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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6jy3:

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

Copper Binding Sites:

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 6jy3

Go back to Copper Binding Sites List in 6jy3
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 6jy3

Go back to Copper Binding Sites List in 6jy3
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 6jy3

Go back to Copper Binding Sites List in 6jy3
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

Reference:

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
Page generated: Mon Jul 14 06:23:20 2025

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