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Copper in PDB 6pw0: Cytochrome C Oxidase Delta 6 Mutant

Enzymatic activity of Cytochrome C Oxidase Delta 6 Mutant

All present enzymatic activity of Cytochrome C Oxidase Delta 6 Mutant:
1.9.3.1;

Protein crystallography data

The structure of Cytochrome C Oxidase Delta 6 Mutant, PDB code: 6pw0 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) 42.84 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.905, 131.477, 176.601, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.8

Other elements in 6pw0:

The structure of Cytochrome C Oxidase Delta 6 Mutant 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 6 Mutant (pdb code 6pw0). 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 6 Mutant, PDB code: 6pw0:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 1 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu617

b:38.4
occ:1.00
 NE2 A:HIS333 2.1 42.2 1.0
NE2 A:HIS334 2.1 38.4 1.0
ND1 A:HIS284 2.2 41.2 1.0
O A:OH601 2.3 40.4 1.0
O A:HOH701 2.7 34.2 1.0
CE1 A:HIS334 2.9 35.4 1.0
CE1 A:HIS333 3.0 43.4 1.0
CG A:HIS284 3.1 38.3 1.0
CD2 A:HIS334 3.1 40.0 1.0
CD2 A:HIS333 3.1 42.6 1.0
CB A:HIS284 3.2 34.3 1.0
CE1 A:HIS284 3.3 39.8 1.0
CA A:HIS284 3.8 38.8 1.0
ND1 A:HIS334 4.0 36.2 1.0
ND1 A:HIS333 4.1 45.3 1.0
CG A:HIS334 4.1 40.9 1.0
CG A:HIS333 4.2 45.7 1.0
CD2 A:HIS284 4.3 38.0 1.0
NE2 A:HIS284 4.3 47.4 1.0
C1A A:HEA603 4.6 29.6 1.0
N A:HIS284 4.7 39.0 1.0
C4A A:HEA603 4.7 32.1 1.0
NA A:HEA603 4.7 41.2 1.0
O A:HOH779 4.8 43.4 1.0
FE A:HEA603 4.8 36.1 1.0
C2A A:HEA603 4.8 38.5 1.0
C3A A:HEA603 4.8 38.4 1.0
C A:HIS284 5.0 40.8 1.0

Copper binding site 2 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 2 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu307

b:37.3
occ:1.00
 ND1 B:HIS260 2.1 33.5 1.0
SG B:CYS252 2.3 36.8 1.0
SG B:CYS256 2.4 33.7 1.0
CU B:CU308 2.6 33.5 1.0
O B:GLU254 2.6 32.7 1.0
CE1 B:HIS260 2.9 32.6 1.0
CG B:HIS260 3.1 33.2 1.0
CB B:CYS256 3.4 31.9 1.0
CB B:CYS252 3.5 29.7 1.0
N B:CYS256 3.5 33.6 1.0
C B:GLU254 3.6 36.0 1.0
CA B:HIS260 3.6 30.4 1.0
CB B:HIS260 3.6 30.8 1.0
O B:HIS260 3.9 31.1 1.0
NE2 B:HIS260 4.1 32.2 1.0
CA B:CYS256 4.1 31.8 1.0
CA B:LEU255 4.1 35.8 1.0
N B:GLU254 4.2 31.9 1.0
C B:HIS260 4.2 33.4 1.0
C B:LEU255 4.2 33.1 1.0
CD2 B:HIS260 4.2 32.2 1.0
N B:LEU255 4.2 35.4 1.0
C B:CYS252 4.2 32.5 1.0
O B:CYS252 4.2 31.1 1.0
ND1 B:HIS217 4.4 31.9 1.0
SD B:MET263 4.5 32.8 1.0
CA B:CYS252 4.5 31.2 1.0
CA B:GLU254 4.5 33.0 1.0
N B:SER253 4.5 33.5 1.0
CG B:MET263 4.7 34.1 1.0
N B:HIS260 4.8 37.5 1.0
CA B:HIS217 5.0 32.2 1.0

Copper binding site 3 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 3 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu308

b:33.5
occ:1.00
 ND1 B:HIS217 2.2 31.9 1.0
SG B:CYS252 2.4 36.8 1.0
SG B:CYS256 2.4 33.7 1.0
SD B:MET263 2.4 32.8 1.0
CU B:CU307 2.6 37.3 1.0
CE B:MET263 3.1 29.6 1.0
CE1 B:HIS217 3.1 31.9 1.0
CG B:HIS217 3.2 35.0 1.0
CB B:CYS256 3.3 31.9 1.0
CB B:HIS217 3.5 29.6 1.0
CG B:MET263 3.5 34.1 1.0
CB B:CYS252 3.6 29.7 1.0
CA B:HIS217 4.2 32.2 1.0
NE2 B:HIS217 4.3 33.5 1.0
O B:GLU254 4.3 32.7 1.0
CD2 B:HIS217 4.3 33.9 1.0
CD1 B:TRP143 4.5 31.6 1.0
ND1 B:HIS260 4.6 33.5 1.0
O B:TYR141 4.6 35.0 1.0
CA B:CYS256 4.7 31.8 1.0
CA B:HIS260 4.8 30.4 1.0
CB B:MET263 4.9 31.6 1.0
N B:CYS256 4.9 33.6 1.0
CA B:CYS252 5.0 31.2 1.0

Copper binding site 4 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 4 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu609

b:44.9
occ:1.00
 NE2 C:HIS333 2.1 42.3 1.0
NE2 C:HIS334 2.2 45.9 1.0
ND1 C:HIS284 2.2 50.4 1.0
O C:OH601 2.7 48.5 1.0
O C:HOH701 2.8 38.8 1.0
CE1 C:HIS333 2.9 42.3 1.0
CG C:HIS284 3.0 45.4 1.0
CD2 C:HIS334 3.1 43.4 1.0
CE1 C:HIS334 3.1 40.7 1.0
CD2 C:HIS333 3.2 41.2 1.0
CB C:HIS284 3.2 41.2 1.0
CE1 C:HIS284 3.3 46.8 1.0
CA C:HIS284 3.8 49.1 1.0
ND1 C:HIS333 4.1 43.8 1.0
ND1 C:HIS334 4.1 42.4 1.0
CG C:HIS334 4.2 42.3 1.0
CD2 C:HIS284 4.2 53.2 1.0
CG C:HIS333 4.2 43.6 1.0
NE2 C:HIS284 4.3 57.6 1.0
N C:HIS284 4.7 44.6 1.0
C1A C:HEA603 4.7 38.2 1.0
C4A C:HEA603 4.7 44.2 1.0
NA C:HEA603 4.8 47.8 1.0
C2A C:HEA603 4.8 41.1 1.0
FE C:HEA603 4.8 42.3 1.0
C3A C:HEA603 4.9 39.1 1.0
C C:HIS284 5.0 48.5 1.0

Copper binding site 5 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 5 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu305

b:40.5
occ:1.00
 ND1 D:HIS260 1.9 40.5 1.0
SG D:CYS252 2.4 35.2 1.0
SG D:CYS256 2.4 38.0 1.0
CU D:CU306 2.5 39.0 1.0
O D:GLU254 2.7 43.4 1.0
CE1 D:HIS260 2.8 38.8 1.0
CG D:HIS260 3.1 37.4 1.0
CB D:CYS252 3.3 39.1 1.0
CB D:CYS256 3.4 33.2 1.0
CB D:HIS260 3.6 39.6 1.0
CA D:HIS260 3.6 36.3 1.0
N D:CYS256 3.6 46.4 1.0
C D:GLU254 3.6 42.3 1.0
O D:HIS260 3.9 37.0 1.0
NE2 D:HIS260 4.0 43.8 1.0
CD2 D:HIS260 4.1 39.3 1.0
CA D:CYS256 4.1 39.9 1.0
C D:CYS252 4.2 39.8 1.0
N D:GLU254 4.2 42.9 1.0
C D:HIS260 4.2 41.2 1.0
C D:LEU255 4.3 38.8 1.0
CA D:LEU255 4.3 38.0 1.0
O D:CYS252 4.3 36.1 1.0
ND1 D:HIS217 4.3 33.8 1.0
N D:LEU255 4.3 40.5 1.0
CA D:CYS252 4.4 41.6 1.0
SD D:MET263 4.4 41.0 1.0
N D:SER253 4.4 43.5 1.0
CA D:GLU254 4.6 39.4 1.0
CG D:MET263 4.6 40.4 1.0
N D:HIS260 4.8 43.1 1.0
CA D:HIS217 4.9 38.5 1.0
CB D:HIS217 4.9 39.8 1.0

Copper binding site 6 out of 6 in 6pw0

Go back to Copper Binding Sites List in 6pw0
Copper binding site 6 out of 6 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu306

b:39.0
occ:1.00
 ND1 D:HIS217 2.2 33.8 1.0
SG D:CYS256 2.4 38.0 1.0
SG D:CYS252 2.4 35.2 1.0
SD D:MET263 2.4 41.0 1.0
CU D:CU305 2.5 40.5 1.0
CE1 D:HIS217 3.1 37.6 1.0
CG D:HIS217 3.2 37.1 1.0
CE D:MET263 3.2 38.1 1.0
CB D:CYS256 3.2 33.2 1.0
CB D:HIS217 3.5 39.8 1.0
CG D:MET263 3.5 40.4 1.0
CB D:CYS252 3.5 39.1 1.0
CA D:HIS217 4.2 38.5 1.0
NE2 D:HIS217 4.3 37.1 1.0
CD2 D:HIS217 4.3 35.1 1.0
O D:GLU254 4.3 43.4 1.0
ND1 D:HIS260 4.4 40.5 1.0
CD1 D:TRP143 4.5 42.3 1.0
O D:TYR141 4.6 41.7 1.0
CA D:CYS256 4.6 39.9 1.0
CA D:HIS260 4.8 36.3 1.0
CB D:MET263 4.9 37.9 1.0
CA D:CYS252 4.9 41.6 1.0
N D:CYS256 4.9 46.4 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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