Atomistry » Copper » PDB 6pvz-6ri0 » 6pw1
Atomistry »
  Copper »
    PDB 6pvz-6ri0 »
      6pw1 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy