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Holmium 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:

Copper (Cu) 4 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 (pdb code 2y9w). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 6 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, PDB code: 2y9w:
Jump to Holmium binding site number: 1; 2; 3; 4; 5; 6;

Holmium binding site 1 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 1 out of 6 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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho402

b:38.5
occ:1.00
 OD2 A:ASP353 2.2 40.5 1.0
OD1 A:ASP336 2.2 32.5 1.0
OE1 A:GLN351 2.2 35.8 1.0
O A:HOH2146 2.2 24.2 1.0
O A:HOH2147 2.7 33.4 1.0
CG A:ASP353 3.1 33.2 1.0
O A:HOH2124 3.3 10.7 1.0
CD A:GLN351 3.4 29.4 1.0
CG A:ASP336 3.4 32.2 1.0
CB A:ASP353 3.5 30.0 1.0
NE2 A:GLN351 4.1 29.2 1.0
OD2 A:ASP336 4.2 34.3 1.0
OD1 A:ASP353 4.3 36.5 1.0
CB A:ASP336 4.4 30.9 1.0
OD1 A:ASP354 4.5 31.9 1.0
CG A:GLN351 4.6 27.2 1.0
CA A:ASP336 4.7 30.0 1.0
CB A:GLN351 4.7 24.7 1.0
O A:HOH2118 4.8 29.1 1.0

Holmium binding site 2 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 2 out of 6 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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho403

b:49.9
occ:0.25
 OE2 A:GLU335 2.2 46.9 1.0
O A:HOH2124 2.3 10.7 1.0
O A:HOH2118 2.9 29.1 1.0
OD1 A:ASP353 3.2 36.5 1.0
CD A:GLU335 3.3 41.3 1.0
O A:HOH2147 3.5 33.4 1.0
OD2 A:ASP353 3.6 40.5 1.0
CG A:ASP353 3.8 33.2 1.0
OE1 A:GLU335 4.2 42.0 1.0
CG A:GLU335 4.2 34.9 1.0
OD2 A:ASP336 4.6 34.3 1.0
OD1 A:ASP336 4.8 32.5 1.0

Holmium binding site 3 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 3 out of 6 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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho404

b:61.5
occ:0.50
 O A:HOH2149 2.2 33.1 1.0
OE2 A:GLU16 2.2 61.7 1.0
O A:HOH2148 2.3 26.8 1.0
OE1 A:GLU16 2.8 53.7 1.0
CD A:GLU16 2.8 53.0 1.0
CG A:GLU16 4.3 46.2 1.0

Holmium binding site 4 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 4 out of 6 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 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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho402

b:32.4
occ:0.70
 O B:HOH2159 2.2 22.6 1.0
OD1 B:ASP336 2.2 29.4 1.0
OE1 B:GLN351 2.2 34.5 1.0
OD2 B:ASP353 2.2 39.2 1.0
O B:HOH2160 2.7 32.4 1.0
OD1 B:ASP353 2.8 34.3 1.0
CG B:ASP353 2.8 31.7 1.0
HO B:HO404 3.2 39.2 0.3
CD B:GLN351 3.4 30.7 1.0
CG B:ASP336 3.4 30.6 1.0
NE2 B:GLN351 4.1 30.9 1.0
OD2 B:ASP336 4.2 33.6 1.0
CB B:ASP353 4.3 28.3 1.0
OD1 B:ASP354 4.4 33.2 1.0
CB B:ASP336 4.5 28.5 1.0
CG B:GLN351 4.6 27.2 1.0
CB B:GLN351 4.7 23.7 1.0
CA B:ASP336 4.8 27.8 1.0

Holmium binding site 5 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 5 out of 6 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 Holmium with other atoms in the Ho binding site number 5 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:Ho403

b:47.9
occ:0.25
 OE1 B:GLU335 2.2 45.3 1.0
CD B:GLU335 2.8 40.2 1.0
OE2 B:GLU335 3.0 41.7 1.0
HO B:HO404 3.2 39.2 0.3
OD2 B:ASP353 3.9 39.2 1.0
O B:HOH2138 4.0 24.9 0.5
CB B:ASP353 4.0 28.3 1.0
CG B:GLU335 4.0 33.8 1.0
CG B:ASP353 4.4 31.7 1.0
CB B:GLU335 4.9 28.5 1.0

Holmium binding site 6 out of 6 in 2y9w

Go back to Holmium Binding Sites List in 2y9w
Holmium binding site 6 out of 6 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 Holmium with other atoms in the Ho binding site number 6 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:Ho404

b:39.2
occ:0.30
 OD2 B:ASP353 2.2 39.2 1.0
OD2 B:ASP336 2.7 33.6 1.0
OD1 B:ASP336 2.7 29.4 1.0
CG B:ASP336 3.1 30.6 1.0
HO B:HO402 3.2 32.4 0.7
HO B:HO403 3.2 47.9 0.2
CG B:ASP353 3.4 31.7 1.0
OE1 B:GLU335 3.5 45.3 1.0
CB B:ASP353 4.2 28.3 1.0
O B:HOH2160 4.2 32.4 1.0
OD1 B:ASP353 4.4 34.3 1.0
CD B:GLU335 4.4 40.2 1.0
CB B:ASP336 4.6 28.5 1.0
O B:HOH2138 4.8 24.9 0.5
CG B:GLU335 4.8 33.8 1.0
CB B:GLU335 4.9 28.5 1.0
OE1 B:GLN351 5.0 34.5 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 Dec 13 19:18:55 2020

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