Zinc in PDB 1v55: Bovine Heart Cytochrome C Oxidase at the Fully Reduced State

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

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State, PDB code: 1v55 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.060, 206.584, 178.298, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Reduced State 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 Reduced State (pdb code 1v55). 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 Reduced State, PDB code: 1v55:
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 Reduced State


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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn99 b:25.5 occ:1.00 SG F:CYS62 2.2 25.1 1.0 SG F:CYS60 2.2 23.9 1.0 SG F:CYS82 2.2 23.4 1.0 SG F:CYS85 2.3 26.4 1.0 CB F:CYS82 3.2 24.7 1.0 CB F:CYS62 3.3 24.4 1.0 CB F:CYS60 3.3 21.8 1.0 CB F:CYS85 3.4 26.6 1.0 CA F:CYS62 3.5 30.4 1.0 N F:CYS85 3.7 27.5 1.0 N F:CYS62 3.8 28.8 1.0 CA F:CYS85 4.1 27.5 1.0 O F:CYS60 4.3 23.7 1.0 C F:CYS60 4.4 22.7 1.0 O F:HOH117 4.5 64.5 1.0 CA F:CYS60 4.5 20.8 1.0 CB F:SER84 4.5 26.3 1.0 CA F:CYS82 4.7 24.4 1.0 C F:SER84 4.7 27.1 1.0 OG F:SER84 4.8 25.5 1.0 C F:ILE61 4.8 27.6 1.0 C F:CYS62 4.9 33.2 1.0 C F:CYS85 4.9 29.1 1.0 OG1 F:THR87 4.9 35.0 1.0 CG1 F:ILE70 4.9 21.2 1.0 CB F:ILE70 5.0 21.4 1.0 N F:GLY86 5.0 30.6 1.0 CA F:SER84 5.0 27.1 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Reduced State


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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn99 b:29.0 occ:1.00 SG S:CYS82 2.2 24.0 1.0 SG S:CYS62 2.3 27.9 1.0 SG S:CYS85 2.3 25.5 1.0 SG S:CYS60 2.3 24.6 1.0 CB S:CYS82 3.1 23.8 1.0 CB S:CYS60 3.3 20.7 1.0 CB S:CYS62 3.4 29.4 1.0 CB S:CYS85 3.4 27.6 1.0 N S:CYS85 3.7 26.9 1.0 CA S:CYS62 3.7 30.4 1.0 N S:CYS62 4.0 30.6 1.0 CA S:CYS85 4.1 28.7 1.0 O S:CYS60 4.3 24.1 1.0 C S:CYS60 4.4 24.1 1.0 CA S:CYS60 4.5 23.1 1.0 CB S:SER84 4.5 29.5 1.0 CA S:CYS82 4.5 27.2 1.0 O S:HOH1303 4.5 75.9 1.0 OG1 S:THR87 4.5 33.8 1.0 C S:SER84 4.7 27.8 1.0 CB S:ILE70 4.8 20.7 1.0 C S:CYS85 4.9 29.3 1.0 N S:GLY86 4.9 31.0 1.0 CA S:SER84 4.9 27.2 1.0 N S:SER84 4.9 29.0 1.0 C S:ILE61 4.9 30.6 1.0 CG2 S:THR87 4.9 35.7 1.0 CG1 S:ILE70 4.9 18.0 1.0

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100