Zinc in PDB 2dys: Bovine Heart Cytochrome C Oxidase Modified By Dccd

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.130, 207.232, 178.242, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd 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 Modified By Dccd (pdb code 2dys). 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 Modified By Dccd, PDB code: 2dys:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:32.8 occ:1.00 SG F:CYS82 2.2 25.1 1.0 SG F:CYS60 2.2 29.8 1.0 SG F:CYS85 2.3 31.4 1.0 SG F:CYS62 2.3 28.2 1.0 CB F:CYS82 3.1 28.0 1.0 CB F:CYS62 3.4 21.2 1.0 CB F:CYS60 3.4 26.5 1.0 CB F:CYS85 3.4 26.3 1.0 CA F:CYS62 3.5 30.1 1.0 N F:CYS85 3.6 33.1 1.0 N F:CYS62 3.8 29.0 1.0 CA F:CYS85 4.1 29.3 1.0 CB F:SER84 4.4 36.8 1.0 O F:HOH226 4.4 66.8 1.0 O F:CYS60 4.4 29.2 1.0 C F:CYS60 4.4 27.1 1.0 CA F:CYS60 4.5 23.5 1.0 CA F:CYS82 4.6 24.7 1.0 CG1 F:ILE70 4.6 27.8 1.0 OG F:SER84 4.7 41.8 1.0 C F:SER84 4.7 35.5 1.0 OG1 F:THR87 4.7 41.9 1.0 C F:ILE61 4.8 30.4 1.0 C F:CYS85 4.8 32.9 1.0 CB F:ILE70 4.9 28.2 1.0 C F:CYS62 4.9 36.5 1.0 CA F:SER84 4.9 35.7 1.0 N F:GLY86 5.0 32.3 1.0 N F:ILE61 5.0 29.4 1.0

Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn101 b:34.9 occ:1.00 SG S:CYS82 2.2 29.6 1.0 SG S:CYS85 2.2 31.0 1.0 SG S:CYS60 2.3 35.4 1.0 SG S:CYS62 2.3 36.1 1.0 CB S:CYS82 2.9 32.7 1.0 CB S:CYS60 3.3 29.5 1.0 CB S:CYS85 3.4 29.2 1.0 CB S:CYS62 3.4 27.2 1.0 N S:CYS85 3.6 29.8 1.0 CA S:CYS62 3.7 35.8 1.0 N S:CYS62 4.0 35.1 1.0 CA S:CYS85 4.1 27.9 1.0 CA S:CYS82 4.4 34.1 1.0 O S:HOH225 4.4 69.9 1.0 O S:CYS60 4.4 33.5 1.0 C S:CYS60 4.5 30.9 1.0 OG1 S:THR87 4.5 42.2 1.0 CA S:CYS60 4.5 31.5 1.0 CB S:SER84 4.5 27.9 1.0 CG1 S:ILE70 4.6 24.6 1.0 C S:SER84 4.6 31.6 1.0 OG S:SER84 4.7 44.3 1.0 CB S:ILE70 4.7 26.5 1.0 C S:CYS85 4.8 31.7 1.0 N S:GLY86 4.8 35.0 1.0 N S:SER84 4.9 35.5 1.0 CA S:SER84 4.9 31.1 1.0 C S:CYS82 4.9 31.4 1.0 C S:ILE61 5.0 36.6 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618