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Copper in PDB 6pw1: Cytochrome C Oxidase Delta 16

Enzymatic activity of Cytochrome C Oxidase Delta 16

All present enzymatic activity of Cytochrome C Oxidase Delta 16:
1.9.3.1;

Protein crystallography data

The structure of Cytochrome C Oxidase Delta 16, PDB code: 6pw1 was solved by J.Liu, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.315, 130.000, 177.539, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.4

Other elements in 6pw1:

The structure of Cytochrome C Oxidase Delta 16 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cytochrome C Oxidase Delta 16 (pdb code 6pw1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cytochrome C Oxidase Delta 16, PDB code: 6pw1:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 1 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu617

b:30.6
occ:1.00
 NE2 A:HIS334 2.0 29.9 1.0
NE2 A:HIS333 2.0 31.3 1.0
ND1 A:HIS284 2.1 27.4 1.0
O A:HOH830 2.4 26.9 1.0
O A:HOH770 2.8 23.4 1.0
CE1 A:HIS334 2.9 25.8 1.0
CE1 A:HIS333 3.0 28.8 1.0
CG A:HIS284 3.0 30.1 1.0
CD2 A:HIS334 3.0 26.9 1.0
CE1 A:HIS284 3.1 27.6 1.0
CD2 A:HIS333 3.1 27.7 1.0
CB A:HIS284 3.3 27.0 1.0
CA A:HIS284 3.9 27.4 1.0
ND1 A:HIS334 4.0 29.5 1.0
CG A:HIS334 4.1 29.6 1.0
ND1 A:HIS333 4.1 31.8 1.0
CD2 A:HIS284 4.2 27.0 1.0
NE2 A:HIS284 4.2 32.2 1.0
CG A:HIS333 4.2 29.7 1.0
C1A A:HEA616 4.6 28.6 1.0
C4A A:HEA616 4.6 26.8 1.0
NA A:HEA616 4.7 30.2 1.0
N A:HIS284 4.8 27.5 1.0
C2A A:HEA616 4.8 27.9 1.0
FE A:HEA616 4.8 27.1 1.0
C3A A:HEA616 4.8 27.0 1.0
O A:HOH824 4.9 34.5 1.0

Copper binding site 2 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 2 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu305

b:25.1
occ:1.00
 ND1 B:HIS260 2.1 24.3 1.0
SG B:CYS252 2.2 25.5 1.0
SG B:CYS256 2.3 25.5 1.0
CU B:CU306 2.5 25.0 1.0
O B:GLU254 2.6 26.4 1.0
CE1 B:HIS260 3.0 24.1 1.0
CG B:HIS260 3.2 26.0 1.0
CB B:CYS252 3.3 23.6 1.0
CB B:CYS256 3.4 25.4 1.0
C B:GLU254 3.5 26.3 1.0
CA B:HIS260 3.6 21.6 1.0
CB B:HIS260 3.6 21.7 1.0
N B:CYS256 3.7 25.3 1.0
O B:HIS260 3.9 22.6 1.0
N B:GLU254 4.1 27.1 1.0
NE2 B:HIS260 4.1 23.4 1.0
C B:CYS252 4.2 26.9 1.0
O B:CYS252 4.2 25.6 1.0
CA B:CYS256 4.2 25.3 1.0
ND1 B:HIS217 4.2 23.7 1.0
C B:HIS260 4.2 23.7 1.0
CD2 B:HIS260 4.2 23.6 1.0
N B:LEU255 4.3 26.5 1.0
CA B:LEU255 4.3 27.1 1.0
C B:LEU255 4.3 24.4 1.0
CA B:CYS252 4.4 25.9 1.0
SD B:MET263 4.4 25.6 1.0
CA B:GLU254 4.5 28.4 1.0
N B:SER253 4.6 25.1 1.0
CG B:MET263 4.7 24.5 1.0
N B:HIS260 4.8 25.1 1.0
CA B:HIS217 4.9 26.2 1.0
CB B:HIS217 5.0 24.0 1.0

Copper binding site 3 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 3 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu306

b:25.0
occ:1.00
 ND1 B:HIS217 2.1 23.7 1.0
SG B:CYS256 2.3 25.5 1.0
SG B:CYS252 2.4 25.5 1.0
SD B:MET263 2.4 25.6 1.0
CU B:CU305 2.5 25.1 1.0
CE1 B:HIS217 2.9 25.2 1.0
CE B:MET263 3.1 21.1 1.0
CG B:HIS217 3.1 25.4 1.0
CB B:CYS256 3.3 25.4 1.0
CB B:CYS252 3.5 23.6 1.0
CG B:MET263 3.5 24.5 1.0
CB B:HIS217 3.6 24.0 1.0
NE2 B:HIS217 4.1 23.7 1.0
O B:GLU254 4.2 26.4 1.0
CD2 B:HIS217 4.2 25.5 1.0
CA B:HIS217 4.2 26.2 1.0
CD1 B:TRP143 4.4 24.1 1.0
ND1 B:HIS260 4.5 24.3 1.0
O B:TYR141 4.7 26.9 1.0
CA B:HIS260 4.7 21.6 1.0
CA B:CYS256 4.7 25.3 1.0
CA B:CYS252 4.9 25.9 1.0
CB B:MET263 4.9 24.7 1.0

Copper binding site 4 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 4 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu606

b:34.4
occ:1.00
 NE2 C:HIS333 2.0 34.6 1.0
NE2 C:HIS334 2.0 36.5 1.0
ND1 C:HIS284 2.2 32.3 1.0
O C:HOH790 2.3 32.4 1.0
O C:HOH740 2.8 27.9 1.0
CE1 C:HIS333 2.9 35.0 1.0
CE1 C:HIS334 2.9 30.0 1.0
CD2 C:HIS334 3.0 30.8 1.0
CD2 C:HIS333 3.1 34.9 1.0
CG C:HIS284 3.1 31.7 1.0
CE1 C:HIS284 3.3 33.3 1.0
CB C:HIS284 3.3 29.6 1.0
CA C:HIS284 3.9 30.7 1.0
ND1 C:HIS334 4.0 32.4 1.0
ND1 C:HIS333 4.1 31.9 1.0
CG C:HIS334 4.1 34.5 1.0
CG C:HIS333 4.2 36.0 1.0
CD2 C:HIS284 4.3 32.8 1.0
NE2 C:HIS284 4.3 37.4 1.0
C1A C:HEA605 4.6 29.8 1.0
C4A C:HEA605 4.6 32.3 1.0
NA C:HEA605 4.7 33.5 1.0
N C:HIS284 4.7 30.1 1.0
C2A C:HEA605 4.8 31.1 1.0
FE C:HEA605 4.8 31.8 1.0
C3A C:HEA605 4.8 31.4 1.0
C C:HIS284 5.0 31.3 1.0

Copper binding site 5 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 5 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu303

b:31.0
occ:1.00
 ND1 D:HIS260 2.0 26.4 1.0
SG D:CYS252 2.3 29.1 1.0
SG D:CYS256 2.3 29.5 1.0
CU D:CU304 2.6 31.2 1.0
O D:GLU254 2.6 31.6 1.0
CE1 D:HIS260 2.9 31.7 1.0
CG D:HIS260 3.1 32.0 1.0
CB D:CYS252 3.3 26.7 1.0
CB D:CYS256 3.4 29.4 1.0
C D:GLU254 3.5 30.8 1.0
CB D:HIS260 3.6 30.7 1.0
CA D:HIS260 3.6 28.7 1.0
N D:CYS256 3.6 31.1 1.0
O D:HIS260 3.9 29.8 1.0
NE2 D:HIS260 4.0 32.0 1.0
N D:GLU254 4.1 31.8 1.0
C D:CYS252 4.1 31.8 1.0
CA D:CYS256 4.1 31.5 1.0
O D:CYS252 4.2 28.1 1.0
CD2 D:HIS260 4.2 31.2 1.0
C D:HIS260 4.2 27.7 1.0
CA D:LEU255 4.2 31.1 1.0
N D:LEU255 4.3 31.1 1.0
C D:LEU255 4.3 32.6 1.0
ND1 D:HIS217 4.3 26.5 1.0
CA D:CYS252 4.4 31.7 1.0
SD D:MET263 4.5 29.7 1.0
CA D:GLU254 4.5 32.0 1.0
N D:SER253 4.6 31.1 1.0
CG D:MET263 4.8 26.6 1.0
N D:HIS260 4.8 29.6 1.0
CA D:HIS217 4.9 31.5 1.0
CB D:HIS217 5.0 28.9 1.0

Copper binding site 6 out of 6 in 6pw1

Go back to Copper Binding Sites List in 6pw1
Copper binding site 6 out of 6 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cytochrome C Oxidase Delta 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu304

b:31.2
occ:1.00
 ND1 D:HIS217 2.1 26.5 1.0
SG D:CYS252 2.3 29.1 1.0
SG D:CYS256 2.4 29.5 1.0
SD D:MET263 2.4 29.7 1.0
CU D:CU303 2.6 31.0 1.0
CE1 D:HIS217 3.0 28.6 1.0
CE D:MET263 3.0 27.8 1.0
CG D:HIS217 3.1 28.6 1.0
CB D:CYS256 3.3 29.4 1.0
CB D:CYS252 3.5 26.7 1.0
CB D:HIS217 3.5 28.9 1.0
CG D:MET263 3.6 26.6 1.0
NE2 D:HIS217 4.1 26.0 1.0
CA D:HIS217 4.2 31.5 1.0
CD2 D:HIS217 4.2 29.7 1.0
O D:GLU254 4.3 31.6 1.0
CD1 D:TRP143 4.5 32.0 1.0
ND1 D:HIS260 4.5 26.4 1.0
O D:TYR141 4.7 32.3 1.0
CA D:CYS256 4.7 31.5 1.0
CA D:HIS260 4.8 28.7 1.0
CA D:CYS252 4.9 31.7 1.0
CB D:MET263 4.9 28.7 1.0
N D:CYS256 5.0 31.1 1.0

Reference:

J.Berg, J.Liu, E.Svahn, S.Ferguson-Miller, P.Brzezinski. Structural Changes at the Surface of Cytochrome C Oxidase Alter the Proton-Pumping Stoichiometry. Biochim Biophys Acta 48116 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 31733183
DOI: 10.1016/J.BBABIO.2019.148116
Page generated: Wed Jul 31 06:47:00 2024

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