Copper in PDB 7d5w: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution:
7.1.1.9;
Protein crystallography data
The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w
was solved by
T.Tsukihara,
A.Shimada,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.92 /
1.84
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.435,
203.092,
177.794,
90,
90,
90
|
R / Rfree (%)
|
15.4 /
18.4
|
Other elements in 7d5w:
The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
(pdb code 7d5w). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 1 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_01.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu603
b:23.3
occ:1.00
|
NE2
|
A:HIS291
|
2.0
|
22.5
|
1.0
|
NE2
|
A:HIS290
|
2.0
|
22.0
|
1.0
|
ND1
|
A:HIS240
|
2.1
|
20.3
|
1.0
|
O2
|
A:PER609
|
2.2
|
20.6
|
0.4
|
O1
|
A:PER609
|
2.7
|
24.8
|
0.4
|
O
|
A:HOH909
|
2.7
|
27.0
|
0.4
|
CE1
|
A:HIS291
|
2.9
|
23.9
|
1.0
|
CE1
|
A:HIS290
|
3.0
|
21.6
|
1.0
|
CD2
|
A:HIS291
|
3.0
|
22.1
|
1.0
|
CG
|
A:HIS240
|
3.1
|
24.5
|
1.0
|
CD2
|
A:HIS290
|
3.1
|
18.8
|
1.0
|
CE1
|
A:HIS240
|
3.1
|
23.6
|
1.0
|
O
|
A:HOH721
|
3.2
|
15.1
|
0.5
|
CB
|
A:HIS240
|
3.3
|
20.7
|
1.0
|
CA
|
A:HIS240
|
3.9
|
21.6
|
1.0
|
ND1
|
A:HIS291
|
4.0
|
18.4
|
1.0
|
CG
|
A:HIS291
|
4.1
|
18.2
|
1.0
|
ND1
|
A:HIS290
|
4.1
|
20.9
|
1.0
|
CG
|
A:HIS290
|
4.2
|
18.5
|
1.0
|
CD2
|
A:HIS240
|
4.2
|
19.7
|
1.0
|
NE2
|
A:HIS240
|
4.2
|
19.7
|
1.0
|
NA
|
A:HEA602
|
4.4
|
21.9
|
1.0
|
C1A
|
A:HEA602
|
4.4
|
22.7
|
1.0
|
C4A
|
A:HEA602
|
4.6
|
22.8
|
1.0
|
N
|
A:HIS240
|
4.7
|
21.8
|
1.0
|
C2A
|
A:HEA602
|
4.7
|
21.3
|
1.0
|
CHA
|
A:HEA602
|
4.8
|
17.2
|
1.0
|
FE
|
A:HEA602
|
4.8
|
21.5
|
1.0
|
CG2
|
A:VAL243
|
4.8
|
20.6
|
1.0
|
C3A
|
A:HEA602
|
4.9
|
26.5
|
1.0
|
ND
|
A:HEA602
|
5.0
|
22.3
|
1.0
|
|
Copper binding site 2 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 2 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_02.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu301
b:23.2
occ:1.00
|
CU1
|
B:CUA301
|
0.0
|
23.2
|
1.0
|
ND1
|
B:HIS161
|
2.1
|
23.9
|
1.0
|
SG
|
B:CYS196
|
2.3
|
24.9
|
1.0
|
SG
|
B:CYS200
|
2.3
|
22.0
|
1.0
|
SD
|
B:MET207
|
2.4
|
25.8
|
1.0
|
CU2
|
B:CUA301
|
2.5
|
23.0
|
1.0
|
CE1
|
B:HIS161
|
2.9
|
21.6
|
1.0
|
CG
|
B:HIS161
|
3.2
|
28.0
|
1.0
|
CE
|
B:MET207
|
3.2
|
22.2
|
1.0
|
CB
|
B:CYS200
|
3.2
|
23.5
|
1.0
|
CB
|
B:CYS196
|
3.4
|
26.6
|
1.0
|
CG
|
B:MET207
|
3.5
|
22.0
|
1.0
|
CB
|
B:HIS161
|
3.6
|
21.1
|
1.0
|
NE2
|
B:HIS161
|
4.1
|
22.9
|
1.0
|
O
|
B:GLU198
|
4.1
|
24.7
|
1.0
|
CA
|
B:HIS161
|
4.2
|
19.8
|
1.0
|
CD2
|
B:HIS161
|
4.2
|
23.2
|
1.0
|
ND1
|
B:HIS204
|
4.4
|
23.3
|
1.0
|
CA
|
B:CYS200
|
4.7
|
25.6
|
1.0
|
O
|
B:HIS102
|
4.7
|
24.7
|
1.0
|
CA
|
B:HIS204
|
4.7
|
21.0
|
1.0
|
CD1
|
B:TRP104
|
4.7
|
22.8
|
1.0
|
O
|
B:LEU160
|
4.7
|
23.7
|
1.0
|
CA
|
B:CYS196
|
4.8
|
21.1
|
1.0
|
CB
|
B:MET207
|
4.9
|
27.5
|
1.0
|
O
|
B:HIS204
|
4.9
|
26.2
|
1.0
|
N
|
B:CYS200
|
5.0
|
23.2
|
1.0
|
|
Copper binding site 3 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 3 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_03.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu301
b:23.0
occ:1.00
|
CU2
|
B:CUA301
|
0.0
|
23.0
|
1.0
|
ND1
|
B:HIS204
|
2.0
|
23.3
|
1.0
|
SG
|
B:CYS200
|
2.3
|
22.0
|
1.0
|
SG
|
B:CYS196
|
2.3
|
24.9
|
1.0
|
CU1
|
B:CUA301
|
2.5
|
23.2
|
1.0
|
O
|
B:GLU198
|
2.6
|
24.7
|
1.0
|
CE1
|
B:HIS204
|
2.9
|
23.8
|
1.0
|
CG
|
B:HIS204
|
3.1
|
23.3
|
1.0
|
CB
|
B:CYS196
|
3.3
|
26.6
|
1.0
|
CB
|
B:CYS200
|
3.3
|
23.5
|
1.0
|
CB
|
B:HIS204
|
3.5
|
20.1
|
1.0
|
C
|
B:GLU198
|
3.6
|
21.2
|
1.0
|
CA
|
B:HIS204
|
3.6
|
21.0
|
1.0
|
N
|
B:CYS200
|
3.7
|
23.2
|
1.0
|
O
|
B:HIS204
|
3.9
|
26.2
|
1.0
|
NE2
|
B:HIS204
|
4.0
|
22.9
|
1.0
|
ND1
|
B:HIS161
|
4.1
|
23.9
|
1.0
|
CA
|
B:CYS200
|
4.1
|
25.6
|
1.0
|
N
|
B:GLU198
|
4.1
|
22.4
|
1.0
|
C
|
B:ILE199
|
4.2
|
23.1
|
1.0
|
CD2
|
B:HIS204
|
4.2
|
24.1
|
1.0
|
C
|
B:CYS196
|
4.2
|
20.4
|
1.0
|
C
|
B:HIS204
|
4.2
|
26.4
|
1.0
|
CA
|
B:ILE199
|
4.2
|
23.9
|
1.0
|
O
|
B:CYS196
|
4.2
|
25.0
|
1.0
|
N
|
B:ILE199
|
4.3
|
18.3
|
1.0
|
SD
|
B:MET207
|
4.3
|
25.8
|
1.0
|
CA
|
B:CYS196
|
4.4
|
21.1
|
1.0
|
CA
|
B:GLU198
|
4.5
|
25.1
|
1.0
|
CG
|
B:MET207
|
4.6
|
22.0
|
1.0
|
N
|
B:SER197
|
4.6
|
21.2
|
1.0
|
N
|
B:HIS204
|
4.8
|
25.0
|
1.0
|
CA
|
B:HIS161
|
4.9
|
19.8
|
1.0
|
CE1
|
B:HIS161
|
5.0
|
21.6
|
1.0
|
|
Copper binding site 4 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 4 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_04.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Cu604
b:24.1
occ:1.00
|
NE2
|
N:HIS291
|
2.0
|
23.6
|
1.0
|
NE2
|
N:HIS290
|
2.1
|
22.9
|
1.0
|
ND1
|
N:HIS240
|
2.1
|
20.3
|
1.0
|
O2
|
N:PER611
|
2.2
|
20.6
|
0.4
|
O
|
N:HOH908
|
2.7
|
28.5
|
0.4
|
O1
|
N:PER611
|
2.8
|
31.0
|
0.4
|
CE1
|
N:HIS291
|
2.9
|
21.5
|
1.0
|
CD2
|
N:HIS291
|
3.0
|
24.9
|
1.0
|
CD2
|
N:HIS290
|
3.0
|
24.9
|
1.0
|
CG
|
N:HIS240
|
3.0
|
26.5
|
1.0
|
CE1
|
N:HIS290
|
3.1
|
26.9
|
1.0
|
CE1
|
N:HIS240
|
3.1
|
22.4
|
1.0
|
O
|
N:HOH725
|
3.3
|
15.9
|
0.5
|
CB
|
N:HIS240
|
3.3
|
20.3
|
1.0
|
CA
|
N:HIS240
|
3.9
|
21.6
|
1.0
|
ND1
|
N:HIS291
|
4.0
|
23.8
|
1.0
|
CG
|
N:HIS291
|
4.1
|
21.1
|
1.0
|
ND1
|
N:HIS290
|
4.2
|
21.5
|
1.0
|
CG
|
N:HIS290
|
4.2
|
20.3
|
1.0
|
CD2
|
N:HIS240
|
4.2
|
21.6
|
1.0
|
NE2
|
N:HIS240
|
4.2
|
22.5
|
1.0
|
NA
|
N:HEA603
|
4.4
|
21.4
|
1.0
|
C1A
|
N:HEA603
|
4.4
|
24.8
|
1.0
|
C4A
|
N:HEA603
|
4.6
|
21.5
|
1.0
|
N
|
N:HIS240
|
4.7
|
22.6
|
1.0
|
C2A
|
N:HEA603
|
4.8
|
23.4
|
1.0
|
CHA
|
N:HEA603
|
4.8
|
18.1
|
1.0
|
FE
|
N:HEA603
|
4.8
|
23.3
|
1.0
|
CG2
|
N:VAL243
|
4.9
|
21.1
|
1.0
|
C3A
|
N:HEA603
|
4.9
|
25.1
|
1.0
|
ND
|
N:HEA603
|
5.0
|
22.3
|
1.0
|
|
Copper binding site 5 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 5 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_05.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cu301
b:27.0
occ:1.00
|
CU1
|
O:CUA301
|
0.0
|
27.0
|
1.0
|
ND1
|
O:HIS161
|
2.0
|
30.2
|
1.0
|
SG
|
O:CYS196
|
2.3
|
29.7
|
1.0
|
SG
|
O:CYS200
|
2.3
|
28.4
|
1.0
|
SD
|
O:MET207
|
2.4
|
31.4
|
1.0
|
CU2
|
O:CUA301
|
2.5
|
27.0
|
1.0
|
CE1
|
O:HIS161
|
2.9
|
27.6
|
1.0
|
CG
|
O:HIS161
|
3.2
|
30.9
|
1.0
|
CE
|
O:MET207
|
3.2
|
28.2
|
1.0
|
CB
|
O:CYS200
|
3.3
|
28.8
|
1.0
|
CB
|
O:CYS196
|
3.4
|
32.1
|
1.0
|
CG
|
O:MET207
|
3.5
|
27.0
|
1.0
|
CB
|
O:HIS161
|
3.6
|
26.6
|
1.0
|
NE2
|
O:HIS161
|
4.0
|
28.1
|
1.0
|
O
|
O:GLU198
|
4.2
|
27.5
|
1.0
|
CD2
|
O:HIS161
|
4.2
|
28.9
|
1.0
|
CA
|
O:HIS161
|
4.2
|
25.7
|
1.0
|
ND1
|
O:HIS204
|
4.4
|
27.9
|
1.0
|
CD1
|
O:TRP104
|
4.6
|
28.4
|
1.0
|
O
|
O:HIS102
|
4.7
|
30.2
|
1.0
|
CA
|
O:CYS200
|
4.7
|
27.4
|
1.0
|
O
|
O:LEU160
|
4.7
|
27.6
|
1.0
|
CA
|
O:HIS204
|
4.7
|
32.7
|
1.0
|
CA
|
O:CYS196
|
4.8
|
30.1
|
1.0
|
CB
|
O:MET207
|
4.9
|
31.6
|
1.0
|
O
|
O:HIS204
|
5.0
|
28.5
|
1.0
|
|
Copper binding site 6 out
of 6 in 7d5w
Go back to
Copper Binding Sites List in 7d5w
Copper binding site 6 out
of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_06.jpg) Mono view
![](/pictures/CU/pdb/d5/7d5w-CU-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cu301
b:27.0
occ:1.00
|
CU2
|
O:CUA301
|
0.0
|
27.0
|
1.0
|
ND1
|
O:HIS204
|
2.0
|
27.9
|
1.0
|
SG
|
O:CYS200
|
2.2
|
28.4
|
1.0
|
SG
|
O:CYS196
|
2.3
|
29.7
|
1.0
|
CU1
|
O:CUA301
|
2.5
|
27.0
|
1.0
|
O
|
O:GLU198
|
2.6
|
27.5
|
1.0
|
CE1
|
O:HIS204
|
2.9
|
27.0
|
1.0
|
CG
|
O:HIS204
|
3.1
|
26.4
|
1.0
|
CB
|
O:CYS196
|
3.3
|
32.1
|
1.0
|
CB
|
O:CYS200
|
3.3
|
28.8
|
1.0
|
CB
|
O:HIS204
|
3.5
|
29.7
|
1.0
|
CA
|
O:HIS204
|
3.6
|
32.7
|
1.0
|
C
|
O:GLU198
|
3.6
|
27.9
|
1.0
|
N
|
O:CYS200
|
3.7
|
31.4
|
1.0
|
O
|
O:HIS204
|
3.9
|
28.5
|
1.0
|
NE2
|
O:HIS204
|
4.0
|
27.5
|
1.0
|
CA
|
O:CYS200
|
4.1
|
27.4
|
1.0
|
ND1
|
O:HIS161
|
4.1
|
30.2
|
1.0
|
CD2
|
O:HIS204
|
4.1
|
27.1
|
1.0
|
N
|
O:GLU198
|
4.2
|
27.0
|
1.0
|
C
|
O:HIS204
|
4.2
|
32.9
|
1.0
|
C
|
O:ILE199
|
4.2
|
30.5
|
1.0
|
C
|
O:CYS196
|
4.2
|
33.8
|
1.0
|
CA
|
O:ILE199
|
4.2
|
23.4
|
1.0
|
O
|
O:CYS196
|
4.3
|
27.7
|
1.0
|
N
|
O:ILE199
|
4.3
|
24.7
|
1.0
|
SD
|
O:MET207
|
4.4
|
31.4
|
1.0
|
CA
|
O:CYS196
|
4.4
|
30.1
|
1.0
|
CA
|
O:GLU198
|
4.5
|
28.9
|
1.0
|
CG
|
O:MET207
|
4.7
|
27.0
|
1.0
|
N
|
O:SER197
|
4.7
|
30.0
|
1.0
|
N
|
O:HIS204
|
4.8
|
33.4
|
1.0
|
CE1
|
O:HIS161
|
4.9
|
27.6
|
1.0
|
CA
|
O:HIS161
|
4.9
|
25.7
|
1.0
|
|
Reference:
A.Shimada,
F.Hara,
K.Shinzawa-Itoh,
N.Kanehisa,
E.Yamashita,
K.Muramoto,
T.Tsukihara,
S.Yoshikawa.
Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Wed Jul 31 08:26:45 2024
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