Copper in PDB 4p6t: Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site

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

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site, PDB code: 4p6t 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)	56.23 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.690, 78.090, 84.280, 90.00, 105.96, 90.00
R / Rfree (%)	20.8 / 26.1

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site (pdb code 4p6t). 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 P- Tyrosol in the Active Site, PDB code: 4p6t:
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 P- Tyrosol 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 P- Tyrosol in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:32.1 occ:1.00 O A:HOH490 1.6 56.2 1.0 H041 A:YRL301 1.9 49.1 1.0 NE2 A:HIS60 2.0 22.7 1.0 O07 A:YRL301 2.1 51.1 1.0 NE2 A:HIS42 2.1 17.2 1.0 C04 A:YRL301 2.5 49.1 1.0 NE2 A:HIS69 2.6 18.7 1.0 H071 A:YRL301 2.6 51.1 1.0 C06 A:YRL301 2.8 47.1 1.0 CD2 A:HIS60 2.8 20.3 1.0 CE1 A:HIS42 2.9 17.2 1.0 CE1 A:HIS60 3.2 21.0 1.0 CE1 A:HIS69 3.2 18.5 1.0 CD2 A:HIS42 3.3 14.9 1.0 CU A:CU303 3.3 15.2 1.0 CD2 A:HIS69 3.7 16.8 1.0 C02 A:YRL301 3.8 50.5 1.0 CZ A:PHE227 3.8 13.8 1.0 CE2 A:PHE227 4.0 14.6 1.0 CG A:HIS60 4.0 20.9 1.0 ND1 A:HIS42 4.1 16.9 1.0 C05 A:YRL301 4.1 51.0 1.0 ND1 A:HIS60 4.2 22.0 1.0 H021 A:YRL301 4.2 50.5 1.0 NE2 A:HIS231 4.3 14.5 1.0 CG A:HIS42 4.3 14.9 1.0 ND1 A:HIS69 4.4 15.5 1.0 H051 A:YRL301 4.6 51.0 1.0 CG A:HIS69 4.7 19.0 1.0 NE2 A:HIS208 4.8 22.4 1.0 CG1 A:VAL218 4.8 33.5 1.0 CE1 A:HIS231 4.8 11.8 1.0 NE2 A:HIS204 4.9 15.0 1.0 C01 A:YRL301 4.9 51.5 1.0 CE1 A:HIS208 4.9 22.4 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol 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 P- Tyrosol in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu303 b:15.2 occ:1.00 O A:HOH490 1.8 56.2 1.0 NE2 A:HIS208 2.0 22.4 1.0 H041 A:YRL301 2.1 49.1 1.0 NE2 A:HIS204 2.1 15.0 1.0 NE2 A:HIS231 2.1 14.5 1.0 C04 A:YRL301 2.6 49.1 1.0 H021 A:YRL301 2.7 50.5 1.0 CE1 A:HIS208 2.8 22.4 1.0 C02 A:YRL301 2.9 50.5 1.0 CD2 A:HIS231 3.0 13.6 1.0 CD2 A:HIS204 3.1 13.4 1.0 CE1 A:HIS204 3.1 15.5 1.0 CD2 A:HIS208 3.2 22.9 1.0 CE1 A:HIS231 3.2 11.8 1.0 CU A:CU302 3.3 32.1 1.0 C06 A:YRL301 3.5 47.1 1.0 CE2 A:PHE227 3.8 14.6 1.0 O07 A:YRL301 3.9 51.1 1.0 ND1 A:HIS208 3.9 22.9 1.0 H071 A:YRL301 4.0 51.1 1.0 C01 A:YRL301 4.1 51.5 1.0 NE2 A:HIS69 4.1 18.7 1.0 CZ A:PHE227 4.2 13.8 1.0 CG A:HIS208 4.2 23.8 1.0 ND1 A:HIS204 4.2 16.1 1.0 CG A:HIS231 4.2 11.3 1.0 CG A:HIS204 4.2 15.5 1.0 ND1 A:HIS231 4.2 9.9 1.0 CE1 A:HIS230 4.3 20.2 1.0 CD2 A:HIS69 4.4 16.8 1.0 C05 A:YRL301 4.5 51.0 1.0 ND1 A:HIS230 4.6 18.6 1.0 H082 A:YRL301 4.7 51.2 1.0 CD2 A:PHE227 4.7 13.9 1.0 CE1 A:PHE65 4.7 14.6 1.0 C03 A:YRL301 4.7 49.1 1.0 CE1 A:HIS69 4.8 18.5 1.0 CD2 A:HIS60 4.9 20.3 1.0 NE2 A:HIS60 4.9 22.7 1.0 C08 A:YRL301 5.0 51.2 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol 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 P- Tyrosol in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:36.2 occ:1.00 O B:HOH465 1.5 0.1 1.0 H071 B:YRL301 1.7 44.5 1.0 O07 B:YRL301 1.8 44.5 1.0 NE2 B:HIS60 1.9 24.7 1.0 NE2 B:HIS42 2.2 19.6 1.0 CE1 B:HIS60 2.7 20.9 1.0 CD2 B:HIS60 3.0 23.9 1.0 CE1 B:HIS42 3.0 17.4 1.0 NE2 B:HIS69 3.0 11.2 1.0 C06 B:YRL301 3.2 42.6 1.0 CD2 B:HIS42 3.2 15.4 1.0 CU B:CU303 3.2 20.5 1.0 H051 B:YRL301 3.6 45.1 1.0 CE1 B:HIS69 3.7 11.7 1.0 C05 B:YRL301 3.9 45.1 1.0 ND1 B:HIS60 3.9 24.2 1.0 CG B:HIS60 4.0 23.4 1.0 C04 B:YRL301 4.2 46.7 1.0 CE2 B:PHE227 4.2 13.9 1.0 H041 B:YRL301 4.2 46.7 1.0 ND1 B:HIS42 4.2 15.2 1.0 CD2 B:HIS69 4.2 9.2 1.0 CZ B:PHE227 4.2 12.2 1.0 NE2 B:HIS231 4.2 14.8 1.0 CG B:HIS42 4.3 16.1 1.0 NE2 B:HIS204 4.6 18.4 1.0 NE2 B:HIS208 4.7 10.5 1.0 CE1 B:HIS231 4.8 13.9 1.0 CE1 B:HIS204 4.9 22.2 1.0 ND1 B:HIS69 4.9 9.5 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol 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 P- Tyrosol in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu303 b:20.5 occ:1.00 O B:HOH465 1.8 0.1 1.0 NE2 B:HIS231 2.0 14.8 1.0 NE2 B:HIS208 2.1 10.5 1.0 NE2 B:HIS204 2.2 18.4 1.0 CE1 B:HIS231 2.9 13.9 1.0 CD2 B:HIS208 3.0 12.8 1.0 CE1 B:HIS204 3.1 22.2 1.0 CD2 B:HIS231 3.1 13.8 1.0 CD2 B:HIS204 3.1 20.3 1.0 CE1 B:HIS208 3.1 12.4 1.0 CU B:CU302 3.2 36.2 1.0 O07 B:YRL301 3.3 44.5 1.0 H051 B:YRL301 3.5 45.1 1.0 C06 B:YRL301 3.8 42.6 1.0 C05 B:YRL301 3.8 45.1 1.0 CE2 B:PHE227 3.9 13.9 1.0 H071 B:YRL301 4.0 44.5 1.0 NE2 B:HIS69 4.0 11.2 1.0 ND1 B:HIS231 4.1 13.8 1.0 CG B:HIS208 4.1 15.3 1.0 CG B:HIS231 4.2 13.7 1.0 ND1 B:HIS208 4.2 14.2 1.0 CZ B:PHE227 4.2 12.2 1.0 ND1 B:HIS204 4.2 20.1 1.0 CG B:HIS204 4.3 20.7 1.0 CD2 B:HIS69 4.5 9.2 1.0 NE2 B:HIS60 4.6 24.7 1.0 CE1 B:HIS230 4.6 21.8 1.0 CD2 B:PHE227 4.7 13.2 1.0 ND1 B:HIS230 4.7 21.7 1.0 CE1 B:HIS69 4.8 11.7 1.0 C04 B:YRL301 4.9 46.7 1.0 CE1 B:PHE65 4.9 18.2 1.0 C03 B:YRL301 4.9 49.9 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