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Copper in PDB 2y9w: Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit

Enzymatic activity of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit

All present enzymatic activity of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, PDB code: 2y9w was solved by W.T.Ismaya, H.J.Rozeboom, A.Weijn, J.J.Mes, F.Fusetti, H.J.Wichers, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.13 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.060, 104.520, 109.050, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.7

Other elements in 2y9w:

The structure of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit also contains other interesting chemical elements:

Holmium (Ho) 6 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit (pdb code 2y9w). 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 PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, PDB code: 2y9w:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2y9w

Go back to Copper Binding Sites List in 2y9w
Copper binding site 1 out of 4 in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit


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 PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu400

b:35.1
occ:1.00
NE2 A:HIS94 2.1 28.9 1.0
NE2 A:HIS61 2.1 33.2 1.0
NE2 A:HIS85 2.1 33.0 1.0
CE1 A:HIS94 2.7 27.6 1.0
CD2 A:HIS61 2.9 29.3 1.0
O A:HOH2094 3.0 44.4 1.0
CE1 A:HIS85 3.0 32.4 1.0
CD2 A:HIS85 3.1 30.3 1.0
CE1 A:HIS61 3.2 31.3 1.0
CD2 A:HIS94 3.3 24.8 1.0
CB A:CYS83 3.5 28.7 1.0
SG A:CYS83 3.5 32.5 1.0
ND1 A:HIS94 4.0 25.9 1.0
CG A:HIS61 4.0 28.6 1.0
ND1 A:HIS85 4.1 30.9 1.0
ND1 A:HIS61 4.2 30.3 1.0
CG A:HIS85 4.2 29.8 1.0
CG A:HIS94 4.3 23.4 1.0
CU A:CU401 4.5 34.0 1.0
CZ A:PHE292 4.5 18.3 1.0
NE2 A:HIS296 4.6 30.7 1.0
CE1 A:HIS296 4.7 27.9 1.0
CZ3 A:TRP93 4.8 17.8 1.0
CE1 A:PHE90 4.9 16.7 1.0
CA A:CYS83 4.9 29.4 1.0
CE1 A:PHE292 4.9 16.6 1.0

Copper binding site 2 out of 4 in 2y9w

Go back to Copper Binding Sites List in 2y9w
Copper binding site 2 out of 4 in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit


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 PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:34.0
occ:1.00
NE2 A:HIS296 2.0 30.7 1.0
NE2 A:HIS259 2.1 33.7 1.0
NE2 A:HIS263 2.1 32.5 1.0
O A:HOH2094 2.6 44.4 1.0
CE1 A:HIS296 2.9 27.9 1.0
CD2 A:HIS259 3.0 29.6 1.0
CD2 A:HIS296 3.0 27.3 1.0
CE1 A:HIS263 3.1 30.9 1.0
CD2 A:HIS263 3.1 29.6 1.0
CE1 A:HIS259 3.1 31.2 1.0
CE1 A:PHE292 3.7 16.6 1.0
CD2 A:HIS295 4.0 24.4 1.0
ND1 A:HIS296 4.1 28.3 1.0
CG A:HIS259 4.1 29.0 1.0
CG A:HIS296 4.1 25.7 1.0
ND1 A:HIS259 4.2 31.1 1.0
ND1 A:HIS263 4.2 29.8 1.0
CZ A:PHE292 4.2 18.3 1.0
NE2 A:HIS295 4.2 25.2 1.0
CG A:HIS263 4.2 29.7 1.0
CU A:CU400 4.5 35.1 1.0
CD1 A:PHE292 4.5 17.9 1.0
NE2 A:HIS94 4.9 28.9 1.0
NE2 A:HIS61 4.9 33.2 1.0

Copper binding site 3 out of 4 in 2y9w

Go back to Copper Binding Sites List in 2y9w
Copper binding site 3 out of 4 in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit


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 PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu400

b:31.5
occ:1.00
NE2 B:HIS61 2.1 27.4 1.0
NE2 B:HIS94 2.1 24.7 1.0
NE2 B:HIS85 2.1 28.0 1.0
O B:HOH2105 2.7 29.1 1.0
CD2 B:HIS61 2.9 24.6 1.0
CE1 B:HIS94 2.9 21.1 1.0
CE1 B:HIS85 3.0 27.8 1.0
CD2 B:HIS85 3.1 25.9 1.0
CD2 B:HIS94 3.2 20.4 1.0
CE1 B:HIS61 3.2 24.2 1.0
CB B:CYS83 3.7 25.1 1.0
SG B:CYS83 3.7 28.8 1.0
CG B:HIS61 4.1 24.1 1.0
ND1 B:HIS94 4.1 19.1 1.0
ND1 B:HIS85 4.1 27.1 1.0
ND1 B:HIS61 4.2 23.2 1.0
CG B:HIS94 4.2 19.7 1.0
CG B:HIS85 4.2 25.9 1.0
CU B:CU401 4.4 30.0 1.0
NE2 B:HIS296 4.5 25.9 1.0
CE1 B:HIS296 4.6 24.6 1.0
CZ B:PHE292 4.6 20.3 1.0
CE1 B:PHE90 4.7 17.2 1.0
CZ3 B:TRP93 4.8 18.0 1.0
CE2 B:PHE292 4.8 19.2 1.0

Copper binding site 4 out of 4 in 2y9w

Go back to Copper Binding Sites List in 2y9w
Copper binding site 4 out of 4 in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit


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 PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:30.0
occ:1.00
NE2 B:HIS296 2.0 25.9 1.0
NE2 B:HIS263 2.1 26.9 1.0
NE2 B:HIS259 2.1 25.2 1.0
O B:HOH2105 2.4 29.1 1.0
CD2 B:HIS296 2.9 24.4 1.0
CD2 B:HIS263 2.9 25.4 1.0
CD2 B:HIS259 3.0 20.1 1.0
CE1 B:HIS296 3.1 24.6 1.0
CE1 B:HIS259 3.1 21.6 1.0
CE1 B:HIS263 3.1 25.6 1.0
CE2 B:PHE292 3.8 19.2 1.0
CD2 B:HIS295 4.1 23.4 1.0
CG B:HIS296 4.1 23.5 1.0
CG B:HIS263 4.1 25.4 1.0
ND1 B:HIS296 4.1 23.4 1.0
NE2 B:HIS295 4.1 23.6 1.0
CG B:HIS259 4.1 21.1 1.0
ND1 B:HIS259 4.2 20.5 1.0
ND1 B:HIS263 4.2 25.4 1.0
CZ B:PHE292 4.4 20.3 1.0
CU B:CU400 4.4 31.5 1.0
CD2 B:PHE292 4.5 18.9 1.0

Reference:

W.T.Ismaya, H.J.Rozeboom, A.Weijn, J.J.Mes, F.Fusetti, H.J.Wichers, B.W.Dijkstra. Crystal Structure of Agaricus Bisporus Mushroom Tyrosinase: Identity of the Tetramer Subunits and Interaction with Tropolone. Biochemistry V. 50 5477 2011.
ISSN: ISSN 0006-2960
PubMed: 21598903
DOI: 10.1021/BI200395T
Page generated: Mon Jul 14 01:39:35 2025

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