Atomistry » Copper » PDB 2xv2-2z7w » 2y9w
Atomistry »
  Copper »
    PDB 2xv2-2z7w »
      2y9w »

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: Wed Jul 31 00:19:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy