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Copper in PDB 2yev: Structure of CAA3-Type Cytochrome Oxidase

Enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase

All present enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase:
1.9.3.1;

Protein crystallography data

The structure of Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev was solved by J.A.Lyons, D.Aragao, T.Soulimane, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.18 / 2.36
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.250, 76.030, 300.267, 90.00, 92.21, 90.00
R / Rfree (%) 17.1 / 21.8

Other elements in 2yev:

The structure of Structure of CAA3-Type Cytochrome Oxidase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of CAA3-Type Cytochrome Oxidase (pdb code 2yev). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 1 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1017

b:37.6
occ:1.00
NE2 A:HIS300 2.0 34.6 1.0
NE2 A:HIS299 2.1 37.5 1.0
ND1 A:HIS250 2.2 29.2 1.0
O A:HOH2076 2.2 49.4 1.0
O A:HOH2077 2.8 25.9 1.0
CD2 A:HIS300 2.9 20.8 1.0
CE1 A:HIS299 2.9 36.2 1.0
CG A:HIS250 3.0 38.2 1.0
CE1 A:HIS300 3.1 36.5 1.0
CD2 A:HIS299 3.2 45.3 1.0
CB A:HIS250 3.2 32.7 1.0
CE1 A:HIS250 3.2 60.3 1.0
CA A:HIS250 3.8 44.4 1.0
CG A:HIS300 4.0 50.7 1.0
ND1 A:HIS300 4.1 35.9 1.0
ND1 A:HIS299 4.1 49.6 1.0
CD2 A:HIS250 4.2 29.5 1.0
CG A:HIS299 4.2 42.6 1.0
NE2 A:HIS250 4.3 37.2 1.0
ND A:HAS1016 4.3 40.2 1.0
C4D A:HAS1016 4.5 35.1 1.0
C1D A:HAS1016 4.7 48.0 1.0
O A:HOH2075 4.7 50.0 1.0
N A:HIS250 4.7 39.5 1.0
CHA A:HAS1016 4.8 27.8 1.0
NA A:HAS1016 4.8 32.0 1.0
FE A:HAS1016 4.9 31.7 1.0
C1A A:HAS1016 4.9 38.2 1.0
C A:HIS250 4.9 31.8 1.0

Copper binding site 2 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 2 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu585

b:36.1
occ:1.00
CU1 B:CUA585 0.0 36.1 1.0
ND1 B:HIS162 2.0 45.9 1.0
SD B:MET208 2.4 33.5 1.0
SG B:CYS201 2.5 33.0 1.0
SG B:CYS197 2.5 32.4 1.0
CU2 B:CUA585 2.5 35.8 1.0
CE1 B:HIS162 2.8 31.1 1.0
CG B:HIS162 3.1 40.1 1.0
CE B:MET208 3.2 26.9 1.0
CB B:CYS201 3.3 18.5 1.0
CB B:CYS197 3.4 26.2 1.0
CB B:HIS162 3.6 32.3 1.0
CG B:MET208 3.7 43.1 1.0
NE2 B:HIS162 4.0 36.4 1.0
O B:GLU199 4.1 41.8 1.0
CA B:HIS162 4.1 36.1 1.0
CD2 B:HIS162 4.1 33.9 1.0
CB B:MET208 4.2 29.9 1.0
ND1 B:HIS205 4.6 51.3 1.0
CA B:CYS201 4.7 46.5 1.0
CA B:CYS197 4.8 27.0 1.0
O B:ILE161 4.8 35.8 1.0
O B:TYR124 4.8 40.2 1.0
N B:CYS201 4.9 33.5 1.0
CZ2 B:TRP128 5.0 38.0 1.0

Copper binding site 3 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 3 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu585

b:35.8
occ:1.00
CU2 B:CUA585 0.0 35.8 1.0
ND1 B:HIS205 2.1 51.3 1.0
SG B:CYS201 2.3 33.0 1.0
SG B:CYS197 2.5 32.4 1.0
O B:GLU199 2.5 41.8 1.0
CU1 B:CUA585 2.5 36.1 1.0
CE1 B:HIS205 2.9 27.3 1.0
CG B:HIS205 3.2 40.8 1.0
CB B:CYS201 3.2 18.5 1.0
CB B:CYS197 3.4 26.2 1.0
N B:CYS201 3.4 33.5 1.0
C B:GLU199 3.5 47.7 1.0
CB B:HIS205 3.7 34.2 1.0
CA B:HIS205 3.7 35.5 1.0
CA B:CYS201 4.0 46.5 1.0
NE2 B:HIS205 4.1 42.6 1.0
C B:LEU200 4.1 41.8 1.0
N B:GLU199 4.1 39.2 1.0
O B:HIS205 4.1 36.2 1.0
CA B:LEU200 4.2 37.2 1.0
CD2 B:HIS205 4.2 44.2 1.0
N B:LEU200 4.2 32.9 1.0
ND1 B:HIS162 4.2 45.9 1.0
C B:CYS197 4.4 41.0 1.0
C B:HIS205 4.4 46.2 1.0
CA B:GLU199 4.4 32.0 1.0
SD B:MET208 4.4 33.5 1.0
O B:CYS197 4.4 41.4 1.0
CA B:CYS197 4.5 27.0 1.0
CB B:MET208 4.8 29.9 1.0
N B:ALA198 4.9 33.3 1.0
N B:HIS205 4.9 35.0 1.0
C B:CYS201 5.0 47.8 1.0

Copper binding site 4 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 4 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1017

b:42.6
occ:1.00
ND1 D:HIS250 2.1 44.0 1.0
NE2 D:HIS299 2.1 41.1 1.0
NE2 D:HIS300 2.1 51.9 1.0
O D:HOH2053 2.2 50.7 1.0
O D:HOH2054 2.3 35.8 1.0
CE1 D:HIS299 2.9 47.3 1.0
CD2 D:HIS300 3.0 31.1 1.0
CG D:HIS250 3.0 40.0 1.0
CE1 D:HIS250 3.1 39.5 1.0
CE1 D:HIS300 3.2 43.1 1.0
CD2 D:HIS299 3.2 51.9 1.0
CB D:HIS250 3.2 24.1 1.0
CA D:HIS250 3.8 42.8 1.0
ND1 D:HIS299 4.1 50.4 1.0
CG D:HIS300 4.2 44.9 1.0
CD2 D:HIS250 4.2 41.0 1.0
NE2 D:HIS250 4.2 43.1 1.0
ND1 D:HIS300 4.2 49.3 1.0
CG D:HIS299 4.3 50.5 1.0
ND D:HAS1016 4.3 37.5 1.0
C4D D:HAS1016 4.5 36.9 1.0
C1D D:HAS1016 4.7 57.7 1.0
N D:HIS250 4.8 38.6 1.0
CHA D:HAS1016 4.8 28.8 1.0
FE D:HAS1016 4.8 42.5 1.0
NA D:HAS1016 4.9 29.3 1.0
C D:HIS250 4.9 36.6 1.0
C1A D:HAS1016 4.9 39.8 1.0

Copper binding site 5 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 5 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu585

b:44.1
occ:1.00
CU1 E:CUA585 0.0 44.1 1.0
ND1 E:HIS162 2.1 37.3 1.0
SG E:CYS197 2.4 40.1 1.0
SG E:CYS201 2.4 43.6 1.0
SD E:MET208 2.5 48.2 1.0
CU2 E:CUA585 2.5 43.4 1.0
CE1 E:HIS162 3.0 31.9 1.0
CE E:MET208 3.2 45.6 1.0
CG E:HIS162 3.2 51.9 1.0
CB E:CYS197 3.3 28.9 1.0
CB E:CYS201 3.3 27.1 1.0
CG E:MET208 3.6 42.3 1.0
CB E:HIS162 3.7 50.4 1.0
CB E:MET208 4.1 48.1 1.0
O E:GLU199 4.1 59.8 1.0
NE2 E:HIS162 4.2 43.9 1.0
CA E:HIS162 4.2 36.5 1.0
CD2 E:HIS162 4.3 41.7 1.0
ND1 E:HIS205 4.5 52.8 1.0
CA E:CYS197 4.7 42.3 1.0
CA E:CYS201 4.7 53.4 1.0
O E:ILE161 4.9 44.4 1.0
N E:CYS201 4.9 43.1 1.0
CZ2 E:TRP128 4.9 45.4 1.0
O E:TYR124 5.0 46.1 1.0

Copper binding site 6 out of 6 in 2yev

Go back to Copper Binding Sites List in 2yev
Copper binding site 6 out of 6 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu585

b:43.4
occ:1.00
CU2 E:CUA585 0.0 43.4 1.0
ND1 E:HIS205 2.0 52.8 1.0
SG E:CYS197 2.4 40.1 1.0
SG E:CYS201 2.4 43.6 1.0
CU1 E:CUA585 2.5 44.1 1.0
O E:GLU199 2.6 59.8 1.0
CE1 E:HIS205 2.8 42.0 1.0
CG E:HIS205 3.1 52.9 1.0
CB E:CYS197 3.3 28.9 1.0
CB E:CYS201 3.3 27.1 1.0
N E:CYS201 3.5 43.1 1.0
C E:GLU199 3.5 40.2 1.0
CB E:HIS205 3.6 50.5 1.0
CA E:HIS205 3.7 46.2 1.0
NE2 E:HIS205 3.9 43.8 1.0
CA E:CYS201 4.0 53.4 1.0
O E:HIS205 4.1 34.9 1.0
CD2 E:HIS205 4.1 51.2 1.0
N E:GLU199 4.1 43.7 1.0
C E:LEU200 4.2 46.4 1.0
CA E:LEU200 4.2 38.0 1.0
N E:LEU200 4.2 41.5 1.0
C E:HIS205 4.3 51.9 1.0
ND1 E:HIS162 4.3 37.3 1.0
C E:CYS197 4.4 47.5 1.0
O E:CYS197 4.4 47.6 1.0
CA E:GLU199 4.4 39.6 1.0
CA E:CYS197 4.5 42.3 1.0
SD E:MET208 4.5 48.2 1.0
CB E:MET208 4.8 48.1 1.0
N E:ALA198 4.9 48.0 1.0
N E:HIS205 4.9 49.1 1.0

Reference:

J.A.Lyons, D.Aragao, O.Slattery, A.V.Pisliakov, T.Soulimane, M.Caffrey. Structural Insights Into Electron Transfer in CAA3-Type Cytochrome Oxidases. Nature V. 487 514 2012.
ISSN: ISSN 0028-0836
PubMed: 22763450
DOI: 10.1038/NATURE11182
Page generated: Sun Dec 13 11:08:10 2020

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