.0 OE1 N:GLU40 4.4 38.0 1.0 N N:LEU47 4.4 60.6 1.0 CA N:LEU41 4.5 33.3 1.0 N N:GLY45 4.5 36.3 1.0 CA N:GLY45 4.6 28.8 1.0 CA N:SER441 4.6 36.2 1.0 CD2 N:LEU41 4.7 27.3 1.0 C N:THR46 4.7 56.2 1.0 CB N:SER441 4.9 34.0 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