Copper in PDB 6jy3: Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

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

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3 was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.529, 152.131, 174.083, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.2

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Iron	(Fe)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Copper atom in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 6jy3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 6jy3:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:26.7 occ:1.00 NE2 A:HIS291 2.0 25.0 1.0 ND1 A:HIS240 2.0 26.0 1.0 NE2 A:HIS290 2.0 27.1 1.0 O2 A:PER607 2.2 33.6 1.0 O1 A:PER607 2.7 25.1 1.0 CE1 A:HIS291 2.9 25.6 1.0 CE1 A:HIS290 3.0 27.1 1.0 CE1 A:HIS240 3.0 27.2 1.0 CD2 A:HIS291 3.0 28.0 1.0 CG A:HIS240 3.0 26.3 1.0 CD2 A:HIS290 3.1 24.1 1.0 CB A:HIS240 3.3 22.3 1.0 CA A:HIS240 3.9 24.8 1.0 ND1 A:HIS291 4.0 26.2 1.0 CG A:HIS291 4.1 23.7 1.0 ND1 A:HIS290 4.1 28.4 1.0 NE2 A:HIS240 4.1 29.5 1.0 CD2 A:HIS240 4.1 26.0 1.0 CG A:HIS290 4.2 24.1 1.0 NA A:HEA602 4.5 25.0 1.0 C1A A:HEA602 4.6 25.6 1.0 C4A A:HEA602 4.7 25.8 1.0 N A:HIS240 4.7 25.2 1.0 C2A A:HEA602 4.8 24.7 1.0 FE A:HEA602 4.8 26.2 1.0 CG2 A:VAL243 4.9 26.1 1.0 C3A A:HEA602 4.9 29.1 1.0 CHA A:HEA602 5.0 22.6 1.0

Copper binding site 2 out of 3 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:31.3 occ:1.00 CU1 B:CUA302 0.0 31.3 1.0 ND1 B:HIS161 2.1 28.4 1.0 SG B:CYS196 2.3 29.8 1.0 SG B:CYS200 2.3 31.9 1.0 SD B:MET207 2.3 32.7 1.0 CU2 B:CUA302 2.5 31.0 1.0 CE1 B:HIS161 2.9 31.0 1.0 CG B:HIS161 3.2 29.7 1.0 CE B:MET207 3.2 32.5 1.0 CB B:CYS200 3.3 29.6 1.0 CB B:CYS196 3.4 33.7 1.0 CG B:MET207 3.5 35.3 1.0 CB B:HIS161 3.6 30.6 1.0 O B:GLU198 3.9 31.5 1.0 NE2 B:HIS161 4.1 32.1 1.0 CA B:HIS161 4.2 32.0 1.0 CD2 B:HIS161 4.2 35.4 1.0 ND1 B:HIS204 4.5 33.0 1.0 O B:HIS102 4.6 35.6 1.0 CA B:CYS200 4.7 28.5 1.0 CA B:HIS204 4.7 29.6 1.0 CD1 B:TRP104 4.7 33.4 1.0 O B:LEU160 4.7 29.4 1.0 CA B:CYS196 4.8 32.2 1.0 CB B:MET207 4.9 35.6 1.0 O B:HIS204 4.9 33.2 1.0

Copper binding site 3 out of 3 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:31.0 occ:1.00 CU2 B:CUA302 0.0 31.0 1.0 ND1 B:HIS204 2.0 33.0 1.0 O B:GLU198 2.2 31.5 1.0 SG B:CYS196 2.3 29.8 1.0 SG B:CYS200 2.3 31.9 1.0 CU1 B:CUA302 2.5 31.3 1.0 CE1 B:HIS204 2.9 32.0 1.0 CG B:HIS204 3.1 31.2 1.0 CB B:CYS196 3.4 33.7 1.0 CB B:CYS200 3.4 29.6 1.0 C B:GLU198 3.4 25.3 1.0 CB B:HIS204 3.5 28.1 1.0 CA B:HIS204 3.6 29.6 1.0 N B:CYS200 3.7 31.2 1.0 O B:HIS204 3.9 33.2 1.0 NE2 B:HIS204 4.1 31.7 1.0 CA B:CYS200 4.1 28.5 1.0 CD2 B:HIS204 4.1 27.3 1.0 N B:GLU198 4.1 28.0 1.0 N B:ILE199 4.2 29.3 1.0 C B:HIS204 4.2 30.0 1.0 C B:ILE199 4.2 32.2 1.0 ND1 B:HIS161 4.2 28.4 1.0 CA B:ILE199 4.2 28.7 1.0 O B:CYS196 4.2 29.4 1.0 C B:CYS196 4.3 31.2 1.0 SD B:MET207 4.3 32.7 1.0 CA B:GLU198 4.4 29.2 1.0 CA B:CYS196 4.4 32.2 1.0 N B:SER197 4.7 33.9 1.0 CG B:MET207 4.7 35.3 1.0 N B:HIS204 4.9 33.7 1.0 CA B:HIS161 4.9 32.0 1.0 CB B:HIS161 5.0 30.6 1.0

K.Shinzawa-Itoh, T.Sugimura, T.Misaki, Y.Tadehara, S.Yamamoto, M.Hanada, N.Yano, T.Nakagawa, S.Uene, T.Yamada, H.Aoyama, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. Monomeric Structure of An Active Form of Bovine Cytochromecoxidase. Proc.Natl.Acad.Sci.Usa V. 116 19945 2019.
ISSN: ESSN 1091-6490
PubMed: 31533957
DOI: 10.1073/PNAS.1907183116