Zinc in PDB 6juw: Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw was solved by A.Shimada, K.Muramoto, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.88 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	182.217, 204.650, 177.397, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.8

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	4 atoms

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution (pdb code 6juw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:55.6 occ:1.00 SG F:CYS85 2.3 76.9 1.0 SG F:CYS62 2.4 84.0 1.0 SG F:CYS60 2.4 41.3 1.0 SG F:CYS82 2.5 45.0 1.0 CB F:CYS85 3.3 57.0 1.0 CB F:CYS60 3.4 35.0 1.0 CB F:CYS82 3.5 38.7 1.0 CB F:CYS62 3.5 49.0 1.0 CA F:CYS62 3.6 50.1 1.0 N F:CYS85 3.7 47.6 1.0 CA F:CYS85 4.0 71.3 1.0 N F:CYS62 4.1 44.5 1.0 O F:CYS60 4.1 33.8 1.0 C F:CYS60 4.2 44.0 1.0 O A:HOH725 4.3 56.2 1.0 CA F:CYS60 4.4 32.3 1.0 CB F:SER84 4.4 88.4 1.0 OG1 F:THR87 4.5 41.1 1.0 C F:CYS85 4.6 39.1 1.0 C F:ILE61 4.7 50.4 1.0 C F:SER84 4.7 92.0 1.0 OG F:SER84 4.8 67.3 1.0 CG1 F:ILE70 4.8 33.5 1.0 N F:SER84 4.8 44.7 1.0 N F:GLY86 4.8 35.2 1.0 CB F:THR87 4.9 39.4 1.0 N F:ILE61 4.9 39.8 1.0 CA F:SER84 4.9 75.0 1.0 CA F:CYS82 4.9 31.1 1.0 CB F:ILE70 4.9 32.4 1.0 C F:CYS62 5.0 68.7 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:55.5 occ:1.00 SG S:CYS85 2.3 59.1 1.0 SG S:CYS62 2.4 79.5 1.0 SG S:CYS60 2.4 40.5 1.0 SG S:CYS82 2.4 50.7 1.0 CB S:CYS60 3.3 36.4 1.0 CB S:CYS82 3.4 35.2 1.0 CB S:CYS62 3.6 62.5 1.0 CB S:CYS85 3.6 0.6 1.0 N S:CYS85 3.7 41.6 1.0 CA S:CYS62 3.7 43.8 1.0 N S:CYS62 4.1 46.5 1.0 CA S:CYS85 4.2 49.5 1.0 CB S:SER84 4.2 65.7 1.0 C S:CYS60 4.2 39.8 1.0 O S:CYS60 4.2 33.7 1.0 CG2 S:THR87 4.3 31.2 1.0 O N:HOH860 4.4 56.6 1.0 CA S:CYS60 4.4 33.5 1.0 C S:ILE61 4.7 45.6 1.0 C S:CYS85 4.7 36.6 1.0 C S:SER84 4.7 59.6 1.0 N S:ILE61 4.8 38.3 1.0 N S:SER84 4.8 44.5 1.0 CA S:SER84 4.8 0.4 1.0 CG1 S:ILE70 4.8 36.1 1.0 CA S:CYS82 4.8 37.8 1.0 N S:GLY86 4.8 41.7 1.0 CB S:ILE70 4.8 35.4 1.0 OG S:SER84 4.9 86.0 1.0

A.Shimada, Y.Etoh, R.Kitoh-Fujisawa, A.Sasaki, K.Shinzawa-Itoh, T.Hiromoto, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structures of Catalytic Intermediates of Cytochromecoxidase Provide Insights Into Its O2-Activation and Unidirectional Proton-Pump Mechanisms. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32165497
DOI: 10.1074/JBC.RA119.009596