Zinc in PDB 2eij: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eij 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 / 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 (%)	20.6 / 23.4

The structure of Bovine Heart Cytochrome C Oxidase in 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 in the Fully Reduced State (pdb code 2eij). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eij:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the 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 Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn262 b:29.2 occ:0.30 O C:HOH2027 2.1 25.6 0.3 NE2 C:HIS148 2.2 35.9 1.0 NE2 C:HIS232 2.2 25.8 1.0 OE1 C:GLU236 2.5 50.2 1.0 CD C:GLU236 2.9 48.9 1.0 CE1 C:HIS148 3.0 37.3 1.0 CD2 C:HIS232 3.0 23.4 1.0 CG C:GLU236 3.3 40.4 1.0 CD2 C:HIS148 3.3 32.6 1.0 CE1 C:HIS232 3.4 25.9 1.0 OE2 C:GLU236 3.8 50.7 1.0 ND1 C:HIS148 4.2 37.4 1.0 CG C:HIS232 4.3 22.1 1.0 CG C:MET152 4.3 26.9 1.0 CG C:HIS148 4.4 32.1 1.0 ND1 C:HIS232 4.4 25.2 1.0 SD C:MET152 4.4 34.9 1.0 CB C:GLU236 4.7 24.8 1.0 O C:HOH2230 4.7 21.7 1.0

Zinc binding site 2 out of 4 in the 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 Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn99 b:25.3 occ:1.00 SG F:CYS62 2.2 25.4 1.0 SG F:CYS60 2.2 24.1 1.0 SG F:CYS85 2.2 25.2 1.0 SG F:CYS82 2.3 26.0 1.0 CB F:CYS82 3.2 26.0 1.0 CB F:CYS62 3.3 22.1 1.0 CB F:CYS60 3.4 21.1 1.0 CB F:CYS85 3.4 26.0 1.0 CA F:CYS62 3.5 28.0 1.0 N F:CYS85 3.7 27.3 1.0 N F:CYS62 3.9 26.9 1.0 CA F:CYS85 4.1 27.2 1.0 O F:CYS60 4.3 21.2 1.0 C F:CYS60 4.4 22.2 1.0 CB F:SER84 4.5 24.4 1.0 CA F:CYS60 4.5 20.6 1.0 O F:HOH2339 4.5 51.8 1.0 CA F:CYS82 4.7 24.2 1.0 OG F:SER84 4.7 25.5 1.0 C F:SER84 4.7 25.3 1.0 OG1 F:THR87 4.8 37.2 1.0 C F:ILE61 4.8 25.6 1.0 C F:CYS85 4.8 29.0 1.0 C F:CYS62 4.9 32.0 1.0 CG1 F:ILE70 4.9 19.0 1.0 CG2 F:THR87 4.9 32.4 1.0 CB F:ILE70 5.0 20.5 1.0 N F:GLY86 5.0 29.6 1.0 CA F:SER84 5.0 25.4 1.0

Zinc binding site 3 out of 4 in the 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 3 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn1262 b:25.9 occ:0.30 NE2 P:HIS148 2.2 33.3 1.0 O P:HOH3027 2.2 21.4 0.3 NE2 P:HIS232 2.2 20.2 1.0 OE1 P:GLU236 2.5 51.9 1.0 CD2 P:HIS232 3.0 21.9 1.0 CD P:GLU236 3.1 49.8 1.0 CE1 P:HIS148 3.1 32.3 1.0 CD2 P:HIS148 3.2 30.3 1.0 CE1 P:HIS232 3.3 19.8 1.0 CG P:GLU236 3.4 39.7 1.0 OE2 P:GLU236 4.0 52.6 1.0 SD P:MET152 4.2 36.0 1.0 CG P:HIS232 4.2 23.0 1.0 CG P:MET152 4.3 27.6 1.0 ND1 P:HIS148 4.3 31.2 1.0 ND1 P:HIS232 4.4 21.9 1.0 CG P:HIS148 4.4 30.7 1.0 O P:HOH3230 4.8 23.9 1.0 CB P:GLU236 4.8 27.6 1.0

Zinc binding site 4 out of 4 in the 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 4 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:28.8 occ:1.00 SG S:CYS82 2.2 25.0 1.0 SG S:CYS85 2.3 27.2 1.0 SG S:CYS62 2.3 28.8 1.0 SG S:CYS60 2.3 25.5 1.0 CB S:CYS82 3.1 24.5 1.0 CB S:CYS60 3.3 21.6 1.0 CB S:CYS85 3.4 25.1 1.0 CB S:CYS62 3.4 29.5 1.0 CA S:CYS62 3.7 29.7 1.0 N S:CYS85 3.7 25.2 1.0 N S:CYS62 4.0 30.2 1.0 CA S:CYS85 4.1 25.9 1.0 O S:CYS60 4.4 23.0 1.0 C S:CYS60 4.4 23.6 1.0 CA S:CYS60 4.5 23.5 1.0 OG1 S:THR87 4.5 35.3 1.0 CB S:SER84 4.6 28.4 1.0 CA S:CYS82 4.6 26.3 1.0 O S:HOH3339 4.6 62.9 1.0 C S:SER84 4.7 25.8 1.0 C S:CYS85 4.8 27.6 1.0 CB S:ILE70 4.9 22.6 1.0 CG2 S:THR87 4.9 34.1 1.0 C S:ILE61 4.9 28.9 1.0 CG1 S:ILE70 4.9 19.4 1.0 N S:GLY86 4.9 29.3 1.0 OG S:SER84 4.9 32.6 1.0 CA S:SER84 5.0 25.4 1.0 N S:SER84 5.0 27.4 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