Copper in PDB 5i38: Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid in the Active Site

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid in the Active Site, PDB code: 5i38 was solved by M.Kanteev, M.Goldfeder, B.Deri, N.Adir, A.Fishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.82 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.240, 74.970, 121.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.1

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid in the Active Site (pdb code 5i38). 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 Inhibitor Kojic Acid in the Active Site, PDB code: 5i38:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid 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 Inhibitor Kojic Acid in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:25.9 occ:1.00 NE2 A:HIS231 2.0 22.5 1.0 NE2 A:HIS208 2.1 24.2 1.0 NE2 A:HIS204 2.1 24.5 1.0 O A:HOH401 2.3 22.9 1.0 CE1 A:HIS231 2.7 21.7 1.0 CD2 A:HIS208 2.9 27.3 1.0 CD2 A:HIS204 3.0 19.8 1.0 CE1 A:HIS204 3.1 26.8 1.0 CE1 A:HIS208 3.1 28.0 1.0 CD2 A:HIS231 3.2 18.4 1.0 O2 A:KOJ303 3.5 42.9 1.0 CE2 A:PHE227 3.7 23.1 1.0 ND1 A:HIS231 3.8 16.4 1.0 C2 A:KOJ303 3.9 34.2 1.0 CG A:HIS208 4.1 25.7 1.0 CG A:HIS231 4.1 18.0 1.0 ND1 A:HIS208 4.1 22.9 1.0 CG A:HIS204 4.1 22.4 1.0 ND1 A:HIS204 4.1 23.9 1.0 CD2 A:HIS230 4.1 25.8 1.0 CZ A:PHE227 4.2 26.4 1.0 CU A:CU302 4.2 31.9 1.0 NE2 A:HIS230 4.2 21.9 1.0 C1 A:KOJ303 4.3 34.8 1.0 CD2 A:PHE227 4.4 22.6 1.0 NE2 A:HIS69 4.6 19.9 1.0 C3 A:KOJ303 4.6 29.2 1.0 CE1 A:PHE65 4.9 21.8 1.0 O3 A:KOJ303 4.9 34.0 1.0 NE2 A:HIS60 5.0 28.7 1.0 CD2 A:HIS69 5.0 20.6 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid 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 Inhibitor Kojic Acid in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:31.9 occ:1.00 NE2 A:HIS69 2.0 19.9 1.0 NE2 A:HIS42 2.0 24.2 1.0 O A:HOH401 2.1 22.9 1.0 NE2 A:HIS60 2.2 28.7 1.0 CD2 A:HIS42 2.6 16.8 1.0 CE1 A:HIS69 2.8 23.1 1.0 CE1 A:HIS60 2.9 33.3 1.0 CD2 A:HIS69 3.2 20.6 1.0 CD2 A:HIS60 3.3 25.5 1.0 CE1 A:HIS42 3.3 24.6 1.0 O2 A:KOJ303 3.3 42.9 1.0 CZ A:PHE227 3.7 26.4 1.0 CG A:HIS42 3.9 18.2 1.0 ND1 A:HIS69 4.0 23.2 1.0 ND1 A:HIS60 4.1 26.5 1.0 NE2 A:HIS231 4.1 22.5 1.0 ND1 A:HIS42 4.2 16.9 1.0 CE2 A:PHE227 4.2 23.1 1.0 CG A:HIS69 4.2 23.3 1.0 CU A:CU301 4.2 25.9 1.0 CG A:HIS60 4.3 29.2 1.0 CE1 A:HIS231 4.3 21.7 1.0 CZ3 A:TRP68 4.5 20.7 1.0 CB A:ALA59 4.7 22.4 1.0 O A:ALA59 4.8 18.2 1.0 C2 A:KOJ303 4.8 34.2 1.0 CE1 A:PHE227 4.8 21.2 1.0 CE3 A:TRP68 4.9 20.7 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid 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 Inhibitor Kojic Acid in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:31.2 occ:1.00 NE2 B:HIS60 2.0 30.3 1.0 NE2 B:HIS42 2.0 26.8 1.0 O B:HOH401 2.1 28.6 1.0 NE2 B:HIS69 2.2 18.9 1.0 CD2 B:HIS42 2.7 19.2 1.0 CE1 B:HIS60 2.7 31.3 1.0 CE1 B:HIS69 2.9 25.2 1.0 CD2 B:HIS60 3.2 26.7 1.0 CE1 B:HIS42 3.2 28.5 1.0 CD2 B:HIS69 3.4 20.1 1.0 O2 B:KOJ303 3.5 35.5 1.0 CZ B:PHE227 3.7 24.8 1.0 ND1 B:HIS60 3.9 22.4 1.0 CG B:HIS42 3.9 19.4 1.0 NE2 B:HIS231 4.1 24.3 1.0 CU B:CU302 4.1 30.2 1.0 ND1 B:HIS69 4.1 24.8 1.0 CE2 B:PHE227 4.1 25.2 1.0 O3 B:KOJ303 4.2 32.1 1.0 ND1 B:HIS42 4.2 21.9 1.0 CG B:HIS60 4.2 25.8 1.0 CE1 B:HIS231 4.2 25.6 1.0 CG B:HIS69 4.4 23.4 1.0 C2 B:KOJ303 4.8 28.3 1.0 CZ3 B:TRP68 4.8 23.4 1.0 CE1 B:PHE227 4.8 23.1 1.0 CB B:ALA59 4.8 24.8 1.0 O B:ALA59 4.9 27.6 1.0 C3 B:KOJ303 5.0 30.6 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Inhibitor Kojic Acid 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 Inhibitor Kojic Acid in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:30.2 occ:1.00 NE2 B:HIS231 2.0 24.3 1.0 NE2 B:HIS208 2.1 24.9 1.0 NE2 B:HIS204 2.1 23.5 1.0 O B:HOH401 2.1 28.6 1.0 CE1 B:HIS231 2.6 25.6 1.0 CD2 B:HIS208 2.9 21.7 1.0 CD2 B:HIS204 3.0 19.7 1.0 CE1 B:HIS208 3.1 26.0 1.0 CE1 B:HIS204 3.1 25.8 1.0 O2 B:KOJ303 3.2 35.5 1.0 CD2 B:HIS231 3.2 24.5 1.0 C2 B:KOJ303 3.7 28.3 1.0 ND1 B:HIS231 3.8 18.1 1.0 CE2 B:PHE227 3.8 25.2 1.0 O3 B:KOJ303 4.0 32.1 1.0 CG B:HIS208 4.1 23.3 1.0 CG B:HIS231 4.1 22.0 1.0 ND1 B:HIS208 4.1 26.0 1.0 C3 B:KOJ303 4.1 30.6 1.0 CU B:CU301 4.1 31.2 1.0 ND1 B:HIS204 4.1 25.1 1.0 CG B:HIS204 4.2 25.3 1.0 CD2 B:HIS230 4.3 20.4 1.0 CZ B:PHE227 4.3 24.8 1.0 NE2 B:HIS230 4.4 20.3 1.0 NE2 B:HIS69 4.5 18.9 1.0 CD2 B:PHE227 4.6 24.0 1.0 C1 B:KOJ303 4.6 25.9 1.0 CE1 B:PHE65 4.8 26.4 1.0 NE2 B:HIS60 4.9 30.3 1.0

B.Deri, M.Kanteev, M.Goldfeder, D.Lecina, V.Guallar, N.Adir, A.Fishman. The Unravelling of the Complex Pattern of Tyrosinase Inhibition. Sci Rep V. 6 34993 2016.
ISSN: ESSN 2045-2322
PubMed: 27725765
DOI: 10.1038/SREP34993