Zinc in PDB 2eik: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, 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 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.8

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn99 b:24.1 occ:1.00 SG F:CYS62 2.2 29.2 1.0 SG F:CYS60 2.3 29.8 1.0 SG F:CYS85 2.3 31.6 1.0 SG F:CYS82 2.3 25.7 1.0 CB F:CYS82 3.2 27.7 1.0 CB F:CYS62 3.3 26.5 1.0 CB F:CYS60 3.4 25.2 1.0 CB F:CYS85 3.4 28.8 1.0 CA F:CYS62 3.5 33.3 1.0 N F:CYS85 3.6 30.1 1.0 N F:CYS62 3.8 30.9 1.0 CA F:CYS85 4.1 31.0 1.0 O F:CYS60 4.3 26.8 1.0 O F:HOH2339 4.3 48.2 1.0 C F:CYS60 4.4 24.5 1.0 CB F:SER84 4.5 28.0 1.0 CA F:CYS60 4.5 22.7 1.0 OG F:SER84 4.6 28.4 1.0 CA F:CYS82 4.7 25.7 1.0 C F:SER84 4.7 28.7 1.0 CG1 F:ILE70 4.8 19.9 1.0 C F:ILE61 4.8 29.0 1.0 C F:CYS85 4.8 32.6 1.0 C F:CYS62 4.9 38.6 1.0 OG1 F:THR87 4.9 42.6 1.0 CB F:ILE70 4.9 23.0 1.0 CA F:SER84 5.0 27.3 1.0 N F:GLY86 5.0 34.6 1.0

Zinc binding site 2 out of 2 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn99 b:29.4 occ:1.00 SG S:CYS85 2.2 34.6 1.0 SG S:CYS62 2.2 32.9 1.0 SG S:CYS82 2.2 31.0 1.0 SG S:CYS60 2.3 32.9 1.0 CB S:CYS82 3.0 29.9 1.0 CB S:CYS60 3.3 28.7 1.0 CB S:CYS85 3.4 31.3 1.0 CB S:CYS62 3.4 35.1 1.0 N S:CYS85 3.6 31.8 1.0 CA S:CYS62 3.7 37.1 1.0 N S:CYS62 4.0 36.0 1.0 CA S:CYS85 4.1 32.2 1.0 OG1 S:THR87 4.3 41.5 1.0 O N:HOH3339 4.4 64.3 1.0 O S:CYS60 4.4 29.2 1.0 C S:CYS60 4.4 29.0 1.0 CA S:CYS60 4.5 30.0 1.0 CA S:CYS82 4.5 32.2 1.0 CB S:SER84 4.5 36.5 1.0 NZ N:LYS514 4.7 74.4 1.0 C S:SER84 4.7 33.0 1.0 C S:CYS85 4.8 31.3 1.0 CB S:ILE70 4.8 26.1 1.0 CG1 S:ILE70 4.8 24.3 1.0 N S:GLY86 4.9 33.6 1.0 N S:SER84 4.9 34.7 1.0 CA S:SER84 4.9 33.6 1.0 C S:ILE61 4.9 35.4 1.0

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104