Zinc in PDB 5i3a: Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site, PDB code: 5i3a was solved by M.Kanteev, 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)	35.54 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.648, 74.360, 120.910, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.9

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site (pdb code 5i3a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site, PDB code: 5i3a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.7 occ:1.00 O A:HOH414 2.0 15.8 1.0 NE2 A:HIS60 2.1 24.4 1.0 CE1 A:HIS42 2.1 25.0 1.0 O6 A:HQE303 2.2 37.0 1.0 C5 A:HQE303 2.3 37.4 1.0 C6 A:HQE303 2.6 37.7 1.0 NE2 A:HIS42 2.6 26.2 1.0 CD2 A:HIS60 3.0 22.7 1.0 CE1 A:HIS60 3.0 24.3 1.0 ND1 A:HIS42 3.3 28.2 1.0 ZN A:ZN302 3.5 22.3 1.0 C4 A:HQE303 3.6 39.2 1.0 NE2 A:HIS69 3.8 23.8 1.0 C1 A:HQE303 3.9 42.1 1.0 CD2 A:HIS42 4.0 21.5 1.0 CE2 A:PHE227 4.0 24.4 1.0 CZ A:PHE227 4.1 23.1 1.0 ND1 A:HIS60 4.1 25.9 1.0 CG A:HIS60 4.2 25.4 1.0 CG A:HIS42 4.3 25.1 1.0 CE1 A:HIS69 4.5 23.1 1.0 NE2 A:HIS231 4.6 20.8 1.0 C3 A:HQE303 4.7 44.0 1.0 NE2 A:HIS208 4.7 27.1 1.0 CE1 A:HIS208 4.7 27.0 1.0 CG1 A:VAL218 4.8 28.2 1.0 C2 A:HQE303 4.8 47.1 0.5 O A:VAL218 4.9 29.6 1.0 CG2 A:VAL218 5.0 32.1 1.0 CD2 A:HIS69 5.0 21.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:22.3 occ:1.00 NE2 A:HIS231 2.0 20.8 1.0 O A:HOH414 2.1 15.8 1.0 NE2 A:HIS208 2.2 27.1 1.0 NE2 A:HIS204 2.2 19.6 1.0 CE1 A:HIS231 2.7 23.7 1.0 CE1 A:HIS208 3.0 27.0 1.0 CE1 A:HIS204 3.1 20.4 1.0 CD2 A:HIS208 3.1 27.3 1.0 CD2 A:HIS204 3.2 21.2 1.0 CD2 A:HIS231 3.2 19.8 1.0 C5 A:HQE303 3.5 37.4 1.0 ZN A:ZN301 3.5 26.7 1.0 C4 A:HQE303 3.7 39.2 1.0 CE2 A:PHE227 3.8 24.4 1.0 ND1 A:HIS231 3.9 20.8 1.0 C6 A:HQE303 3.9 37.7 1.0 CZ A:PHE227 4.1 23.1 1.0 NE2 A:HIS69 4.1 23.8 1.0 ND1 A:HIS208 4.1 30.0 1.0 CG A:HIS231 4.1 21.0 1.0 C3 A:HQE303 4.2 44.0 1.0 CG A:HIS208 4.2 30.7 1.0 ND1 A:HIS204 4.2 20.2 1.0 CG A:HIS204 4.3 20.2 1.0 C1 A:HQE303 4.4 42.1 1.0 O6 A:HQE303 4.4 37.0 1.0 C2 A:HQE303 4.6 47.1 0.5 CE1 A:PHE65 4.6 21.5 1.0 CD2 A:HIS230 4.6 23.2 1.0 CD2 A:PHE227 4.6 22.1 1.0 CD2 A:HIS69 4.7 21.6 1.0 NE2 A:HIS230 4.7 22.4 1.0 NE2 A:HIS60 4.8 24.4 1.0 CE1 A:HIS69 4.8 23.1 1.0 CD2 A:HIS60 4.9 22.7 1.0 CZ A:PHE65 4.9 21.7 1.0 O3 A:HQE303 5.0 40.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:32.3 occ:1.00 O B:HOH409 2.0 28.4 1.0 NE2 B:HIS60 2.1 32.4 1.0 CE1 B:HIS42 2.2 25.1 1.0 O3 B:HQE304 2.2 42.3 1.0 NE2 B:HIS42 2.7 24.1 1.0 C4 B:HQE304 2.8 41.9 1.0 C3 B:HQE304 2.9 42.5 1.0 CD2 B:HIS60 3.0 28.8 1.0 CE1 B:HIS60 3.2 30.7 1.0 ZN B:ZN302 3.4 24.8 1.0 ND1 B:HIS42 3.4 27.1 1.0 NE2 B:HIS69 3.7 24.8 1.0 CE1 B:PHE227 4.0 25.8 1.0 CZ B:PHE227 4.1 26.9 1.0 CD2 B:HIS42 4.1 22.4 1.0 C5 B:HQE304 4.1 42.2 1.0 CG B:HIS60 4.2 29.9 1.0 C2 B:HQE304 4.2 43.5 0.5 ND1 B:HIS60 4.2 31.8 1.0 CG B:HIS42 4.4 23.5 1.0 CE1 B:HIS69 4.4 24.1 1.0 NE2 B:HIS231 4.6 22.9 1.0 CG1 B:VAL218 4.6 30.8 1.0 NE2 B:HIS208 4.6 25.7 1.0 CE1 B:HIS208 4.7 26.4 1.0 CD2 B:HIS69 4.8 24.8 1.0 NE2 B:HIS204 4.9 23.7 1.0 O B:VAL218 4.9 28.5 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:24.8 occ:1.00 NE2 B:HIS231 2.0 22.9 1.0 O B:HOH409 2.1 28.4 1.0 NE2 B:HIS208 2.1 25.7 1.0 NE2 B:HIS204 2.2 23.7 1.0 CE1 B:HIS231 2.8 21.1 1.0 CE1 B:HIS208 3.0 26.4 1.0 CD2 B:HIS208 3.1 25.8 1.0 CE1 B:HIS204 3.1 26.0 1.0 CD2 B:HIS204 3.2 26.3 1.0 CD2 B:HIS231 3.2 23.3 1.0 ZN B:ZN301 3.4 32.3 1.0 C4 B:HQE304 3.4 41.9 1.0 CE1 B:PHE227 3.7 25.8 1.0 C3 B:HQE304 3.9 42.5 1.0 O3 B:HQE304 3.9 42.3 1.0 ND1 B:HIS231 4.0 21.5 1.0 CZ B:PHE227 4.1 26.9 1.0 ND1 B:HIS208 4.1 25.3 1.0 CG B:HIS208 4.1 26.4 1.0 C5 B:HQE304 4.2 42.2 1.0 CG B:HIS231 4.2 22.1 1.0 NE2 B:HIS69 4.2 24.8 1.0 ND1 B:HIS204 4.2 24.2 1.0 CG B:HIS204 4.3 26.2 1.0 CD2 B:HIS230 4.6 28.4 1.0 CD1 B:PHE227 4.6 25.1 1.0 CE1 B:PHE65 4.7 25.8 1.0 CD2 B:HIS69 4.7 24.8 1.0 NE2 B:HIS230 4.8 26.6 1.0 C2 B:HQE304 4.9 43.5 0.5 CE1 B:HIS69 5.0 24.1 1.0 NE2 B:HIS60 5.0 32.4 1.0 CZ B:PHE65 5.0 26.4 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration A of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:59.1 occ:1.00 NE2 B:HIS13 2.4 46.3 1.0 CD2 B:HIS13 3.3 44.6 1.0 CE1 B:HIS13 3.5 48.2 1.0 CG B:HIS13 4.5 44.6 1.0 ND1 B:HIS13 4.5 46.4 1.0 O B:HOH470 4.7 32.7 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