Atomistry » Holmium » PDB 1buu-9c90 » 2y9x
Atomistry »
  Holmium »
    PDB 1buu-9c90 »
      2y9x »

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: Sun Aug 11 09:14:18 2024

Last articles

Cl in 5IGN
Cl in 5IH5
Cl in 5IG6
Cl in 5IFU
Cl in 5IFT
Cl in 5IFP
Cl in 5IF8
Cl in 5IEZ
Cl in 5IFB
Cl in 5IF5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy