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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:

Fluorine (F) 2 atoms

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

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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: Sun Dec 13 11:22:12 2020

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