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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6jy4:

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

Copper Binding Sites:

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 6jy4

Go back to Copper Binding Sites List in 6jy4
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 6jy4

Go back to Copper Binding Sites List in 6jy4
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 6jy4

Go back to Copper Binding Sites List in 6jy4
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

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: Sun Dec 13 11:23:27 2020

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