Zinc in PDB 5i3b: Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B of Hydroquinone Inhibitor in the Active Site

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B of Hydroquinone Inhibitor in the Active Site, PDB code: 5i3b 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)	33.43 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.620, 74.420, 119.690, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.7

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B of Hydroquinone Inhibitor in the Active Site (pdb code 5i3b). 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 B of Hydroquinone Inhibitor in the Active Site, PDB code: 5i3b:
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 B 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 B of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.2 occ:1.00 O A:HOH426 2.0 16.7 1.0 NE2 A:HIS60 2.1 19.4 1.0 NE2 A:HIS42 2.1 23.4 1.0 C5 A:HQE303 2.1 22.3 1.0 O6 A:HQE303 2.2 30.0 0.8 C6 A:HQE303 2.4 23.5 1.0 CE1 A:HIS42 2.9 23.7 1.0 CD2 A:HIS60 3.0 19.0 1.0 CE1 A:HIS60 3.0 25.0 1.0 C4 A:HQE303 3.2 33.1 1.0 CD2 A:HIS42 3.2 20.5 1.0 ZN A:ZN302 3.5 21.4 1.0 C1 A:HQE303 3.5 30.0 1.0 NE2 A:HIS69 3.9 22.0 1.0 CE2 A:PHE227 3.9 20.8 1.0 CZ A:PHE227 4.1 21.7 1.0 ND1 A:HIS42 4.1 23.0 1.0 ND1 A:HIS60 4.1 21.2 1.0 CG A:HIS60 4.2 24.4 1.0 C3 A:HQE303 4.2 24.4 0.4 CG A:HIS42 4.3 21.9 1.0 C2 A:HQE303 4.3 26.2 0.3 CE1 A:HIS69 4.4 22.5 1.0 CG1 A:VAL218 4.5 25.3 1.0 NE2 A:HIS208 4.5 22.1 1.0 NE2 A:HIS231 4.7 17.8 1.0 CE1 A:HIS208 4.8 23.4 1.0 CG2 A:VAL218 4.9 25.6 1.0 NE2 A:HIS204 5.0 18.2 1.0 O A:VAL218 5.0 25.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B 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 B of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.4 occ:1.00 NE2 A:HIS231 1.9 17.8 1.0 O A:HOH426 2.0 16.7 1.0 NE2 A:HIS208 2.1 22.1 1.0 NE2 A:HIS204 2.2 18.2 1.0 CE1 A:HIS231 2.7 21.4 1.0 CD2 A:HIS208 3.0 20.0 1.0 CD2 A:HIS231 3.1 16.6 1.0 CD2 A:HIS204 3.1 20.0 1.0 CE1 A:HIS208 3.1 23.4 1.0 CE1 A:HIS204 3.1 21.3 1.0 ZN A:ZN301 3.5 22.2 1.0 CE2 A:PHE227 3.8 20.8 1.0 ND1 A:HIS231 3.9 17.3 1.0 C4 A:HQE303 4.0 33.1 1.0 C5 A:HQE303 4.0 22.3 1.0 CZ A:PHE227 4.1 21.7 1.0 CG A:HIS231 4.1 19.4 1.0 NE2 A:HIS69 4.1 22.0 1.0 CG A:HIS208 4.2 24.6 1.0 ND1 A:HIS208 4.2 24.9 1.0 ND1 A:HIS204 4.2 19.5 1.0 CG A:HIS204 4.3 21.0 1.0 C3 A:HQE303 4.3 24.4 0.4 C6 A:HQE303 4.3 23.5 1.0 CD2 A:HIS230 4.5 23.6 1.0 CE1 A:PHE65 4.6 21.2 1.0 C2 A:HQE303 4.6 26.2 0.3 C1 A:HQE303 4.6 30.0 1.0 CD2 A:PHE227 4.6 20.3 1.0 NE2 A:HIS230 4.7 21.4 1.0 CD2 A:HIS69 4.7 23.2 1.0 CE1 A:HIS69 4.8 22.5 1.0 NE2 A:HIS60 4.8 19.4 1.0 O3 A:HQE303 4.8 31.0 1.0 CD2 A:HIS60 4.9 19.0 1.0 O6 A:HQE303 5.0 30.0 0.8 CZ A:PHE65 5.0 19.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B 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 B of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:35.0 occ:1.00 O6 B:HQE303 1.6 20.8 0.7 C6 B:HQE303 1.8 27.7 0.8 O B:HOH412 1.9 42.6 1.0 NE2 B:HIS42 2.3 25.3 1.0 NE2 B:HIS60 2.3 31.3 1.0 C1 B:HQE303 2.4 30.1 0.5 C5 B:HQE303 2.7 26.7 1.0 ZN B:ZN302 3.1 25.2 1.0 CD2 B:HIS60 3.1 30.0 1.0 CD2 B:HIS42 3.2 26.2 1.0 CE1 B:HIS42 3.3 22.9 1.0 NE2 B:HIS69 3.4 24.3 1.0 CE1 B:HIS60 3.4 28.0 1.0 C2 B:HQE303 3.5 32.9 1.0 C4 B:HQE303 3.7 27.7 0.5 CE2 B:PHE227 3.8 24.3 1.0 CZ B:PHE227 3.8 24.0 1.0 C3 B:HQE303 4.0 30.3 0.7 CE1 B:HIS69 4.1 26.7 1.0 NE2 B:HIS231 4.2 28.6 1.0 NE2 B:HIS208 4.3 28.0 1.0 CG B:HIS60 4.3 29.5 1.0 ND1 B:HIS42 4.4 25.2 1.0 CG B:HIS42 4.4 24.4 1.0 ND1 B:HIS60 4.5 27.9 1.0 CD2 B:HIS69 4.5 24.0 1.0 CE1 B:HIS208 4.6 26.5 1.0 NE2 B:HIS204 4.6 25.7 1.0 CE1 B:HIS231 4.8 22.5 1.0 CE1 B:HIS204 5.0 27.6 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B 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 B of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:25.2 occ:1.00 O B:HOH412 1.6 42.6 1.0 NE2 B:HIS231 2.0 28.6 1.0 NE2 B:HIS208 2.1 28.0 1.0 NE2 B:HIS204 2.2 25.7 1.0 CE1 B:HIS231 2.8 22.5 1.0 CD2 B:HIS208 3.0 26.6 1.0 ZN B:ZN301 3.1 35.0 1.0 CD2 B:HIS231 3.1 26.9 1.0 CE1 B:HIS208 3.1 26.5 1.0 CD2 B:HIS204 3.2 25.0 1.0 CE1 B:HIS204 3.2 27.6 1.0 C1 B:HQE303 3.7 30.1 0.5 CE2 B:PHE227 3.8 24.3 1.0 C2 B:HQE303 3.9 32.9 1.0 ND1 B:HIS231 4.0 21.4 1.0 C6 B:HQE303 4.1 27.7 0.8 CZ B:PHE227 4.1 24.0 1.0 CG B:HIS208 4.1 25.8 1.0 CG B:HIS231 4.1 25.9 1.0 ND1 B:HIS208 4.2 27.3 1.0 NE2 B:HIS69 4.2 24.3 1.0 ND1 B:HIS204 4.3 24.8 1.0 CG B:HIS204 4.3 24.9 1.0 C3 B:HQE303 4.5 30.3 0.7 CD2 B:HIS230 4.6 25.0 1.0 O6 B:HQE303 4.6 20.8 0.7 CE1 B:PHE65 4.6 24.5 1.0 C5 B:HQE303 4.6 26.7 1.0 CD2 B:PHE227 4.6 15.5 1.0 CD2 B:HIS69 4.7 24.0 1.0 NE2 B:HIS230 4.7 26.9 1.0 C4 B:HQE303 4.8 27.7 0.5 CE1 B:HIS69 4.9 26.7 1.0 NE2 B:HIS60 4.9 31.3 1.0 CD2 B:HIS60 5.0 30.0 1.0 NE2 B:HIS42 5.0 25.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Configuration B 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 B of Hydroquinone Inhibitor in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:69.3 occ:0.76 CE1 B:HIS13 2.5 50.6 1.0 O B:HOH506 3.1 53.7 1.0 ND1 B:HIS13 3.4 50.6 1.0 NE2 B:HIS13 3.5 53.4 1.0 CG B:HIS13 4.6 41.8 1.0 CD2 B:HIS13 4.6 46.8 1.0 O B:HOH426 4.8 41.2 1.0 CB B:LEU12 4.9 40.0 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