Zinc in PDB 5b1b: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b was solved by N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, 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 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.606, 204.140, 177.653, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.6

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 Angstrom Resolution (pdb code 5b1b). 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 the Fully Reduced State at 1.6 Angstrom Resolution, PDB code: 5b1b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 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 the Fully Reduced State at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:25.3 occ:1.00 SG F:CYS62 2.3 26.8 1.0 SG F:CYS85 2.3 26.1 1.0 SG F:CYS60 2.4 25.1 1.0 SG F:CYS82 2.4 24.8 1.0 CB F:CYS82 3.2 26.2 1.0 CB F:CYS62 3.4 26.2 1.0 CB F:CYS60 3.4 23.7 1.0 CB F:CYS85 3.5 26.6 1.0 CA F:CYS62 3.6 25.9 1.0 N F:CYS85 3.8 25.4 1.0 CA F:CYS85 4.1 27.1 1.0 N F:CYS62 4.3 24.5 1.0 O F:CYS60 4.4 22.8 1.0 C F:CYS60 4.5 24.8 1.0 CA F:CYS60 4.5 24.2 1.0 CB F:SER84 4.5 24.8 1.0 O F:HOH215 4.6 43.3 1.0 CA F:CYS82 4.7 24.9 1.0 OG F:SER84 4.7 30.8 1.0 C F:SER84 4.7 28.1 1.0 CG2 F:THR87 4.8 31.7 1.0 C F:CYS85 4.9 27.9 1.0 C F:ILE61 4.9 27.0 1.0 CB F:ILE70 5.0 21.1 1.0 C F:CYS62 5.0 28.0 1.0 N F:GLY86 5.0 27.4 1.0 N F:SER84 5.0 26.0 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State at 1.6 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 the Fully Reduced State at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:25.3 occ:1.00 SG S:CYS82 2.3 25.3 1.0 SG S:CYS62 2.3 26.9 1.0 SG S:CYS60 2.3 23.6 1.0 SG S:CYS85 2.4 25.9 1.0 CB S:CYS82 3.2 24.6 1.0 CB S:CYS62 3.3 27.4 1.0 CB S:CYS60 3.4 24.6 1.0 CB S:CYS85 3.5 25.1 1.0 CA S:CYS62 3.6 27.9 1.0 N S:CYS85 3.8 26.6 1.0 CA S:CYS85 4.1 28.4 1.0 N S:CYS62 4.2 27.3 1.0 CG2 S:THR87 4.3 24.6 0.5 C S:CYS60 4.4 22.9 1.0 CB S:SER84 4.4 27.2 1.0 O S:CYS60 4.5 21.4 1.0 O S:HOH239 4.5 38.0 1.0 CG2 S:THR87 4.5 29.6 0.5 CA S:CYS60 4.5 24.4 1.0 CA S:CYS82 4.6 24.7 1.0 OG S:SER84 4.7 32.3 1.0 C S:SER84 4.7 28.4 1.0 C S:CYS85 4.8 29.0 1.0 C S:ILE61 4.9 26.0 1.0 CB S:ILE70 4.9 21.8 1.0 C S:CYS62 5.0 32.0 1.0 N S:GLY86 5.0 25.1 1.0 N S:SER84 5.0 27.4 1.0 CG1 S:ILE70 5.0 23.2 1.0

N.Yano, K.Muramoto, A.Shimada, S.Takemura, J.Baba, H.Fujisawa, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770