Zinc in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, 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 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.9

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K 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 Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). 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 Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn99 b:35.3 occ:1.00 SG F:CYS60 2.3 32.8 1.0 SG F:CYS82 2.3 31.5 1.0 SG F:CYS62 2.4 34.5 1.0 SG F:CYS85 2.4 35.1 1.0 CB F:CYS82 3.3 34.2 1.0 CB F:CYS60 3.3 31.6 1.0 CB F:CYS62 3.3 31.4 1.0 CB F:CYS85 3.4 33.0 1.0 CA F:CYS62 3.6 36.2 1.0 N F:CYS85 3.8 35.5 1.0 N F:CYS62 4.1 37.5 1.0 CA F:CYS85 4.1 35.4 1.0 O F:CYS60 4.3 31.0 1.0 C F:CYS60 4.4 32.8 1.0 CA F:CYS60 4.5 31.1 1.0 O F:HOH2514 4.6 45.8 1.0 CB F:SER84 4.6 37.6 1.0 OG F:SER84 4.6 40.7 1.0 CA F:CYS82 4.7 34.0 1.0 CG2 F:THR87 4.8 41.7 1.0 C F:SER84 4.8 36.3 1.0 C F:ILE61 4.8 35.9 1.0 CG1 F:ILE70 4.9 30.7 1.0 CB F:ILE70 4.9 32.9 1.0 C F:CYS85 4.9 36.6 1.0 C F:CYS62 4.9 38.3 1.0 NZ A:LYS514 5.0 50.8 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn99 b:38.7 occ:1.00 SG S:CYS62 2.4 38.5 1.0 SG S:CYS82 2.4 38.2 1.0 SG S:CYS85 2.4 40.6 1.0 SG S:CYS60 2.4 38.2 1.0 CB S:CYS82 3.1 36.6 1.0 CB S:CYS60 3.4 36.4 1.0 CB S:CYS85 3.5 38.8 1.0 CB S:CYS62 3.5 43.1 1.0 CA S:CYS62 3.7 42.5 1.0 N S:CYS85 3.7 39.0 1.0 N S:CYS62 4.1 42.8 1.0 CA S:CYS85 4.2 39.6 1.0 O S:CYS60 4.4 36.5 1.0 C S:CYS60 4.4 37.5 1.0 CA S:CYS60 4.5 37.3 1.0 CA S:CYS82 4.6 37.8 1.0 OG1 S:THR87 4.6 53.2 1.0 C S:SER84 4.6 40.3 1.0 O S:HOH3514 4.7 64.0 1.0 CB S:SER84 4.7 43.2 1.0 OG S:SER84 4.7 41.9 1.0 C S:ILE61 4.8 42.0 1.0 C S:CYS85 4.8 40.8 1.0 CB S:ILE70 4.8 35.7 1.0 CG1 S:ILE70 4.9 35.5 1.0 N S:SER84 4.9 41.3 1.0 CA S:SER84 4.9 40.8 1.0 N S:GLY86 5.0 42.9 1.0

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107