Copper in PDB 6ei4: Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
Protein crystallography data
The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site, PDB code: 6ei4
was solved by
B.Deri,
R.Gitto,
Y.Pazy Benhar,
A.Fishman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.10 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.650,
78.100,
81.050,
90.00,
104.52,
90.00
|
R / Rfree (%)
|
22.7 /
25.1
|
Other elements in 6ei4:
The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
(pdb code 6ei4). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site, PDB code: 6ei4:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 6ei4
Go back to
Copper Binding Sites List in 6ei4
Copper binding site 1 out
of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:24.9
occ:1.00
|
NE2
|
A:HIS60
|
1.9
|
23.1
|
1.0
|
F07
|
A:B5N301
|
1.9
|
35.4
|
1.0
|
NE2
|
A:HIS42
|
1.9
|
17.0
|
1.0
|
NE2
|
A:HIS69
|
2.1
|
11.1
|
1.0
|
CE1
|
A:HIS60
|
2.7
|
12.8
|
1.0
|
CD2
|
A:HIS42
|
2.9
|
15.4
|
1.0
|
CE1
|
A:HIS69
|
3.0
|
11.0
|
1.0
|
CD2
|
A:HIS60
|
3.0
|
18.0
|
1.0
|
CE1
|
A:HIS42
|
3.0
|
17.9
|
1.0
|
C04
|
A:B5N301
|
3.1
|
32.6
|
1.0
|
CD2
|
A:HIS69
|
3.3
|
10.7
|
1.0
|
C02
|
A:B5N301
|
3.7
|
27.5
|
1.0
|
CU
|
A:CU303
|
3.9
|
16.9
|
1.0
|
ND1
|
A:HIS60
|
3.9
|
12.7
|
1.0
|
CZ
|
A:PHE227
|
4.0
|
9.6
|
1.0
|
CG
|
A:HIS42
|
4.0
|
12.9
|
1.0
|
CG
|
A:HIS60
|
4.0
|
15.3
|
1.0
|
NE2
|
A:HIS231
|
4.1
|
19.0
|
1.0
|
ND1
|
A:HIS42
|
4.1
|
19.7
|
1.0
|
C06
|
A:B5N301
|
4.1
|
31.4
|
1.0
|
ND1
|
A:HIS69
|
4.1
|
13.1
|
1.0
|
CE2
|
A:PHE227
|
4.2
|
12.3
|
1.0
|
CE1
|
A:HIS231
|
4.3
|
11.3
|
1.0
|
CG
|
A:HIS69
|
4.3
|
11.7
|
1.0
|
O
|
A:ALA59
|
4.8
|
12.4
|
1.0
|
CB
|
A:ALA59
|
4.8
|
13.2
|
1.0
|
CZ3
|
A:TRP68
|
4.9
|
10.4
|
1.0
|
CE1
|
A:PHE65
|
4.9
|
11.4
|
1.0
|
|
Copper binding site 2 out
of 4 in 6ei4
Go back to
Copper Binding Sites List in 6ei4
Copper binding site 2 out
of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu303
b:16.9
occ:1.00
|
NE2
|
A:HIS204
|
2.0
|
10.3
|
1.0
|
NE2
|
A:HIS231
|
2.0
|
19.0
|
1.0
|
NE2
|
A:HIS208
|
2.0
|
20.6
|
1.0
|
F07
|
A:B5N301
|
2.6
|
35.4
|
1.0
|
CE1
|
A:HIS231
|
2.6
|
11.3
|
1.0
|
CE1
|
A:HIS204
|
2.9
|
13.3
|
1.0
|
C04
|
A:B5N301
|
2.9
|
32.6
|
1.0
|
CD2
|
A:HIS208
|
3.0
|
19.9
|
1.0
|
CD2
|
A:HIS204
|
3.0
|
9.1
|
1.0
|
CE1
|
A:HIS208
|
3.0
|
16.8
|
1.0
|
CD2
|
A:HIS231
|
3.2
|
17.0
|
1.0
|
C02
|
A:B5N301
|
3.2
|
27.5
|
1.0
|
C06
|
A:B5N301
|
3.8
|
31.4
|
1.0
|
ND1
|
A:HIS231
|
3.8
|
9.8
|
1.0
|
CU
|
A:CU302
|
3.9
|
24.9
|
1.0
|
CE2
|
A:PHE227
|
3.9
|
12.3
|
1.0
|
ND1
|
A:HIS204
|
4.0
|
12.8
|
1.0
|
CG
|
A:HIS204
|
4.1
|
13.9
|
1.0
|
CG
|
A:HIS231
|
4.1
|
8.6
|
1.0
|
CG
|
A:HIS208
|
4.1
|
20.5
|
1.0
|
ND1
|
A:HIS208
|
4.1
|
18.6
|
1.0
|
C01
|
A:B5N301
|
4.2
|
35.8
|
1.0
|
NE2
|
A:HIS230
|
4.2
|
13.3
|
1.0
|
CD2
|
A:HIS230
|
4.3
|
10.1
|
1.0
|
CZ
|
A:PHE227
|
4.4
|
9.6
|
1.0
|
NE2
|
A:HIS69
|
4.4
|
11.1
|
1.0
|
CD2
|
A:PHE227
|
4.6
|
11.1
|
1.0
|
C05
|
A:B5N301
|
4.7
|
30.8
|
1.0
|
CE1
|
A:PHE65
|
4.7
|
11.4
|
1.0
|
CD2
|
A:HIS69
|
4.8
|
10.7
|
1.0
|
NE2
|
A:HIS60
|
4.8
|
23.1
|
1.0
|
C03
|
A:B5N301
|
4.9
|
37.1
|
1.0
|
|
Copper binding site 3 out
of 4 in 6ei4
Go back to
Copper Binding Sites List in 6ei4
Copper binding site 3 out
of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu302
b:26.1
occ:1.00
|
F07
|
B:B5N301
|
1.9
|
35.4
|
1.0
|
NE2
|
B:HIS42
|
2.0
|
22.1
|
1.0
|
NE2
|
B:HIS60
|
2.0
|
21.2
|
1.0
|
NE2
|
B:HIS69
|
2.0
|
16.0
|
1.0
|
CD2
|
B:HIS42
|
2.8
|
16.6
|
1.0
|
C04
|
B:B5N301
|
2.9
|
32.6
|
1.0
|
CE1
|
B:HIS69
|
2.9
|
16.3
|
1.0
|
CE1
|
B:HIS60
|
2.9
|
19.2
|
1.0
|
CD2
|
B:HIS60
|
3.1
|
25.1
|
1.0
|
CE1
|
B:HIS42
|
3.1
|
19.3
|
1.0
|
CD2
|
B:HIS69
|
3.1
|
11.3
|
1.0
|
C02
|
B:B5N301
|
3.6
|
27.5
|
1.0
|
C06
|
B:B5N301
|
3.7
|
31.4
|
1.0
|
CU
|
B:CU303
|
3.9
|
25.7
|
1.0
|
ND1
|
B:HIS60
|
4.0
|
17.8
|
1.0
|
CG
|
B:HIS42
|
4.0
|
17.6
|
1.0
|
ND1
|
B:HIS69
|
4.1
|
12.8
|
1.0
|
NE2
|
B:HIS231
|
4.1
|
15.8
|
1.0
|
CZ
|
B:PHE227
|
4.1
|
15.4
|
1.0
|
CG
|
B:HIS60
|
4.1
|
20.9
|
1.0
|
ND1
|
B:HIS42
|
4.1
|
27.8
|
1.0
|
CG
|
B:HIS69
|
4.2
|
15.3
|
1.0
|
CE1
|
B:HIS231
|
4.3
|
13.6
|
1.0
|
CE2
|
B:PHE227
|
4.4
|
13.7
|
1.0
|
O
|
B:ALA59
|
4.8
|
19.6
|
1.0
|
CB
|
B:ALA59
|
4.8
|
15.9
|
1.0
|
C01
|
B:B5N301
|
4.8
|
35.8
|
1.0
|
CZ3
|
B:TRP68
|
4.8
|
7.2
|
1.0
|
C05
|
B:B5N301
|
5.0
|
30.8
|
1.0
|
|
Copper binding site 4 out
of 4 in 6ei4
Go back to
Copper Binding Sites List in 6ei4
Copper binding site 4 out
of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Tyrosinase From Bacillus Megaterium with B5N Inhibitor in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu303
b:25.7
occ:1.00
|
NE2
|
B:HIS231
|
2.0
|
15.8
|
1.0
|
NE2
|
B:HIS208
|
2.0
|
26.7
|
1.0
|
NE2
|
B:HIS204
|
2.1
|
26.7
|
1.0
|
F07
|
B:B5N301
|
2.3
|
35.4
|
1.0
|
C04
|
B:B5N301
|
2.5
|
32.6
|
1.0
|
CE1
|
B:HIS231
|
2.7
|
13.6
|
1.0
|
C02
|
B:B5N301
|
2.7
|
27.5
|
1.0
|
CD2
|
B:HIS208
|
2.9
|
23.9
|
1.0
|
CE1
|
B:HIS208
|
3.1
|
15.2
|
1.0
|
CE1
|
B:HIS204
|
3.1
|
27.1
|
1.0
|
CD2
|
B:HIS204
|
3.1
|
25.5
|
1.0
|
CD2
|
B:HIS231
|
3.1
|
11.4
|
1.0
|
C06
|
B:B5N301
|
3.5
|
31.4
|
1.0
|
C01
|
B:B5N301
|
3.8
|
35.8
|
1.0
|
ND1
|
B:HIS231
|
3.9
|
12.8
|
1.0
|
CU
|
B:CU302
|
3.9
|
26.1
|
1.0
|
CE2
|
B:PHE227
|
4.0
|
13.7
|
1.0
|
CG
|
B:HIS208
|
4.1
|
18.4
|
1.0
|
NE2
|
B:HIS230
|
4.1
|
26.3
|
1.0
|
ND1
|
B:HIS208
|
4.1
|
20.9
|
1.0
|
CG
|
B:HIS231
|
4.1
|
11.3
|
1.0
|
CD2
|
B:HIS230
|
4.1
|
22.2
|
1.0
|
ND1
|
B:HIS204
|
4.2
|
28.0
|
1.0
|
CG
|
B:HIS204
|
4.2
|
24.6
|
1.0
|
C05
|
B:B5N301
|
4.4
|
30.8
|
1.0
|
CZ
|
B:PHE227
|
4.5
|
15.4
|
1.0
|
NE2
|
B:HIS69
|
4.5
|
16.0
|
1.0
|
C03
|
B:B5N301
|
4.5
|
37.1
|
1.0
|
CD2
|
B:PHE227
|
4.8
|
13.4
|
1.0
|
CE1
|
B:PHE65
|
4.8
|
18.0
|
1.0
|
CD2
|
B:HIS69
|
4.9
|
11.3
|
1.0
|
NE2
|
B:HIS60
|
5.0
|
21.2
|
1.0
|
|
Reference:
S.Ferro,
B.Deri,
M.P.Germano,
R.Gitto,
L.Ielo,
M.R.Buemi,
G.Certo,
S.Vittorio,
A.Rapisarda,
Y.Pazy,
A.Fishman,
L.De Luca.
Targeting Tyrosinase: Development and Structural Insights of Novel Inhibitors Bearing Arylpiperidine and Arylpiperazine Fragments. J. Med. Chem. V. 61 3908 2018.
ISSN: ISSN 1520-4804
PubMed: 29634898
DOI: 10.1021/ACS.JMEDCHEM.7B01745
Page generated: Wed Jul 31 05:50:30 2024
|