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Copper in PDB 5iy5: Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

Enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

All present enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5 was solved by S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.290, 183.872, 148.929, 90.00, 102.12, 90.00
R / Rfree (%) 16.7 / 20.7

Other elements in 5iy5:

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution (pdb code 5iy5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5iy5

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Copper binding site 1 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:29.8
occ:1.00
 NE2 A:HIS291 1.9 27.3 1.0
ND1 A:HIS240 2.0 29.2 1.0
NE2 A:HIS290 2.1 27.9 1.0
O2 A:PER606 2.4 54.0 1.0
CE1 A:HIS291 2.9 22.9 1.0
CD2 A:HIS291 2.9 24.8 1.0
O1 A:PER606 2.9 40.3 1.0
CG A:HIS240 3.0 27.4 1.0
CE1 A:HIS290 3.0 28.6 1.0
CE1 A:HIS240 3.0 23.0 1.0
CD2 A:HIS290 3.1 27.1 1.0
CB A:HIS240 3.3 24.4 1.0
CA A:HIS240 3.9 24.7 1.0
ND1 A:HIS291 4.0 22.5 1.0
CG A:HIS291 4.0 26.2 1.0
CD2 A:HIS240 4.2 26.2 1.0
ND1 A:HIS290 4.2 28.5 1.0
NE2 A:HIS240 4.2 28.8 1.0
CG A:HIS290 4.2 29.2 1.0
C1A A:HEA605 4.5 26.1 1.0
NA A:HEA605 4.5 24.3 1.0
CG2 A:VAL243 4.6 23.2 1.0
C4A A:HEA605 4.7 23.6 1.0
N A:HIS240 4.8 24.8 1.0
C2A A:HEA605 4.8 25.8 1.0
FE A:HEA605 4.9 28.5 1.0
CHA A:HEA605 4.9 25.9 1.0
C3A A:HEA605 4.9 23.9 1.0

Copper binding site 2 out of 6 in 5iy5

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Copper binding site 2 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:29.2
occ:1.00
 CU1 B:CUA302 0.0 29.2 1.0
ND1 B:HIS161 2.1 28.4 1.0
SG B:CYS196 2.3 27.0 1.0
SG B:CYS200 2.4 28.9 1.0
SD B:MET207 2.4 30.6 1.0
CU2 B:CUA302 2.5 27.5 1.0
CE1 B:HIS161 3.0 29.5 1.0
CE B:MET207 3.1 28.3 1.0
CG B:HIS161 3.2 25.6 1.0
CB B:CYS200 3.3 26.0 1.0
CB B:CYS196 3.4 27.2 1.0
CG B:MET207 3.5 29.1 1.0
CB B:HIS161 3.6 25.7 1.0
O B:GLU198 3.9 26.9 1.0
CA B:HIS161 4.2 29.6 1.0
NE2 B:HIS161 4.2 27.9 1.0
CD2 B:HIS161 4.3 27.5 1.0
ND1 B:HIS204 4.4 24.5 1.0
CA B:CYS200 4.7 28.2 1.0
CA B:HIS204 4.7 31.0 1.0
CD1 B:TRP104 4.7 30.0 1.0
O B:HIS102 4.7 32.2 1.0
CA B:CYS196 4.8 27.4 1.0
O B:LEU160 4.8 28.2 1.0
O B:HIS204 4.8 32.2 1.0
CB B:MET207 4.9 29.8 1.0
N B:CYS200 5.0 25.2 1.0

Copper binding site 3 out of 6 in 5iy5

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Copper binding site 3 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:27.5
occ:1.00
 CU2 B:CUA302 0.0 27.5 1.0
ND1 B:HIS204 2.0 24.5 1.0
O B:GLU198 2.3 26.9 1.0
SG B:CYS196 2.3 27.0 1.0
SG B:CYS200 2.3 28.9 1.0
CU1 B:CUA302 2.5 29.2 1.0
CE1 B:HIS204 2.8 25.6 1.0
CG B:HIS204 3.1 28.9 1.0
CB B:CYS196 3.3 27.2 1.0
CB B:CYS200 3.3 26.0 1.0
C B:GLU198 3.4 26.5 1.0
CA B:HIS204 3.5 31.0 1.0
CB B:HIS204 3.6 28.6 1.0
O B:HIS204 3.7 32.2 1.0
N B:CYS200 3.7 25.2 1.0
NE2 B:HIS204 4.0 28.6 1.0
N B:GLU198 4.1 26.5 1.0
C B:HIS204 4.1 32.3 1.0
CA B:CYS200 4.1 28.2 1.0
CD2 B:HIS204 4.2 27.0 1.0
ND1 B:HIS161 4.2 28.4 1.0
C B:CYS196 4.2 28.9 1.0
N B:ILE199 4.2 27.0 1.0
CA B:ILE199 4.2 26.6 1.0
C B:ILE199 4.2 25.8 1.0
O B:CYS196 4.3 28.6 1.0
SD B:MET207 4.3 30.6 1.0
CA B:CYS196 4.4 27.4 1.0
CA B:GLU198 4.4 27.7 1.0
N B:SER197 4.6 25.9 1.0
CG B:MET207 4.6 29.1 1.0
N B:HIS204 4.8 31.1 1.0
CA B:HIS161 4.9 29.6 1.0
C B:CYS200 5.0 27.5 1.0

Copper binding site 4 out of 6 in 5iy5

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Copper binding site 4 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu602

b:35.9
occ:1.00
 NE2 N:HIS291 2.0 39.3 1.0
NE2 N:HIS290 2.0 38.2 1.0
ND1 N:HIS240 2.1 31.0 1.0
O2 N:PER607 2.3 48.7 1.0
O1 N:PER607 2.8 36.8 1.0
CE1 N:HIS291 2.9 36.6 1.0
CD2 N:HIS291 3.0 31.5 1.0
CE1 N:HIS290 3.0 39.0 1.0
CD2 N:HIS290 3.0 35.1 1.0
CE1 N:HIS240 3.0 30.4 1.0
CG N:HIS240 3.0 32.1 1.0
CB N:HIS240 3.3 29.7 1.0
CA N:HIS240 3.9 28.9 1.0
ND1 N:HIS291 4.0 38.6 1.0
CG N:HIS291 4.1 38.5 1.0
ND1 N:HIS290 4.2 38.0 1.0
NE2 N:HIS240 4.2 36.9 1.0
CD2 N:HIS240 4.2 30.1 1.0
CG N:HIS290 4.2 34.4 1.0
C1A N:HEA606 4.5 32.1 1.0
NA N:HEA606 4.5 34.8 1.0
C4A N:HEA606 4.6 33.4 1.0
CG2 N:VAL243 4.7 27.9 1.0
N N:HIS240 4.8 30.7 1.0
FE N:HEA606 4.8 35.0 1.0
C2A N:HEA606 4.8 35.2 1.0
C3A N:HEA606 4.9 33.6 1.0
CHA N:HEA606 5.0 31.3 1.0

Copper binding site 5 out of 6 in 5iy5

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Copper binding site 5 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:43.3
occ:1.00
 CU1 O:CUA301 0.0 43.3 1.0
SG O:CYS200 2.0 46.2 1.0
SG O:CYS196 2.0 43.5 1.0
ND1 O:HIS161 2.1 41.2 1.0
SD O:MET207 2.3 42.4 1.0
CU2 O:CUA301 2.8 43.0 1.0
CE1 O:HIS161 3.0 41.7 1.0
CB O:CYS200 3.1 54.0 1.0
CG O:HIS161 3.1 42.4 1.0
CE O:MET207 3.1 44.8 1.0
CB O:CYS196 3.2 46.2 1.0
CB O:HIS161 3.5 39.7 1.0
CG O:MET207 3.5 39.7 1.0
O O:GLU198 4.1 43.2 1.0
CA O:HIS161 4.1 39.3 1.0
NE2 O:HIS161 4.1 45.9 1.0
CD2 O:HIS161 4.2 42.3 1.0
CA O:CYS200 4.6 46.7 1.0
CD1 O:TRP104 4.6 39.1 1.0
CA O:CYS196 4.6 45.8 1.0
O O:HIS102 4.6 41.7 1.0
O O:LEU160 4.7 42.3 1.0
ND1 O:HIS204 4.8 42.3 1.0
CA O:HIS204 4.8 40.6 1.0
CB O:MET207 4.9 43.9 1.0
CZ2 O:TRP106 5.0 43.9 1.0

Copper binding site 6 out of 6 in 5iy5

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Copper binding site 6 out of 6 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:43.0
occ:1.00
 CU2 O:CUA301 0.0 43.0 1.0
SG O:CYS200 2.0 46.2 1.0
SG O:CYS196 2.0 43.5 1.0
ND1 O:HIS204 2.0 42.3 1.0
O O:GLU198 2.1 43.2 1.0
CU1 O:CUA301 2.8 43.3 1.0
CE1 O:HIS204 2.8 37.6 1.0
CB O:CYS196 2.9 46.2 1.0
CG O:HIS204 3.0 43.9 1.0
CB O:CYS200 3.3 54.0 1.0
C O:GLU198 3.3 40.3 1.0
CB O:HIS204 3.5 37.0 1.0
CA O:HIS204 3.6 40.6 1.0
N O:CYS200 3.6 44.8 1.0
O O:HIS204 3.8 42.0 1.0
N O:GLU198 3.9 35.8 1.0
NE2 O:HIS204 4.0 41.6 1.0
CA O:CYS200 4.1 46.7 1.0
C O:CYS196 4.1 41.5 1.0
O O:CYS196 4.1 38.7 1.0
CA O:CYS196 4.1 45.8 1.0
C O:HIS204 4.1 41.8 1.0
CD2 O:HIS204 4.2 42.4 1.0
C O:ILE199 4.2 41.6 1.0
N O:ILE199 4.2 37.3 1.0
CA O:ILE199 4.2 41.0 1.0
CA O:GLU198 4.3 38.3 1.0
ND1 O:HIS161 4.4 41.2 1.0
SD O:MET207 4.6 42.4 1.0
N O:SER197 4.6 40.3 1.0
N O:HIS204 4.8 42.0 1.0
CG O:MET207 4.8 39.7 1.0
CA O:HIS161 5.0 39.3 1.0

Reference:

S.Shimada, K.Shinzawa-Itoh, J.Baba, S.Aoe, A.Shimada, E.Yamashita, J.Kang, M.Tateno, S.Yoshikawa, T.Tsukihara. Complex Structure of Cytochrome C-Cytochrome C Oxidase Reveals A Novel Protein-Protein Interaction Mode Embo J. V. 36 291 2017.
ISSN: ESSN 1460-2075
PubMed: 27979921
DOI: 10.15252/EMBJ.201695021
Page generated: Sun Dec 13 11:18:08 2020

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