Copper in PDB 3nm8: Crystal Structure of Tyrosinase From Bacillus Megaterium

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium:
1.14.18.1;

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium, PDB code: 3nm8 was solved by M.Sendovski, 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)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.210, 84.490, 146.310, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.3

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Zinc	(Zn)	7 atoms

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium (pdb code 3nm8). 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, PDB code: 3nm8:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:25.2 occ:1.00 O A:HOH340 1.8 30.0 1.0 NE2 A:HIS60 2.0 18.4 1.0 NE2 A:HIS42 2.2 17.1 1.0 O A:HOH344 2.2 26.7 1.0 CE1 A:HIS42 2.9 20.6 1.0 CE1 A:HIS60 3.0 19.8 1.0 O A:HOH339 3.0 30.0 1.0 CD2 A:HIS60 3.0 19.5 1.0 CD2 A:HIS42 3.3 15.1 1.0 CU A:CU502 3.6 18.2 1.0 NE2 A:HIS69 3.8 16.3 1.0 O A:HOH338 4.0 30.0 1.0 ND1 A:HIS60 4.1 19.6 1.0 CE2 A:PHE227 4.1 13.8 1.0 CG A:HIS60 4.1 21.9 1.0 ND1 A:HIS42 4.1 19.8 1.0 CG A:HIS42 4.3 19.8 1.0 CE1 A:HIS69 4.4 16.5 1.0 CZ A:PHE227 4.4 18.8 1.0 CG2 A:VAL218 4.6 33.5 1.0 NE2 A:HIS208 4.6 16.3 1.0 CE1 A:HIS208 4.7 17.0 1.0 CG1 A:VAL218 4.7 33.5 1.0 NE2 A:HIS231 4.8 15.8 1.0 CA A:VAL218 4.9 29.3 1.0 O A:VAL218 4.9 27.9 1.0 NE2 A:HIS204 4.9 21.3 1.0 CB A:VAL218 5.0 35.8 1.0 CD2 A:HIS69 5.0 18.0 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:18.2 occ:1.00 NE2 A:HIS231 1.9 15.8 1.0 NE2 A:HIS204 2.0 21.3 1.0 NE2 A:HIS208 2.0 16.3 1.0 O A:HOH344 2.0 26.7 1.0 CE1 A:HIS231 2.7 17.5 1.0 CE1 A:HIS208 2.8 17.0 1.0 CD2 A:HIS204 2.9 16.4 1.0 CE1 A:HIS204 3.0 20.9 1.0 CD2 A:HIS231 3.1 13.4 1.0 CD2 A:HIS208 3.1 15.8 1.0 O A:HOH339 3.3 30.0 1.0 CU A:CU501 3.6 25.2 1.0 CE2 A:PHE227 3.9 13.8 1.0 ND1 A:HIS231 3.9 15.5 1.0 O A:HOH340 3.9 30.0 1.0 ND1 A:HIS208 4.0 16.8 1.0 CG A:HIS204 4.1 20.6 1.0 ND1 A:HIS204 4.1 20.9 1.0 CG A:HIS231 4.1 16.1 1.0 CG A:HIS208 4.1 15.3 1.0 NE2 A:HIS69 4.2 16.3 1.0 CZ A:PHE227 4.3 18.8 1.0 ND1 A:HIS230 4.6 19.9 1.0 CE1 A:HIS230 4.6 18.3 1.0 CE1 A:PHE65 4.6 18.2 1.0 CD2 A:PHE227 4.6 14.8 1.0 CD2 A:HIS69 4.7 18.0 1.0 O A:HOH338 4.7 30.0 1.0 CE1 A:HIS69 4.8 16.5 1.0 NE2 A:HIS60 4.8 18.4 1.0 O A:HOH369 4.9 30.9 1.0 CD2 A:HIS60 5.0 19.5 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:27.8 occ:1.00 NE2 B:HIS42 2.1 16.4 1.0 NE2 B:HIS60 2.2 25.6 1.0 O B:HOH307 2.2 19.3 1.0 O B:HOH454 2.3 30.9 1.0 CE1 B:HIS42 2.9 18.8 1.0 O B:HOH308 3.0 19.0 1.0 CD2 B:HIS60 3.0 26.2 1.0 CD2 B:HIS42 3.2 19.5 1.0 CE1 B:HIS60 3.2 26.3 1.0 CU B:CU502 3.6 22.2 1.0 NE2 B:HIS69 3.9 17.7 1.0 CE2 B:PHE227 4.0 14.1 1.0 ND1 B:HIS42 4.1 18.7 1.0 CG B:HIS60 4.2 26.6 1.0 O B:HOH306 4.3 34.9 1.0 ND1 B:HIS60 4.3 27.7 1.0 CZ B:PHE227 4.3 13.7 1.0 CG B:HIS42 4.3 19.5 1.0 CG1 B:VAL218 4.4 24.5 1.0 CE1 B:HIS69 4.5 15.4 1.0 NE2 B:HIS208 4.5 18.0 1.0 CG2 B:VAL218 4.7 28.0 1.0 CA B:VAL218 4.8 25.6 1.0 CE1 B:HIS208 4.8 20.6 1.0 NE2 B:HIS231 4.9 15.0 1.0 CB B:VAL218 4.9 30.4 1.0 O B:VAL218 4.9 24.9 1.0 CB B:ALA221 5.0 19.1 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:22.2 occ:1.00 NE2 B:HIS231 2.0 15.0 1.0 NE2 B:HIS208 2.1 18.0 1.0 O B:HOH307 2.2 19.3 1.0 NE2 B:HIS204 2.4 21.2 1.0 CE1 B:HIS231 2.8 14.7 1.0 CD2 B:HIS208 3.0 19.5 1.0 CE1 B:HIS208 3.0 20.6 1.0 CD2 B:HIS231 3.1 16.0 1.0 CD2 B:HIS204 3.2 21.6 1.0 CE1 B:HIS204 3.4 20.1 1.0 O B:HOH308 3.5 19.0 1.0 CU B:CU501 3.6 27.8 1.0 CE2 B:PHE227 3.9 14.1 1.0 ND1 B:HIS231 4.0 14.8 1.0 CZ B:PHE227 4.1 13.7 1.0 ND1 B:HIS208 4.1 19.5 1.0 NE2 B:HIS69 4.1 17.7 1.0 CG B:HIS208 4.2 19.8 1.0 CG B:HIS231 4.2 17.6 1.0 O B:HOH454 4.3 30.9 1.0 CG B:HIS204 4.4 23.8 1.0 CE1 B:HIS230 4.4 16.6 1.0 ND1 B:HIS204 4.4 21.1 1.0 ND1 B:HIS230 4.5 21.0 1.0 CD2 B:HIS69 4.6 16.1 1.0 CE1 B:PHE65 4.6 22.5 1.0 CD2 B:PHE227 4.7 12.7 1.0 O B:HOH306 4.9 34.9 1.0 CE1 B:HIS69 4.9 15.4 1.0

M.Sendovski, M.Kanteev, V.Shuster Ben-Yosef, N.Adir, A.Fishman. First Structures of An Active Bacterial Tyrosinase Reveal Copper Plasticity J.Mol.Biol. V. 405 227 2011.
ISSN: ISSN 0022-2836
PubMed: 21040728
DOI: 10.1016/J.JMB.2010.10.048