Copper in PDB 2vz3: Bleached Galactose Oxidase

All present enzymatic activity of Bleached Galactose Oxidase:
1.1.3.9;

The structure of Bleached Galactose Oxidase, PDB code: 2vz3 was solved by M.S.Rogers, R.Hurtado-Guerrero, S.J.Firbank, M.A.Halcrow, D.M.Dooley, S.E.V.Phillips, P.F.Knowles, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.0 / 1.9
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.480, 88.090, 84.940, 90.00, 116.67, 90.00
R / Rfree (%)	16.85 / 20.25

The binding sites of Copper atom in the Bleached Galactose Oxidase (pdb code 2vz3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Bleached Galactose Oxidase, PDB code: 2vz3:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Bleached Galactose Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bleached Galactose Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1642 b:13.7 occ:0.40 ND1 A:HIS334 2.0 9.9 1.0 SG A:CYS383 2.1 12.3 1.0 CU A:CU1643 2.7 13.1 0.4 CE1 A:HIS334 2.9 8.6 1.0 CG A:HIS334 3.0 7.6 1.0 CE2 A:TYR405 3.3 13.5 1.0 CB A:HIS334 3.4 6.7 1.0 SD A:MET382 3.4 9.0 1.0 CB A:CYS383 3.5 7.4 1.0 N A:CYS383 3.6 5.3 1.0 CA A:CYS383 3.7 6.8 1.0 CZ A:TYR405 3.8 12.9 1.0 OH A:TYR405 3.8 12.1 1.0 O A:HOH2240 3.8 6.7 1.0 NE2 A:HIS334 4.0 9.1 1.0 CG A:MET382 4.0 7.1 1.0 CD2 A:HIS334 4.0 5.8 1.0 CD2 A:TYR405 4.0 11.9 1.0 O A:HIS581 4.0 7.4 1.0 O A:HOH2192 4.1 7.7 1.0 OG1 A:THR582 4.4 7.3 1.0 C A:MET382 4.6 7.1 1.0 CE1 A:TYR405 4.8 11.9 1.0 CA A:HIS334 4.8 6.8 1.0 CB A:ASN333 4.9 6.5 1.0 CG A:TYR405 5.0 11.7 1.0

Copper binding site 2 out of 3 in the Bleached Galactose Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bleached Galactose Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1643 b:13.1 occ:0.40 O A:HOH2240 1.8 6.7 1.0 SG A:CYS383 1.9 12.3 1.0 CU A:CU1642 2.7 13.7 0.4 CB A:CYS383 3.1 7.4 1.0 OH A:TYR405 3.3 12.1 1.0 CE1 A:PHE441 3.3 8.7 1.0 CD1 A:PHE441 3.3 10.4 1.0 CZ A:TYR405 3.4 12.9 1.0 CE1 A:TYR495 3.9 16.0 1.0 CE1 A:TYR405 3.9 11.9 1.0 ND1 A:HIS334 3.9 9.9 1.0 CE2 A:TYR405 3.9 13.5 1.0 O A:HIS581 4.0 7.4 1.0 CE1 A:HIS334 4.0 8.6 1.0 CG2 A:THR582 4.1 8.7 1.0 CA A:CYS383 4.1 6.8 1.0 O A:HOH2315 4.2 14.9 1.0 CD1 A:TYR495 4.3 13.3 1.0 CZ A:PHE441 4.6 9.8 1.0 C A:HIS581 4.6 7.7 1.0 OG1 A:THR582 4.6 7.3 1.0 CG A:PHE441 4.6 7.6 1.0 CD1 A:TYR405 4.7 13.2 1.0 CD2 A:TYR405 4.7 11.9 1.0 N A:CYS383 4.8 5.3 1.0 CB A:HIS581 4.9 7.4 1.0 CA A:HIS581 5.0 8.3 1.0 CG A:HIS334 5.0 7.6 1.0 CZ A:TYR495 5.0 16.7 1.0

Copper binding site 3 out of 3 in the Bleached Galactose Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bleached Galactose Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1644 b:12.3 occ:1.00 NE2 A:HIS496 2.0 9.4 1.0 OH A:TYR272 2.1 12.1 1.0 NE2 A:HIS581 2.1 8.1 1.0 OH A:TYR495 2.9 20.1 1.0 CD2 A:HIS496 3.0 10.2 1.0 CD2 A:HIS581 3.0 9.8 1.0 CZ A:TYR272 3.0 13.0 1.0 CE1 A:HIS496 3.0 11.4 1.0 CE1 A:HIS581 3.1 9.7 1.0 CZ A:PHE227 3.3 11.5 1.0 SG A:CYS228 3.4 10.6 1.0 CZ A:TYR495 3.4 16.7 1.0 CE2 A:TYR495 3.6 12.6 1.0 CE1 A:TYR272 3.6 13.1 1.0 CE1 A:PHE227 4.0 9.2 1.0 CE2 A:TYR272 4.0 9.5 1.0 OXT A:ACT1640 4.0 24.5 1.0 ND1 A:HIS496 4.1 8.8 1.0 CE2 A:PHE227 4.1 11.9 1.0 CG A:HIS496 4.1 11.0 1.0 CG A:HIS581 4.2 9.5 1.0 ND1 A:HIS581 4.2 9.4 1.0 CH3 A:ACT1640 4.2 26.5 1.0 CE1 A:TYR495 4.4 16.0 1.0 C A:ACT1640 4.5 27.4 1.0 CD2 A:TYR495 4.7 11.4 1.0 CD1 A:TYR272 4.8 7.5 1.0 OH A:TYR405 4.9 12.1 1.0

M.S.Rogers, R.Hurtado-Guerrero, S.J.Firbank, M.A.Halcrow, D.M.Dooley, S.E.V.Phillips, P.F.Knowles, M.J.Mcpherson. Cross-Link Formation of the Cysteine 228-Tyrosine 272 Catalytic Cofactor of Galactose Oxidase Does Not Require Dioxygen. Biochemistry V. 47 10428 2008.
ISSN: ISSN 0006-2960
PubMed: 18771294
DOI: 10.1021/BI8010835