Zinc in PDB 4p6r: Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine in the Active Site

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine in the Active Site:
1.14.18.1;

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine in the Active Site, PDB code: 4p6r was solved by M.Goldfeder, M.Kanteev, N.Adir, A.Fishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.87 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.800, 78.680, 85.820, 90.00, 102.63, 90.00
R / Rfree (%)	19.1 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine in the Active Site (pdb code 4p6r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine in the Active Site, PDB code: 4p6r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine 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 Tyrosine in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.8 occ:1.00 NE2 A:HIS204 2.0 9.8 1.0 NE2 A:HIS231 2.0 11.6 1.0 NE2 A:HIS208 2.1 16.9 1.0 O A:HOH506 2.1 32.8 1.0 CE1 A:HIS231 2.6 14.8 1.0 CD2 A:HIS204 2.9 15.5 1.0 CE1 A:HIS204 3.0 14.3 1.0 CE1 A:HIS208 3.0 16.2 1.0 CD2 A:HIS208 3.1 18.4 1.0 CD2 A:HIS231 3.2 12.2 1.0 ZN A:ZN302 3.5 32.5 1.0 OH A:TYR303 3.5 22.5 1.0 CE1 A:TYR303 3.8 15.8 1.0 ND1 A:HIS231 3.9 9.5 1.0 CE2 A:PHE227 3.9 14.0 1.0 CZ A:TYR303 3.9 18.5 1.0 ND1 A:HIS204 4.1 14.1 1.0 CG A:HIS204 4.1 13.1 1.0 NE2 A:HIS69 4.1 18.4 1.0 CZ A:PHE227 4.1 13.7 1.0 ND1 A:HIS208 4.1 16.3 1.0 CG A:HIS231 4.2 11.7 1.0 CG A:HIS208 4.2 16.5 1.0 CE1 A:PHE65 4.6 18.1 1.0 CD2 A:HIS69 4.6 12.7 1.0 CD2 A:PHE227 4.7 12.7 1.0 CD2 A:HIS230 4.7 9.7 1.0 CD1 A:TYR303 4.7 16.5 1.0 CE1 A:HIS69 4.8 14.6 1.0 NE2 A:HIS42 4.9 24.0 1.0 CE2 A:TYR303 4.9 20.1 1.0 NE2 A:HIS60 4.9 21.6 1.0 CZ A:PHE65 5.0 17.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine 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 Tyrosine in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:32.5 occ:1.00 OH A:TYR303 1.9 22.5 1.0 O A:HOH506 2.0 32.8 1.0 NE2 A:HIS60 2.0 21.6 1.0 NE2 A:HIS42 2.1 24.0 1.0 CE1 A:HIS42 2.6 17.3 1.0 CD2 A:HIS60 2.9 20.5 1.0 CZ A:TYR303 3.0 18.5 1.0 CE1 A:HIS60 3.1 14.5 1.0 CE1 A:TYR303 3.3 15.8 1.0 CD2 A:HIS42 3.4 20.2 1.0 ZN A:ZN301 3.5 16.8 1.0 NE2 A:HIS69 3.7 18.4 1.0 ND1 A:HIS42 3.9 20.1 1.0 CE2 A:PHE227 4.0 14.0 1.0 CZ A:PHE227 4.1 13.7 1.0 CG A:HIS60 4.1 20.6 1.0 ND1 A:HIS60 4.2 14.7 1.0 CE2 A:TYR303 4.2 20.1 1.0 CE1 A:HIS69 4.2 14.6 1.0 CG A:HIS42 4.3 20.6 1.0 CG1 A:VAL218 4.4 16.7 1.0 NE2 A:HIS208 4.5 16.9 1.0 CE1 A:HIS208 4.6 16.2 1.0 CD1 A:TYR303 4.7 16.5 1.0 NE2 A:HIS231 4.8 11.6 1.0 NE2 A:HIS204 4.8 9.8 1.0 CD2 A:HIS69 4.9 12.7 1.0 O A:VAL218 5.0 18.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine 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 Tyrosine in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:35.4 occ:1.00 O B:HOH514 1.9 36.5 1.0 OH B:TYR303 2.0 24.4 1.0 NE2 B:HIS42 2.0 22.2 1.0 NE2 B:HIS60 2.1 20.5 1.0 CE1 B:HIS42 2.9 16.6 1.0 CD2 B:HIS60 3.0 19.9 1.0 CZ B:TYR303 3.1 21.3 1.0 CE1 B:HIS60 3.1 18.3 1.0 CD2 B:HIS42 3.1 15.9 1.0 NE2 B:HIS69 3.3 18.3 1.0 CE1 B:TYR303 3.4 20.3 1.0 ZN B:ZN302 3.4 18.4 1.0 CE2 B:PHE227 3.9 10.4 1.0 CE1 B:HIS69 3.9 16.8 1.0 CZ B:PHE227 4.0 12.8 1.0 ND1 B:HIS42 4.1 21.6 1.0 CG B:HIS60 4.1 23.2 1.0 ND1 B:HIS60 4.2 17.7 1.0 CG B:HIS42 4.2 20.0 1.0 CE2 B:TYR303 4.3 20.4 1.0 NE2 B:HIS208 4.4 16.1 1.0 CG1 B:VAL218 4.4 25.6 1.0 CD2 B:HIS69 4.4 9.4 1.0 NE2 B:HIS231 4.6 15.6 1.0 CE1 B:HIS208 4.6 11.4 1.0 CD1 B:TYR303 4.8 20.6 1.0 CG2 B:VAL218 4.8 27.2 1.0 NE2 B:HIS204 4.9 19.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Tyrosine 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 Tyrosine in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.4 occ:1.00 O B:HOH514 2.0 36.5 1.0 NE2 B:HIS208 2.0 16.1 1.0 NE2 B:HIS231 2.0 15.6 1.0 NE2 B:HIS204 2.1 19.2 1.0 CE1 B:HIS231 2.8 17.7 1.0 CD2 B:HIS208 3.0 14.1 1.0 CE1 B:HIS208 3.0 11.4 1.0 CE1 B:HIS204 3.1 17.9 1.0 CD2 B:HIS204 3.1 22.4 1.0 CD2 B:HIS231 3.2 14.6 1.0 ZN B:ZN301 3.4 35.4 1.0 OH B:TYR303 3.4 24.4 1.0 CE1 B:TYR303 3.6 20.3 1.0 CZ B:TYR303 3.7 21.3 1.0 CE2 B:PHE227 3.9 10.4 1.0 ND1 B:HIS231 4.0 14.8 1.0 NE2 B:HIS69 4.1 18.3 1.0 ND1 B:HIS208 4.1 14.2 1.0 CG B:HIS208 4.1 13.8 1.0 CZ B:PHE227 4.2 12.8 1.0 ND1 B:HIS204 4.2 16.8 1.0 CG B:HIS231 4.2 13.3 1.0 CG B:HIS204 4.2 20.2 1.0 CD2 B:HIS69 4.4 9.4 1.0 CD1 B:TYR303 4.5 20.6 1.0 CE1 B:PHE65 4.7 19.6 1.0 CD2 B:PHE227 4.7 11.3 1.0 CD2 B:HIS230 4.8 13.4 1.0 CE2 B:TYR303 4.8 20.4 1.0 CE1 B:HIS69 4.8 16.8 1.0 NE2 B:HIS60 4.9 20.5 1.0 CD2 B:HIS60 5.0 19.9 1.0 CZ B:PHE65 5.0 15.9 1.0

M.Goldfeder, M.Kanteev, S.Isaschar-Ovdat, N.Adir, A.Fishman. Determination of Tyrosinase Substrate-Binding Modes Reveals Mechanistic Differences Between Type-3 Copper Proteins. Nat Commun V. 5 4505 2014.
ISSN: ESSN 2041-1723
PubMed: 25074014
DOI: 10.1038/NCOMMS5505