Copper in PDB 5ce9: Structure of Tyrosinase From Walnut (Juglans Regia)

The structure of Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9 was solved by A.Bijelic, M.Pretzler, F.Zekiri, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.10 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.430, 90.940, 86.580, 90.00, 130.18, 90.00
R / Rfree (%)	17 / 18.8

The structure of Structure of Tyrosinase From Walnut (Juglans Regia) also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Copper atom in the Structure of Tyrosinase From Walnut (Juglans Regia) (pdb code 5ce9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Structure of Tyrosinase From Walnut (Juglans Regia), PDB code: 5ce9:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:32.3 occ:1.00 NE2 A:HIS273 2.0 28.4 1.0 NE2 A:HIS239 2.0 28.5 1.0 NE2 A:HIS243 2.0 29.3 1.0 O A:O403 2.1 35.2 1.0 CE1 A:HIS273 2.9 25.4 1.0 CE1 A:HIS243 2.9 27.5 1.0 HE1 A:HIS273 3.0 30.5 1.0 CD2 A:HIS239 3.0 25.9 1.0 CE1 A:HIS239 3.0 28.9 1.0 CD2 A:HIS243 3.0 30.0 1.0 HE1 A:HIS243 3.1 33.0 1.0 CD2 A:HIS273 3.1 26.8 1.0 HD2 A:HIS239 3.1 31.1 1.0 HE1 A:HIS239 3.2 34.6 1.0 HD2 A:HIS243 3.3 36.0 1.0 HD2 A:HIS273 3.4 32.2 1.0 HE2 A:PHE269 3.6 31.9 1.0 HE1 A:PHE113 3.9 31.5 1.0 HD2 A:HIS272 3.9 31.8 1.0 CU A:CU402 4.0 26.0 0.7 ND1 A:HIS273 4.0 26.9 1.0 ND1 A:HIS243 4.0 29.3 1.0 CE2 A:PHE269 4.1 26.6 1.0 ND1 A:HIS239 4.1 29.0 1.0 CG A:HIS239 4.1 27.3 1.0 CG A:HIS243 4.1 29.2 1.0 CG A:HIS273 4.2 26.4 1.0 HZ A:PHE269 4.2 31.8 1.0 NE2 A:HIS117 4.3 25.6 1.0 CZ A:PHE269 4.4 26.5 1.0 HE2 A:HIS272 4.4 33.0 1.0 CD2 A:HIS272 4.5 26.5 1.0 HZ A:PHE113 4.5 30.7 1.0 NE2 A:HIS87 4.6 33.9 1.0 CE1 A:PHE113 4.7 26.2 1.0 NE2 A:HIS272 4.7 27.5 1.0 CD2 A:HIS117 4.7 26.8 1.0 HD1 A:HIS273 4.8 32.3 1.0 HD2 A:HIS117 4.8 32.1 1.0 HD1 A:HIS243 4.8 35.2 1.0 CD2 A:PHE269 4.9 26.1 1.0 HD1 A:HIS239 4.9 34.8 1.0 CE1 A:HIS117 4.9 25.5 1.0 HE1 A:HIS87 4.9 38.2 1.0 HG21 A:VAL276 5.0 28.0 1.0

Copper binding site 2 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:26.0 occ:0.70 NE2 A:HIS108 2.0 30.2 1.0 NE2 A:HIS87 2.0 33.9 1.0 NE2 A:HIS117 2.0 25.6 1.0 O A:O403 2.1 35.2 1.0 CE1 A:HIS117 2.7 25.5 1.0 HE1 A:HIS117 2.7 30.6 1.0 CD2 A:HIS87 2.8 33.3 1.0 HD2 A:HIS87 2.9 40.0 1.0 CE1 A:HIS108 2.9 29.2 1.0 CD2 A:HIS108 3.1 30.4 1.0 HE1 A:HIS108 3.1 35.0 1.0 CE1 A:HIS87 3.1 31.8 1.0 CD2 A:HIS117 3.2 26.8 1.0 HD2 A:HIS108 3.3 36.5 1.0 HE1 A:HIS87 3.4 38.2 1.0 HZ A:PHE269 3.5 31.8 1.0 HD11 A:ILE107 3.5 33.2 1.0 SG A:CYS91 3.6 31.0 1.0 HD2 A:HIS117 3.6 32.1 1.0 ND1 A:HIS117 4.0 24.8 1.0 CU A:CU401 4.0 32.3 1.0 CG A:HIS87 4.0 32.2 1.0 HE2 A:PHE269 4.1 31.9 1.0 ND1 A:HIS108 4.1 29.2 1.0 ND1 A:HIS87 4.1 31.6 1.0 HE1 A:PHE113 4.2 31.5 1.0 CG A:HIS108 4.2 30.1 1.0 CG A:HIS117 4.2 24.5 1.0 HE1 A:HIS273 4.2 30.5 1.0 NE2 A:HIS273 4.3 28.4 1.0 CZ A:PHE269 4.3 26.5 1.0 CD1 A:ILE107 4.4 27.6 1.0 CE1 A:HIS273 4.5 25.4 1.0 HD12 A:ILE107 4.5 33.2 1.0 HE2 A:PHE116 4.6 28.2 1.0 CE2 A:PHE269 4.6 26.6 1.0 HD1 A:PHE260 4.6 51.3 1.0 HD13 A:ILE107 4.6 33.2 1.0 HE1 A:PHE260 4.6 52.9 1.0 HD1 A:HIS117 4.7 29.8 1.0 HD2 A:PHE116 4.7 27.7 1.0 HD1 A:PHE113 4.8 31.0 1.0 HD1 A:HIS108 4.8 35.1 1.0 CE1 A:PHE113 4.9 26.2 1.0 HD1 A:HIS87 4.9 37.9 1.0 HE1 A:HIS239 4.9 34.6 1.0

Copper binding site 3 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:37.3 occ:1.00 NE2 B:HIS243 2.0 27.5 1.0 NE2 B:HIS239 2.0 24.6 1.0 NE2 B:HIS273 2.0 29.1 1.0 O B:O403 2.1 30.1 1.0 CE1 B:HIS273 2.9 27.9 1.0 CE1 B:HIS243 2.9 27.2 1.0 CD2 B:HIS239 3.0 24.3 1.0 HE1 B:HIS273 3.0 33.5 1.0 CE1 B:HIS239 3.0 26.1 1.0 HE1 B:HIS243 3.1 32.7 1.0 CD2 B:HIS243 3.1 28.0 1.0 CD2 B:HIS273 3.1 26.4 1.0 HD2 B:HIS239 3.1 29.2 1.0 HE1 B:HIS239 3.3 31.3 1.0 HD2 B:HIS243 3.3 33.6 1.0 HD2 B:HIS273 3.4 31.7 1.0 HE2 B:PHE269 3.6 27.8 1.0 HD2 B:HIS272 3.9 30.5 1.0 HE1 B:PHE113 4.0 27.2 1.0 CU B:CU402 4.0 30.9 0.7 ND1 B:HIS273 4.0 27.1 1.0 ND1 B:HIS243 4.0 28.7 1.0 CE2 B:PHE269 4.1 23.2 1.0 ND1 B:HIS239 4.1 27.2 1.0 CG B:HIS239 4.1 27.7 1.0 CG B:HIS243 4.1 26.9 1.0 CG B:HIS273 4.1 25.2 1.0 HZ B:PHE269 4.3 27.6 1.0 NE2 B:HIS117 4.3 23.8 1.0 HE2 B:HIS272 4.4 30.0 1.0 CD2 B:HIS272 4.5 25.4 1.0 CZ B:PHE269 4.5 23.0 1.0 HZ B:PHE113 4.5 26.4 1.0 NE2 B:HIS87 4.6 29.7 1.0 NE2 B:HIS272 4.7 25.0 1.0 CD2 B:HIS117 4.7 22.7 1.0 CE1 B:PHE113 4.8 22.7 1.0 HD2 B:HIS117 4.8 27.2 1.0 HD1 B:HIS273 4.8 32.5 1.0 HD1 B:HIS243 4.8 34.4 1.0 HD1 B:HIS239 4.9 32.6 1.0 CD2 B:PHE269 4.9 22.6 1.0 CE1 B:HIS117 5.0 23.0 1.0 HE1 B:PHE260 5.0 49.2 1.0

Copper binding site 4 out of 4 in the Structure of Tyrosinase From Walnut (Juglans Regia)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Tyrosinase From Walnut (Juglans Regia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:30.9 occ:0.70 NE2 B:HIS87 2.0 29.7 1.0 NE2 B:HIS108 2.0 23.0 1.0 NE2 B:HIS117 2.1 23.8 1.0 O B:O403 2.1 30.1 1.0 CD2 B:HIS87 2.8 28.4 1.0 CE1 B:HIS117 2.8 23.0 1.0 HD2 B:HIS87 2.8 34.0 1.0 HE1 B:HIS117 2.9 27.6 1.0 CE1 B:HIS108 2.9 25.4 1.0 HE1 B:HIS108 3.0 30.4 1.0 CD2 B:HIS108 3.1 25.6 1.0 CE1 B:HIS87 3.2 30.3 1.0 CD2 B:HIS117 3.2 22.7 1.0 HD2 B:HIS108 3.4 30.8 1.0 HE1 B:HIS87 3.5 36.3 1.0 SG B:CYS91 3.5 26.4 1.0 HD2 B:HIS117 3.5 27.2 1.0 HZ B:PHE269 3.6 27.6 1.0 HD11 B:ILE107 3.6 29.8 1.0 CG B:HIS87 4.0 28.4 1.0 CU B:CU401 4.0 37.3 1.0 ND1 B:HIS117 4.0 22.1 1.0 ND1 B:HIS108 4.1 23.7 1.0 HE2 B:PHE269 4.1 27.8 1.0 ND1 B:HIS87 4.1 29.6 1.0 CG B:HIS108 4.2 23.8 1.0 CG B:HIS117 4.2 21.9 1.0 NE2 B:HIS273 4.3 29.1 1.0 HE1 B:HIS273 4.3 33.5 1.0 HE1 B:PHE113 4.4 27.2 1.0 CZ B:PHE269 4.4 23.0 1.0 CD1 B:ILE107 4.4 24.8 1.0 HE2 B:PHE116 4.4 25.9 1.0 HE1 B:PHE260 4.5 49.2 1.0 HD12 B:ILE107 4.5 29.8 1.0 CE1 B:HIS273 4.5 27.9 1.0 HD1 B:PHE260 4.6 50.2 1.0 CE2 B:PHE269 4.6 23.2 1.0 HD13 B:ILE107 4.6 29.8 1.0 HD2 B:PHE116 4.7 24.9 1.0 HD1 B:HIS117 4.8 26.5 1.0 CE1 B:PHE260 4.8 41.0 1.0 HD1 B:HIS108 4.8 28.4 1.0 CD1 B:PHE260 4.9 41.8 1.0 HD1 B:HIS87 4.9 35.6 1.0 HE1 B:HIS239 5.0 31.3 1.0 HD1 B:PHE113 5.0 27.4 1.0 HB3 B:CYS91 5.0 29.8 1.0 CB B:CYS91 5.0 24.8 1.0

A.Bijelic, M.Pretzler, C.Molitor, F.Zekiri, A.Rompel. The Structure of A Plant Tyrosinase From Walnut Leaves Reveals the Importance of """"Substrate-Guiding Residues"""" For Enzymatic Specificity. Angew.Chem.Int.Ed.Engl. V. 54 14677 2015.
ISSN: ESSN 1521-3773
PubMed: 26473311
DOI: 10.1002/ANIE.201506994