Zinc in PDB 3abl: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset):
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset), PDB code: 3abl was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.137, 207.514, 178.173, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) 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 at the Fully Oxidized State (15-S X-Ray Exposure Dataset) (pdb code 3abl). 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 at the Fully Oxidized State (15-S X-Ray Exposure Dataset), PDB code: 3abl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn99 b:30.8 occ:1.00 SG F:CYS60 2.3 30.3 1.0 SG F:CYS82 2.3 29.1 1.0 SG F:CYS62 2.3 30.4 1.0 SG F:CYS85 2.4 30.1 1.0 CB F:CYS82 3.2 29.9 1.0 CB F:CYS60 3.3 25.2 1.0 CB F:CYS62 3.4 31.7 1.0 CB F:CYS85 3.5 28.0 1.0 CA F:CYS62 3.5 33.5 1.0 N F:CYS85 3.8 29.5 1.0 N F:CYS62 4.1 33.9 1.0 CA F:CYS85 4.2 29.8 1.0 O F:CYS60 4.4 26.7 1.0 OG F:SER84 4.4 35.6 1.0 C F:CYS60 4.5 28.8 1.0 CA F:CYS60 4.5 26.5 1.0 CA F:CYS82 4.6 31.5 1.0 O F:HOH2330 4.6 42.2 1.0 CG2 F:THR87 4.8 33.3 1.0 C F:SER84 4.8 30.5 1.0 C F:ILE61 4.8 34.6 1.0 C F:CYS85 4.8 32.6 1.0 CB F:SER84 4.9 32.6 1.0 C F:CYS62 4.9 35.8 1.0 CB F:ILE70 4.9 27.6 1.0 N F:GLY86 4.9 31.3 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn99 b:34.9 occ:1.00 SG S:CYS85 2.3 35.2 1.0 SG S:CYS82 2.4 35.0 1.0 SG S:CYS62 2.4 33.1 1.0 SG S:CYS60 2.4 36.2 1.0 CB S:CYS82 3.1 35.4 1.0 CB S:CYS85 3.3 31.4 1.0 CB S:CYS62 3.3 31.6 1.0 CB S:CYS60 3.3 32.2 1.0 CA S:CYS62 3.6 34.8 1.0 N S:CYS85 3.7 32.3 1.0 CA S:CYS85 4.1 33.2 1.0 N S:CYS62 4.1 34.0 1.0 OG S:SER84 4.3 38.1 1.0 O S:CYS60 4.3 33.9 1.0 C S:CYS60 4.4 34.6 1.0 CA S:CYS60 4.5 34.5 1.0 CA S:CYS82 4.6 34.8 1.0 O S:HOH3330 4.6 55.5 1.0 OG1 S:THR87 4.6 50.0 1.0 C S:SER84 4.7 34.0 1.0 CB S:SER84 4.8 36.1 1.0 C S:CYS85 4.8 33.8 1.0 CG1 S:ILE70 4.8 28.6 1.0 CB S:ILE70 4.8 31.7 1.0 C S:ILE61 4.9 36.1 1.0 C S:CYS62 4.9 37.5 1.0 N S:SER84 5.0 35.3 1.0 CA S:SER84 5.0 33.7 1.0 N S:GLY86 5.0 36.1 1.0

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106