Copper in PDB 6jy4: Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 6jy4 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.395, 152.395, 174.040, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 20.5

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State (pdb code 6jy4). 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 Reduced State, PDB code: 6jy4:
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 Reduced 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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:29.1 occ:1.00 NE2 A:HIS291 1.9 30.4 1.0 ND1 A:HIS240 1.9 27.1 1.0 NE2 A:HIS290 2.1 29.6 1.0 CD2 A:HIS291 2.9 32.5 1.0 CG A:HIS240 2.9 26.7 1.0 CE1 A:HIS291 2.9 29.1 1.0 CE1 A:HIS240 3.0 26.2 1.0 CE1 A:HIS290 3.0 27.6 1.0 CD2 A:HIS290 3.1 25.4 1.0 CB A:HIS240 3.2 25.2 1.0 CA A:HIS240 3.9 28.9 1.0 ND1 A:HIS291 4.0 30.7 1.0 CG A:HIS291 4.0 31.4 1.0 CD2 A:HIS240 4.1 31.7 1.0 NE2 A:HIS240 4.1 33.1 1.0 ND1 A:HIS290 4.2 31.1 1.0 CG A:HIS290 4.2 24.4 1.0 C1A A:HEA602 4.5 30.9 1.0 NA A:HEA602 4.6 26.7 1.0 CG2 A:VAL243 4.7 30.0 1.0 N A:HIS240 4.7 28.7 1.0 C4A A:HEA602 4.8 32.9 1.0 C2A A:HEA602 4.8 27.1 1.0 CHA A:HEA602 4.9 26.7 1.0 CG2 A:VAL287 4.9 27.0 1.0 C3A A:HEA602 5.0 31.7 1.0

Copper binding site 2 out of 3 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:34.9 occ:1.00 CU1 B:CUA302 0.0 34.9 1.0 ND1 B:HIS161 2.1 33.5 1.0 SD B:MET207 2.3 35.4 1.0 SG B:CYS196 2.3 32.9 1.0 SG B:CYS200 2.3 36.2 1.0 CU2 B:CUA302 2.5 34.5 1.0 CE1 B:HIS161 2.9 36.6 1.0 CE B:MET207 3.1 30.9 1.0 CG B:HIS161 3.2 35.5 1.0 CB B:CYS200 3.3 33.1 1.0 CB B:CYS196 3.4 38.3 1.0 CG B:MET207 3.5 34.4 1.0 CB B:HIS161 3.6 32.6 1.0 O B:GLU198 3.9 35.3 1.0 NE2 B:HIS161 4.1 36.8 1.0 CA B:HIS161 4.2 36.2 1.0 CD2 B:HIS161 4.2 42.2 1.0 ND1 B:HIS204 4.5 35.1 1.0 CD1 B:TRP104 4.5 37.0 1.0 O B:HIS102 4.6 38.4 1.0 CA B:HIS204 4.7 33.3 1.0 CA B:CYS200 4.7 35.2 1.0 O B:LEU160 4.8 30.5 1.0 CA B:CYS196 4.9 34.2 1.0 CB B:MET207 4.9 43.7 1.0 O B:HIS204 5.0 34.4 1.0

Copper binding site 3 out of 3 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:34.5 occ:1.00 CU2 B:CUA302 0.0 34.5 1.0 ND1 B:HIS204 2.0 35.1 1.0 O B:GLU198 2.2 35.3 1.0 SG B:CYS196 2.2 32.9 1.0 SG B:CYS200 2.4 36.2 1.0 CU1 B:CUA302 2.5 34.9 1.0 CE1 B:HIS204 2.9 38.3 1.0 CG B:HIS204 3.1 36.7 1.0 CB B:CYS196 3.3 38.3 1.0 CB B:CYS200 3.4 33.1 1.0 C B:GLU198 3.4 29.1 1.0 CB B:HIS204 3.5 29.7 1.0 CA B:HIS204 3.5 33.3 1.0 N B:CYS200 3.7 34.0 1.0 O B:HIS204 3.9 34.4 1.0 NE2 B:HIS204 4.0 38.3 1.0 CD2 B:HIS204 4.1 32.6 1.0 N B:GLU198 4.2 31.3 1.0 C B:HIS204 4.2 33.0 1.0 CA B:CYS200 4.2 35.2 1.0 ND1 B:HIS161 4.2 33.5 1.0 C B:CYS196 4.2 35.2 1.0 CA B:ILE199 4.2 30.4 1.0 N B:ILE199 4.2 32.2 1.0 O B:CYS196 4.3 32.0 1.0 C B:ILE199 4.3 34.5 1.0 SD B:MET207 4.3 35.4 1.0 CA B:CYS196 4.3 34.2 1.0 CA B:GLU198 4.4 35.1 1.0 N B:SER197 4.6 32.2 1.0 CG B:MET207 4.7 34.4 1.0 N B:HIS204 4.8 35.2 1.0 CA B:HIS161 4.9 36.2 1.0 CB B:HIS161 5.0 32.6 1.0 CE1 B:HIS161 5.0 36.6 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