Atomistry » Copper » PDB 6pw0-6ri2 » 6pw0
Atomistry »
  Copper »
    PDB 6pw0-6ri2 »
      6pw0 »

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: Sun Dec 13 11:24:49 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy