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Holmium in PDB 2y9x: Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone

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

All present enzymatic activity of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone:
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, with Inhibitor Tropolone, PDB code: 2y9x 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) 58.03 / 2.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.840, 104.820, 119.360, 90.00, 110.45, 90.00
R / Rfree (%) 23.5 / 28.9

Other elements in 2y9x:

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

Copper (Cu) 8 atoms

Holmium Binding Sites:

The binding sites of Holmium atom in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone (pdb code 2y9x). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 4 binding sites of Holmium where determined in the Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone, PDB code: 2y9x:
Jump to Holmium binding site number: 1; 2; 3; 4;

Holmium binding site 1 out of 4 in 2y9x

Go back to Holmium Binding Sites List in 2y9x
Holmium 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, with Inhibitor Tropolone


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho402

b:63.7
occ:1.00
 OE1 A:GLN351 2.7 47.3 1.0
OD1 A:ASP336 2.9 43.0 1.0
OD2 A:ASP353 3.0 46.9 1.0
OD1 B:ASP312 3.3 44.2 1.0
O A:HOH2002 3.6 13.9 1.0
CB A:ASP353 3.6 43.7 1.0
CG A:ASP353 3.7 45.4 1.0
CG A:ASP336 3.8 42.6 1.0
CD A:GLN351 3.9 45.6 1.0
CG B:ASP312 4.2 43.6 1.0
OD1 A:ASP354 4.3 44.3 1.0
OD2 A:ASP336 4.5 43.5 1.0
CB B:ASP312 4.5 42.9 1.0
NZ B:LYS376 4.6 47.9 1.0
OE2 B:GLU356 4.6 42.7 1.0
CB A:ASP336 4.7 41.8 1.0
NE2 A:GLN351 4.7 46.3 1.0
CA B:ASP312 4.7 42.2 1.0
OE1 B:GLU356 4.7 43.3 1.0
CB A:GLN351 4.7 42.2 1.0
CA A:ASP336 4.8 41.0 1.0
OD1 A:ASP353 4.9 46.7 1.0
CG A:GLN351 4.9 43.4 1.0

Holmium binding site 2 out of 4 in 2y9x

Go back to Holmium Binding Sites List in 2y9x
Holmium 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, with Inhibitor Tropolone


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho402

b:59.7
occ:1.00
 OE1 B:GLN351 2.2 52.3 1.0
OD1 A:ASP312 2.5 43.7 1.0
OD2 B:ASP353 2.8 48.2 1.0
OD2 B:ASP336 3.0 44.0 1.0
CD B:GLN351 3.4 47.5 1.0
O B:HOH2005 3.5 18.3 1.0
CB B:ASP353 3.6 44.5 1.0
CG B:ASP353 3.6 46.2 1.0
CG A:ASP312 3.6 43.3 1.0
CG B:ASP336 3.9 43.0 1.0
NE2 B:GLN351 4.0 47.6 1.0
CB A:ASP312 4.1 42.7 1.0
OD1 B:ASP354 4.3 45.7 1.0
CB B:ASP336 4.4 42.2 1.0
CA A:ASP312 4.5 42.0 1.0
CA B:ASP336 4.5 41.5 1.0
CG B:GLN351 4.6 45.0 1.0
OD2 A:ASP312 4.6 43.9 1.0
CB B:GLN351 4.6 43.2 1.0
NZ A:LYS376 4.6 48.0 1.0
OE1 A:GLU356 4.7 42.5 1.0
OE2 A:GLU356 4.7 42.0 1.0
OD1 B:ASP353 4.8 47.6 1.0
O B:GLU335 4.9 40.7 1.0
OD1 B:ASP336 4.9 43.4 1.0

Holmium binding site 3 out of 4 in 2y9x

Go back to Holmium Binding Sites List in 2y9x
Holmium 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, with Inhibitor Tropolone


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ho402

b:72.9
occ:1.00
 O C:HOH2002 2.6 10.5 1.0
OD2 C:ASP353 2.8 48.6 1.0
OD1 C:ASP336 2.8 43.6 1.0
OE1 C:GLN351 2.8 48.9 1.0
OD1 D:ASP312 3.1 43.5 1.0
CB C:ASP353 3.6 45.3 1.0
CG C:ASP353 3.6 46.9 1.0
CG C:ASP336 3.6 43.2 1.0
CG D:ASP312 3.8 43.1 1.0
CD C:GLN351 4.0 47.6 1.0
CB C:ASP336 4.2 42.5 1.0
OE2 D:GLU356 4.3 43.4 1.0
CB D:ASP312 4.3 42.5 1.0
CA D:ASP312 4.5 42.4 1.0
CA C:ASP336 4.5 41.9 1.0
OD2 C:ASP336 4.5 43.8 1.0
OE1 D:GLU356 4.6 44.2 1.0
OD1 C:ASP354 4.7 46.5 1.0
OD2 D:ASP312 4.7 43.3 1.0
NE2 C:GLN351 4.7 48.3 1.0
NZ D:LYS376 4.8 47.2 1.0
OD1 C:ASP353 4.8 48.7 1.0
CD D:GLU356 4.9 43.9 1.0
CB C:GLN351 5.0 44.3 1.0

Holmium binding site 4 out of 4 in 2y9x

Go back to Holmium Binding Sites List in 2y9x
Holmium 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, with Inhibitor Tropolone


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 4 of Crystal Structure of PPO3, A Tyrosinase From Agaricus Bisporus, in Deoxy-Form That Contains Additional Unknown Lectin-Like Subunit, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ho402

b:64.6
occ:1.00
 OD2 D:ASP353 2.2 54.6 1.0
O D:HOH2003 2.7 10.3 1.0
OD1 D:ASP336 2.8 44.1 1.0
OD1 C:ASP312 3.0 43.2 1.0
OE1 D:GLN351 3.2 49.2 1.0
CG D:ASP353 3.3 48.4 1.0
CB D:ASP353 3.7 46.5 1.0
CG D:ASP336 4.0 43.4 1.0
CG C:ASP312 4.0 42.8 1.0
OD1 D:ASP354 4.1 47.2 1.0
CB C:ASP312 4.3 41.9 1.0
CD D:GLN351 4.3 47.9 1.0
OD1 D:ASP353 4.4 50.1 1.0
CA C:ASP312 4.5 41.4 1.0
CB D:ASP336 4.5 42.9 1.0
OE1 C:GLU356 4.6 43.2 1.0
CA D:ASP336 4.7 42.6 1.0
OE2 C:GLU356 4.7 43.3 1.0
OD2 D:ASP336 5.0 43.7 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: Fri Aug 8 11:38:26 2025

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