Copper in PDB 3w6w: Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae

The structure of Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae, PDB code: 3w6w was solved by N.Fujieda, S.Yabuta, T.Ikeda, T.Oyama, N.Muraki, G.Kurisu, S.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.07 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.313, 118.086, 84.207, 90.00, 97.40, 90.00
R / Rfree (%)	17.7 / 19.9

The binding sites of Copper atom in the Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae (pdb code 3w6w). 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 Melb Holo-Protyrosinase From Asperugillus Oryzae, PDB code: 3w6w:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae


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 Melb Holo-Protyrosinase From Asperugillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu701 b:15.9 occ:1.00 NE2 A:HIS67 2.0 9.0 1.0 O A:HOH1002 2.0 25.2 1.0 NE2 A:HIS103 2.1 10.2 1.0 NE2 A:HIS94 2.2 11.1 1.0 O A:HOH1001 2.3 19.8 1.0 CE1 A:HIS67 2.9 9.3 1.0 CE1 A:HIS103 2.9 10.8 1.0 CD2 A:HIS67 3.0 9.0 1.0 CD2 A:HIS94 3.1 11.7 1.0 CE1 A:HIS94 3.2 11.9 1.0 CD2 A:HIS103 3.2 9.3 1.0 CU A:CU702 3.6 15.3 1.0 CB A:CYS92 3.7 11.3 1.0 SG A:CYS92 3.8 12.4 1.0 ND1 A:HIS67 4.0 9.7 1.0 NE2 A:HIS372 4.1 8.3 1.0 CG A:HIS67 4.1 9.5 1.0 ND1 A:HIS103 4.1 10.3 1.0 CG A:HIS103 4.3 9.4 1.0 ND1 A:HIS94 4.3 13.0 1.0 CG A:HIS94 4.3 12.9 1.0 CZ A:PHE368 4.3 8.0 1.0 CE2 A:PHE368 4.4 8.0 1.0 CE1 A:HIS372 4.4 8.5 1.0 NE2 A:HIS328 4.7 8.5 1.0 CE2 A:PHE513 4.8 12.3 1.0 CZ3 A:TRP102 4.8 9.2 1.0 CE1 A:PHE99 4.9 10.1 1.0 CG2 A:VAL359 4.9 11.6 0.5 O A:VAL93 5.0 12.2 1.0 CD2 A:HIS372 5.0 8.1 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae


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 Melb Holo-Protyrosinase From Asperugillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:15.3 occ:1.00 O A:HOH1001 1.9 19.8 1.0 NE2 A:HIS328 1.9 8.5 1.0 NE2 A:HIS332 2.1 8.9 1.0 NE2 A:HIS372 2.1 8.3 1.0 O A:HOH1002 2.2 25.2 1.0 CD2 A:HIS328 2.9 8.4 1.0 CE1 A:HIS372 3.0 8.5 1.0 CE1 A:HIS328 3.0 9.0 1.0 CE1 A:HIS332 3.1 8.7 1.0 CD2 A:HIS332 3.1 9.2 1.0 CD2 A:HIS372 3.2 8.1 1.0 CU A:CU701 3.6 15.9 1.0 CE2 A:PHE513 3.9 12.3 1.0 CE2 A:PHE368 4.0 8.0 1.0 ND1 A:HIS328 4.0 9.4 1.0 CG A:HIS328 4.0 9.0 1.0 ND1 A:HIS372 4.1 8.5 1.0 ND1 A:HIS332 4.2 8.9 1.0 CG A:HIS332 4.2 9.1 1.0 CG A:HIS372 4.3 8.3 1.0 CZ A:PHE513 4.3 12.2 1.0 NE2 A:HIS103 4.4 10.2 1.0 NE2 A:HIS67 4.6 9.0 1.0 CZ A:PHE368 4.7 8.0 1.0 CD2 A:PHE368 4.7 8.1 1.0 CE1 A:PHE99 4.7 10.1 1.0 CD2 A:HIS103 4.7 9.3 1.0 ND1 A:HIS371 4.7 8.3 1.0 CD2 A:PHE513 4.8 12.2 1.0 CE1 A:HIS371 4.8 8.6 1.0 NE2 A:HIS94 4.9 11.1 1.0 CE1 A:HIS67 5.0 9.3 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae


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 Melb Holo-Protyrosinase From Asperugillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu701 b:17.2 occ:1.00 O B:HOH801 2.0 16.2 1.0 NE2 B:HIS67 2.0 11.9 1.0 NE2 B:HIS94 2.1 13.7 1.0 NE2 B:HIS103 2.2 12.2 1.0 O B:HOH802 2.3 31.0 1.0 CE1 B:HIS67 2.9 12.7 1.0 CE1 B:HIS103 3.0 12.4 1.0 CD2 B:HIS67 3.0 11.8 1.0 CD2 B:HIS94 3.1 13.8 1.0 CE1 B:HIS94 3.1 14.1 1.0 CD2 B:HIS103 3.3 11.3 1.0 CU B:CU702 3.5 17.5 1.0 CB B:CYS92 3.8 13.7 1.0 SG B:CYS92 3.8 14.3 1.0 NE2 B:HIS372 4.0 9.3 1.0 ND1 B:HIS67 4.1 12.7 1.0 CG B:HIS67 4.1 12.5 1.0 ND1 B:HIS103 4.2 11.8 1.0 ND1 B:HIS94 4.2 14.4 1.0 CG B:HIS94 4.2 14.3 1.0 CG B:HIS103 4.3 11.1 1.0 CE1 B:HIS372 4.3 9.5 1.0 CE2 B:PHE368 4.4 9.3 1.0 CZ B:PHE368 4.4 9.8 1.0 CE2 B:PHE513 4.6 16.9 1.0 NE2 B:HIS328 4.7 10.3 1.0 CZ3 B:TRP102 4.8 13.2 1.0 CE1 B:PHE99 4.9 12.8 1.0 CG2 B:VAL359 4.9 12.4 0.5 O B:VAL93 5.0 14.6 1.0 CD2 B:HIS372 5.0 9.6 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Melb Holo-Protyrosinase From Asperugillus Oryzae


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 Melb Holo-Protyrosinase From Asperugillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu702 b:17.5 occ:1.00 O B:HOH802 1.9 31.0 1.0 NE2 B:HIS328 1.9 10.3 1.0 NE2 B:HIS332 2.1 10.5 1.0 NE2 B:HIS372 2.1 9.3 1.0 O B:HOH801 2.3 16.2 1.0 CD2 B:HIS328 2.9 10.5 1.0 CE1 B:HIS372 2.9 9.5 1.0 CE1 B:HIS328 3.0 10.2 1.0 CD2 B:HIS332 3.0 10.3 1.0 CE1 B:HIS332 3.1 10.5 1.0 CD2 B:HIS372 3.2 9.6 1.0 CU B:CU701 3.5 17.2 1.0 CE2 B:PHE513 3.9 16.9 1.0 CE2 B:PHE368 4.0 9.3 1.0 CG B:HIS328 4.0 10.5 1.0 ND1 B:HIS328 4.0 10.3 1.0 ND1 B:HIS372 4.1 9.9 1.0 ND1 B:HIS332 4.2 10.2 1.0 CG B:HIS332 4.2 10.1 1.0 CZ B:PHE513 4.3 16.8 1.0 CG B:HIS372 4.3 10.0 1.0 NE2 B:HIS103 4.4 12.2 1.0 NE2 B:HIS67 4.6 11.9 1.0 CE1 B:PHE99 4.7 12.8 1.0 CZ B:PHE368 4.7 9.8 1.0 CD2 B:PHE368 4.7 9.3 1.0 CD2 B:HIS103 4.7 11.3 1.0 CD2 B:HIS371 4.7 8.9 1.0 CD2 B:PHE513 4.8 15.9 1.0 NE2 B:HIS94 4.9 13.7 1.0 NE2 B:HIS371 4.9 8.9 1.0 CE1 B:HIS67 5.0 12.7 1.0

N.Fujieda, S.Yabuta, T.Ikeda, T.Oyama, N.Muraki, G.Kurisu, S.Itoh. Crystal Structures of Copper-Depleted and Copper-Bound Fungal Pro-Tyrosinase: Insights Into Endogenous Cysteine-Dependent Copper Incorporation. J.Biol.Chem. V. 288 22128 2013.
ISSN: ESSN 1083-351X
PubMed: 23749993
DOI: 10.1074/JBC.M113.477612