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Copper in PDB 5xdx: Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.044, 205.691, 177.797, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.3

Other elements in 5xdx:

The structure of Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution (pdb code 5xdx). 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution, PDB code: 5xdx:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5xdx

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:28.8
occ:1.00
 NE2 A:HIS291 2.0 28.1 1.0
ND1 A:HIS240 2.0 24.8 1.0
NE2 A:HIS290 2.0 28.6 1.0
CD2 A:HIS291 2.9 26.4 1.0
CG A:HIS240 2.9 25.6 1.0
CE1 A:HIS291 2.9 26.4 1.0
CE1 A:HIS290 3.0 28.5 1.0
CD2 A:HIS290 3.0 28.1 1.0
CE1 A:HIS240 3.1 25.7 1.0
CB A:HIS240 3.2 24.2 1.0
CA A:HIS240 3.9 25.1 1.0
ND1 A:HIS291 4.0 26.8 1.0
CG A:HIS291 4.0 26.2 1.0
CD2 A:HIS240 4.1 25.1 1.0
ND1 A:HIS290 4.1 28.4 1.0
NE2 A:HIS240 4.2 26.9 1.0
CG A:HIS290 4.2 27.7 1.0
C1A A:HEA602 4.6 28.1 1.0
NA A:HEA602 4.7 28.4 1.0
CG2 A:VAL243 4.7 25.6 1.0
N A:HIS240 4.7 25.2 1.0
C4A A:HEA602 4.8 28.5 1.0
C2A A:HEA602 4.9 28.2 1.0
CHA A:HEA602 5.0 27.1 1.0

Copper binding site 2 out of 6 in 5xdx

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.9
occ:1.00
 CU1 B:CUA301 0.0 30.9 1.0
ND1 B:HIS161 2.0 28.5 1.0
SD B:MET207 2.3 32.1 1.0
SG B:CYS196 2.3 30.7 1.0
SG B:CYS200 2.4 30.9 1.0
CU2 B:CUA301 2.6 30.2 1.0
CE1 B:HIS161 2.9 29.0 1.0
CE B:MET207 3.1 30.9 1.0
CG B:HIS161 3.1 28.5 1.0
CB B:CYS200 3.3 29.4 1.0
CB B:CYS196 3.4 28.9 1.0
CG B:MET207 3.5 32.6 1.0
CB B:HIS161 3.6 28.7 1.0
O B:GLU198 3.9 31.8 1.0
NE2 B:HIS161 4.1 28.3 1.0
CD2 B:HIS161 4.2 28.2 1.0
CA B:HIS161 4.2 28.1 1.0
ND1 B:HIS204 4.5 30.8 1.0
CD1 B:TRP104 4.6 31.9 1.0
O B:HIS102 4.6 32.9 1.0
CA B:CYS200 4.7 29.9 1.0
CA B:HIS204 4.8 31.4 1.0
O B:LEU160 4.8 28.7 1.0
CA B:CYS196 4.8 28.8 1.0
CB B:MET207 4.8 31.4 1.0
CZ2 B:TRP106 5.0 28.3 1.0

Copper binding site 3 out of 6 in 5xdx

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.2
occ:1.00
 CU2 B:CUA301 0.0 30.2 1.0
ND1 B:HIS204 2.0 30.8 1.0
O B:GLU198 2.1 31.8 1.0
SG B:CYS200 2.3 30.9 1.0
SG B:CYS196 2.3 30.7 1.0
CU1 B:CUA301 2.6 30.9 1.0
CE1 B:HIS204 2.9 30.4 1.0
CG B:HIS204 3.1 30.1 1.0
CB B:CYS196 3.3 28.9 1.0
C B:GLU198 3.3 29.5 1.0
CB B:CYS200 3.4 29.4 1.0
CB B:HIS204 3.5 29.1 1.0
CA B:HIS204 3.5 31.4 1.0
N B:CYS200 3.7 28.6 1.0
O B:HIS204 3.8 29.9 1.0
NE2 B:HIS204 4.0 30.9 1.0
C B:HIS204 4.1 30.5 1.0
N B:GLU198 4.2 28.4 1.0
CD2 B:HIS204 4.2 29.5 1.0
CA B:CYS200 4.2 29.9 1.0
N B:ILE199 4.2 28.6 1.0
CA B:ILE199 4.2 29.3 1.0
C B:CYS196 4.2 28.1 1.0
ND1 B:HIS161 4.2 28.5 1.0
C B:ILE199 4.2 27.7 1.0
O B:CYS196 4.3 27.6 1.0
CA B:CYS196 4.4 28.8 1.0
SD B:MET207 4.4 32.1 1.0
CA B:GLU198 4.4 29.4 1.0
N B:SER197 4.6 26.8 1.0
CG B:MET207 4.7 32.6 1.0
N B:HIS204 4.7 31.9 1.0
CA B:HIS161 4.9 28.1 1.0

Copper binding site 4 out of 6 in 5xdx

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:37.2
occ:1.00
 NE2 N:HIS291 2.0 36.4 1.0
ND1 N:HIS240 2.0 34.2 1.0
NE2 N:HIS290 2.0 34.6 1.0
CD2 N:HIS291 2.9 35.7 1.0
CE1 N:HIS291 2.9 35.6 1.0
CG N:HIS240 2.9 34.4 1.0
CE1 N:HIS290 2.9 34.2 1.0
CE1 N:HIS240 3.0 34.9 1.0
CD2 N:HIS290 3.1 34.4 1.0
CB N:HIS240 3.2 33.5 1.0
CA N:HIS240 4.0 33.2 1.0
ND1 N:HIS291 4.0 36.8 1.0
CG N:HIS291 4.0 36.3 1.0
ND1 N:HIS290 4.1 33.8 1.0
CD2 N:HIS240 4.1 33.7 1.0
NE2 N:HIS240 4.2 34.7 1.0
CG N:HIS290 4.2 34.8 1.0
C1A N:HEA602 4.6 37.0 1.0
NA N:HEA602 4.7 37.5 1.0
CG2 N:VAL243 4.7 32.0 1.0
N N:HIS240 4.7 32.5 1.0
C4A N:HEA602 4.8 37.0 1.0
C2A N:HEA602 4.9 37.1 1.0
CHA N:HEA602 5.0 35.8 1.0

Copper binding site 5 out of 6 in 5xdx

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu303

b:43.2
occ:1.00
 CU1 O:CUA303 0.0 43.2 1.0
ND1 O:HIS161 2.0 40.4 1.0
SD O:MET207 2.3 45.5 1.0
SG O:CYS196 2.3 41.8 1.0
SG O:CYS200 2.3 43.7 1.0
CU2 O:CUA303 2.7 42.5 1.0
CE1 O:HIS161 2.8 40.7 1.0
CE O:MET207 3.0 43.8 1.0
CG O:HIS161 3.1 40.2 1.0
CB O:CYS200 3.3 42.6 1.0
CB O:CYS196 3.4 42.8 1.0
CG O:MET207 3.5 45.3 1.0
CB O:HIS161 3.6 40.5 1.0
O O:GLU198 4.0 46.0 1.0
NE2 O:HIS161 4.0 40.5 1.0
CD2 O:HIS161 4.2 40.4 1.0
CA O:HIS161 4.3 40.7 1.0
CD1 O:TRP104 4.4 48.2 1.0
O O:HIS102 4.5 45.8 1.0
ND1 O:HIS204 4.6 43.8 1.0
CA O:CYS200 4.7 43.0 1.0
O O:LEU160 4.8 40.8 1.0
CA O:HIS204 4.8 46.0 1.0
CB O:MET207 4.8 46.4 1.0
CA O:CYS196 4.8 42.4 1.0

Copper binding site 6 out of 6 in 5xdx

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Reduced State with pH 7.3 at 1.99 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 the Reduced State with pH 7.3 at 1.99 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu303

b:42.5
occ:1.00
 CU2 O:CUA303 0.0 42.5 1.0
ND1 O:HIS204 2.0 43.8 1.0
O O:GLU198 2.0 46.0 1.0
SG O:CYS200 2.3 43.7 1.0
SG O:CYS196 2.3 41.8 1.0
CU1 O:CUA303 2.7 43.2 1.0
CE1 O:HIS204 2.9 43.0 1.0
CG O:HIS204 3.1 43.7 1.0
C O:GLU198 3.3 42.7 1.0
CB O:CYS196 3.3 42.8 1.0
CB O:CYS200 3.4 42.6 1.0
CA O:HIS204 3.5 46.0 1.0
CB O:HIS204 3.5 44.3 1.0
N O:CYS200 3.6 43.5 1.0
O O:HIS204 3.8 45.8 1.0
NE2 O:HIS204 4.0 43.0 1.0
N O:GLU198 4.1 40.7 1.0
N O:ILE199 4.1 42.1 1.0
CA O:ILE199 4.1 43.1 1.0
C O:HIS204 4.1 46.3 1.0
CA O:CYS200 4.1 43.0 1.0
CD2 O:HIS204 4.1 43.3 1.0
C O:ILE199 4.2 42.7 1.0
ND1 O:HIS161 4.2 40.4 1.0
C O:CYS196 4.2 41.4 1.0
CA O:GLU198 4.3 41.8 1.0
O O:CYS196 4.3 40.6 1.0
CA O:CYS196 4.4 42.4 1.0
SD O:MET207 4.5 45.5 1.0
N O:SER197 4.6 40.9 1.0
N O:HIS204 4.7 47.0 1.0
CG O:MET207 4.7 45.3 1.0
CA O:HIS161 4.9 40.7 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr F Struct V. 74 92 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29400318
DOI: 10.1107/S2053230X17018532
Page generated: Wed Jul 31 05:21:47 2024

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