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Copper in PDB 6juw: Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw was solved by A.Shimada, K.Muramoto, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.217, 204.650, 177.397, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.8

Other elements in 6juw:

The structure of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution (pdb code 6juw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution, PDB code: 6juw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6juw

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:29.6
occ:1.00
 NE2 A:HIS291 2.0 27.0 1.0
NE2 A:HIS290 2.0 26.9 1.0
O A:HOH803 2.1 25.1 0.7
O A:HOH803 2.2 18.1 0.1
ND1 A:HIS240 2.2 26.9 1.0
O A:HOH711 2.5 11.7 0.1
CE1 A:HIS291 2.8 28.6 1.0
CE1 A:HIS290 3.0 26.9 1.0
CD2 A:HIS291 3.0 27.0 1.0
O A:HOH711 3.0 23.0 0.7
CG A:HIS240 3.1 29.4 1.0
CD2 A:HIS290 3.1 27.4 1.0
CE1 A:HIS240 3.2 27.3 1.0
CB A:HIS240 3.4 21.9 1.0
CA A:HIS240 3.9 24.6 1.0
ND1 A:HIS291 4.0 26.7 1.0
CG A:HIS291 4.1 21.9 1.0
ND1 A:HIS290 4.1 26.7 1.0
CG A:HIS290 4.2 25.4 1.0
CD2 A:HIS240 4.2 24.2 1.0
NE2 A:HIS240 4.2 23.8 1.0
NA A:HEA602 4.3 23.3 1.0
C1A A:HEA602 4.3 26.4 1.0
C4A A:HEA602 4.6 26.3 1.0
FE A:HEA602 4.6 28.1 1.0
CHA A:HEA602 4.7 23.8 1.0
CG2 A:VAL243 4.7 26.2 1.0
N A:HIS240 4.7 26.1 1.0
C2A A:HEA602 4.7 27.6 1.0
ND A:HEA602 4.8 28.0 1.0
C3A A:HEA602 4.9 27.2 1.0
C4D A:HEA602 4.9 26.5 1.0
C A:HIS240 5.0 22.7 1.0

Copper binding site 2 out of 6 in 6juw

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:29.3
occ:1.00
 CU1 B:CUA301 0.0 29.3 1.0
ND1 B:HIS161 2.1 28.3 1.0
SG B:CYS196 2.3 28.2 1.0
SD B:MET207 2.4 29.9 1.0
SG B:CYS200 2.4 29.1 1.0
CU2 B:CUA301 2.5 28.2 1.0
CE1 B:HIS161 2.9 24.8 1.0
CG B:HIS161 3.2 27.4 1.0
CE B:MET207 3.2 28.2 1.0
CB B:CYS200 3.3 24.3 1.0
CB B:CYS196 3.3 33.1 1.0
CG B:MET207 3.4 26.6 1.0
CB B:HIS161 3.6 26.9 1.0
NE2 B:HIS161 4.1 27.0 1.0
O B:GLU198 4.2 29.4 1.0
CD2 B:HIS161 4.2 25.1 1.0
CA B:HIS161 4.2 24.6 1.0
ND1 B:HIS204 4.5 26.5 1.0
O B:HIS102 4.7 28.8 1.0
CA B:HIS204 4.7 26.1 1.0
CD1 B:TRP104 4.7 26.8 1.0
CA B:CYS196 4.7 30.0 1.0
CA B:CYS200 4.7 28.6 1.0
O B:LEU160 4.8 29.7 1.0
CB B:MET207 4.9 28.5 1.0
O B:HIS204 5.0 29.2 1.0

Copper binding site 3 out of 6 in 6juw

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:28.2
occ:1.00
 CU2 B:CUA301 0.0 28.2 1.0
ND1 B:HIS204 2.0 26.5 1.0
SG B:CYS200 2.3 29.1 1.0
SG B:CYS196 2.3 28.2 1.0
CU1 B:CUA301 2.5 29.3 1.0
O B:GLU198 2.6 29.4 1.0
CE1 B:HIS204 3.0 29.1 1.0
CG B:HIS204 3.1 29.3 1.0
CB B:CYS196 3.3 33.1 1.0
CB B:CYS200 3.4 24.3 1.0
CB B:HIS204 3.4 25.2 1.0
CA B:HIS204 3.6 26.1 1.0
C B:GLU198 3.6 27.0 1.0
N B:CYS200 3.7 26.9 1.0
O B:HIS204 3.8 29.2 1.0
NE2 B:HIS204 4.1 27.5 1.0
C B:HIS204 4.1 29.3 1.0
CD2 B:HIS204 4.1 26.9 1.0
CA B:CYS200 4.2 28.6 1.0
C B:ILE199 4.2 26.9 1.0
N B:GLU198 4.2 26.9 1.0
ND1 B:HIS161 4.2 28.3 1.0
O B:CYS196 4.2 26.2 1.0
C B:CYS196 4.2 30.7 1.0
CA B:ILE199 4.3 28.4 1.0
SD B:MET207 4.3 29.9 1.0
N B:ILE199 4.3 25.4 1.0
CA B:CYS196 4.4 30.0 1.0
CG B:MET207 4.5 26.6 1.0
CA B:GLU198 4.5 29.6 1.0
N B:SER197 4.7 29.0 1.0
N B:HIS204 4.9 28.8 1.0
CA B:HIS161 5.0 24.6 1.0

Copper binding site 4 out of 6 in 6juw

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:30.6
occ:1.00
 NE2 N:HIS291 2.0 25.0 1.0
NE2 N:HIS290 2.1 30.6 1.0
O N:HOH843 2.1 31.4 0.8
O N:HOH843 2.2 34.1 0.1
ND1 N:HIS240 2.2 27.5 1.0
O N:HOH717 2.5 13.7 0.1
CE1 N:HIS291 2.9 27.8 1.0
CD2 N:HIS291 3.0 25.5 1.0
CE1 N:HIS290 3.0 30.1 1.0
CD2 N:HIS290 3.1 29.8 1.0
CG N:HIS240 3.1 29.2 1.0
CE1 N:HIS240 3.1 28.5 1.0
O N:HOH717 3.1 28.8 0.8
CB N:HIS240 3.3 26.1 1.0
CA N:HIS240 3.9 24.7 1.0
ND1 N:HIS291 4.0 28.6 1.0
CG N:HIS291 4.1 29.4 1.0
ND1 N:HIS290 4.2 26.3 1.0
NE2 N:HIS240 4.2 24.9 1.0
CG N:HIS290 4.2 26.2 1.0
CD2 N:HIS240 4.2 22.9 1.0
NA N:HEA602 4.3 28.8 1.0
C1A N:HEA602 4.3 30.8 1.0
C4A N:HEA602 4.5 26.5 1.0
FE N:HEA602 4.6 29.4 1.0
C2A N:HEA602 4.7 26.8 1.0
CG2 N:VAL243 4.7 28.1 1.0
CHA N:HEA602 4.7 28.2 1.0
C3A N:HEA602 4.8 26.9 1.0
N N:HIS240 4.8 24.6 1.0
ND N:HEA602 4.8 29.0 1.0
C4D N:HEA602 4.9 28.0 1.0
O N:HOH776 5.0 36.0 0.8

Copper binding site 5 out of 6 in 6juw

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:33.4
occ:1.00
 CU1 O:CUA301 0.0 33.4 1.0
ND1 O:HIS161 2.1 30.9 1.0
SG O:CYS200 2.3 33.6 1.0
SG O:CYS196 2.3 33.5 1.0
SD O:MET207 2.4 34.1 1.0
CU2 O:CUA301 2.5 32.7 1.0
CE1 O:HIS161 2.9 29.7 1.0
CE O:MET207 3.2 33.7 1.0
CG O:HIS161 3.2 31.6 1.0
CB O:CYS200 3.2 29.8 1.0
CB O:CYS196 3.4 35.0 1.0
CG O:MET207 3.5 30.2 1.0
CB O:HIS161 3.7 33.0 1.0
NE2 O:HIS161 4.1 31.2 1.0
O O:GLU198 4.2 30.8 1.0
CD2 O:HIS161 4.3 31.4 1.0
CA O:HIS161 4.3 30.2 1.0
ND1 O:HIS204 4.4 29.3 1.0
CD1 O:TRP104 4.6 35.3 1.0
CA O:CYS200 4.6 33.1 1.0
O O:HIS102 4.7 33.8 1.0
O O:LEU160 4.7 31.6 1.0
CA O:HIS204 4.7 32.7 1.0
CA O:CYS196 4.8 32.5 1.0
CB O:MET207 4.9 33.4 1.0
N O:CYS200 4.9 32.1 1.0
O O:HIS204 4.9 32.7 1.0

Copper binding site 6 out of 6 in 6juw

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Bovine Heart Cytochrome C Oxidase in Catalitic Intermediates at 1.80 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:32.7
occ:1.00
 CU2 O:CUA301 0.0 32.7 1.0
ND1 O:HIS204 2.0 29.3 1.0
SG O:CYS200 2.3 33.6 1.0
SG O:CYS196 2.3 33.5 1.0
CU1 O:CUA301 2.5 33.4 1.0
O O:GLU198 2.5 30.8 1.0
CE1 O:HIS204 2.9 32.2 1.0
CG O:HIS204 3.0 34.1 1.0
CB O:CYS196 3.3 35.0 1.0
CB O:CYS200 3.3 29.8 1.0
CB O:HIS204 3.5 32.4 1.0
C O:GLU198 3.6 34.1 1.0
N O:CYS200 3.6 32.1 1.0
CA O:HIS204 3.6 32.7 1.0
O O:HIS204 3.8 32.7 1.0
NE2 O:HIS204 4.0 32.6 1.0
CA O:CYS200 4.1 33.1 1.0
CD2 O:HIS204 4.1 30.6 1.0
N O:GLU198 4.1 31.6 1.0
C O:HIS204 4.2 35.3 1.0
C O:ILE199 4.2 32.7 1.0
C O:CYS196 4.2 35.2 1.0
O O:CYS196 4.2 31.9 1.0
ND1 O:HIS161 4.2 30.9 1.0
CA O:ILE199 4.2 29.3 1.0
N O:ILE199 4.3 29.5 1.0
SD O:MET207 4.3 34.1 1.0
CA O:CYS196 4.4 32.5 1.0
CA O:GLU198 4.5 30.8 1.0
CG O:MET207 4.6 30.2 1.0
N O:SER197 4.6 31.6 1.0
N O:HIS204 4.8 33.2 1.0
CA O:HIS161 5.0 30.2 1.0
C O:CYS200 5.0 31.1 1.0

Reference:

A.Shimada, Y.Etoh, R.Kitoh-Fujisawa, A.Sasaki, K.Shinzawa-Itoh, T.Hiromoto, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structures of Catalytic Intermediates of Cytochromecoxidase Provide Insights Into Its O2-Activation and Unidirectional Proton-Pump Mechanisms. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32165497
DOI: 10.1074/JBC.RA119.009596
Page generated: Wed Jul 31 06:24:59 2024

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