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Copper 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:

Holmium (Ho) 4 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, with Inhibitor Tropolone (pdb code 2y9x). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 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, with Inhibitor Tropolone, PDB code: 2y9x:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 1 out of 8 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 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, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu400

b:43.9
occ:1.00
NE2 A:HIS61 2.1 47.1 1.0
NE2 A:HIS94 2.1 43.7 1.0
NE2 A:HIS85 2.1 45.7 1.0
CE1 A:HIS94 2.9 42.4 1.0
CD2 A:HIS61 2.9 45.5 1.0
CD2 A:HIS85 3.0 44.4 1.0
CE1 A:HIS85 3.1 45.0 1.0
CE1 A:HIS61 3.1 46.8 1.0
CD2 A:HIS94 3.2 41.5 1.0
CB A:CYS83 3.7 43.2 1.0
SG A:CYS83 3.7 44.2 1.0
ND1 A:HIS94 4.0 41.7 1.0
CG A:HIS61 4.1 45.1 1.0
ND1 A:HIS85 4.2 45.2 1.0
CG A:HIS94 4.2 40.7 1.0
ND1 A:HIS61 4.2 46.3 1.0
CG A:HIS85 4.2 44.6 1.0
NE2 A:HIS296 4.3 45.4 1.0
CU A:CU401 4.4 40.5 1.0
CE1 A:HIS296 4.4 45.0 1.0
OA2 A:0TR410 4.4 82.8 1.0
CZ A:PHE292 4.4 41.5 1.0
CE2 A:PHE292 4.7 40.7 1.0
CE1 A:PHE90 4.9 37.7 1.0

Copper binding site 2 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 2 out of 8 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 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, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:40.5
occ:1.00
NE2 A:HIS296 2.1 45.4 1.0
NE2 A:HIS259 2.1 45.0 1.0
NE2 A:HIS263 2.1 46.0 1.0
CE1 A:HIS259 2.9 45.1 1.0
CD2 A:HIS263 2.9 45.9 1.0
CD2 A:HIS296 3.0 43.9 1.0
CE1 A:HIS296 3.1 45.0 1.0
CD2 A:HIS259 3.1 43.8 1.0
CE1 A:HIS263 3.1 45.5 1.0
OA2 A:0TR410 3.5 82.8 1.0
CE2 A:PHE292 4.0 40.7 1.0
ND1 A:HIS259 4.0 44.6 1.0
CG A:HIS296 4.1 43.5 1.0
CG A:HIS263 4.1 45.9 1.0
ND1 A:HIS296 4.1 44.1 1.0
CG A:HIS259 4.2 43.8 1.0
ND1 A:HIS263 4.2 45.6 1.0
CD2 A:HIS295 4.3 41.5 1.0
CU A:CU400 4.4 43.9 1.0
NE2 A:HIS295 4.5 41.3 1.0
CZ A:PHE292 4.5 41.5 1.0
OA1 A:0TR410 4.6 82.7 1.0
CA2 A:0TR410 4.6 82.8 1.0
CD2 A:PHE292 4.7 40.8 1.0

Copper binding site 3 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 3 out of 8 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 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, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu400

b:42.1
occ:1.00
NE2 B:HIS61 2.1 48.4 1.0
NE2 B:HIS85 2.1 46.4 1.0
NE2 B:HIS94 2.1 44.8 1.0
CE1 B:HIS85 2.9 45.5 1.0
CE1 B:HIS94 3.0 43.3 1.0
CD2 B:HIS61 3.0 47.3 1.0
CE1 B:HIS61 3.1 48.4 1.0
CD2 B:HIS94 3.1 42.9 1.0
CD2 B:HIS85 3.2 44.9 1.0
SG B:CYS83 3.5 45.5 1.0
CB B:CYS83 3.7 44.5 1.0
OA1 B:0TR410 3.9 71.8 1.0
CU B:CU401 4.0 42.7 1.0
ND1 B:HIS85 4.1 45.4 1.0
ND1 B:HIS94 4.1 42.4 1.0
ND1 B:HIS61 4.2 47.9 1.0
CG B:HIS61 4.2 47.0 1.0
CG B:HIS94 4.2 41.9 1.0
CG B:HIS85 4.2 44.8 1.0
NE2 B:HIS296 4.3 47.8 1.0
CE1 B:HIS296 4.4 46.9 1.0
CZ B:PHE292 4.5 42.6 1.0
CE2 B:PHE292 4.9 42.7 1.0
CE1 B:PHE90 4.9 38.2 1.0

Copper binding site 4 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 4 out of 8 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 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, with Inhibitor Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:42.7
occ:1.00
NE2 B:HIS296 2.1 47.8 1.0
NE2 B:HIS259 2.1 48.3 1.0
NE2 B:HIS263 2.1 49.9 1.0
CE1 B:HIS296 2.9 46.9 1.0
CD2 B:HIS259 2.9 47.1 1.0
CD2 B:HIS263 2.9 49.6 1.0
CE1 B:HIS259 3.1 48.0 1.0
CE1 B:HIS263 3.1 49.1 1.0
OA1 B:0TR410 3.2 71.8 1.0
CD2 B:HIS296 3.2 46.1 1.0
CA1 B:0TR410 4.0 71.9 1.0
CU B:CU400 4.0 42.1 1.0
ND1 B:HIS296 4.1 46.1 1.0
CG B:HIS259 4.1 47.1 1.0
ND1 B:HIS259 4.1 48.0 1.0
CG B:HIS263 4.1 49.5 1.0
ND1 B:HIS263 4.1 49.3 1.0
OA2 B:0TR410 4.2 71.6 1.0
CG B:HIS296 4.2 45.5 1.0
CE2 B:PHE292 4.3 42.7 1.0
CD2 B:HIS295 4.3 44.9 1.0
NE2 B:HIS295 4.3 44.8 1.0
CA2 B:0TR410 4.5 71.8 1.0
CZ B:PHE292 4.6 42.6 1.0
NE2 B:HIS94 4.8 44.8 1.0
CA6 B:0TR410 4.9 71.9 1.0
CD2 B:HIS94 5.0 42.9 1.0

Copper binding site 5 out of 8 in 2y9x

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Copper binding site 5 out of 8 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 Copper with other atoms in the Cu binding site number 5 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:Cu400

b:42.6
occ:1.00
NE2 C:HIS94 2.1 46.4 1.0
NE2 C:HIS61 2.1 50.9 1.0
NE2 C:HIS85 2.1 47.2 1.0
CE1 C:HIS94 2.9 44.7 1.0
CD2 C:HIS61 2.9 49.9 1.0
CE1 C:HIS85 3.0 46.6 1.0
OA2 C:0TR410 3.0 0.1 1.0
CD2 C:HIS94 3.1 45.1 1.0
CD2 C:HIS85 3.1 45.4 1.0
CE1 C:HIS61 3.2 50.9 1.0
SG C:CYS83 3.3 46.9 1.0
CB C:CYS83 3.5 46.3 1.0
ND1 C:HIS94 4.0 44.3 1.0
ND1 C:HIS85 4.1 46.2 1.0
CG C:HIS61 4.1 49.5 1.0
CG C:HIS94 4.2 43.8 1.0
ND1 C:HIS61 4.2 50.5 1.0
CG C:HIS85 4.2 45.3 1.0
CA2 C:0TR410 4.3 0.6 1.0
CU C:CU401 4.4 42.1 1.0
NE2 C:HIS296 4.5 50.7 1.0
CE1 C:HIS296 4.6 49.5 1.0
CZ C:PHE292 4.6 47.5 1.0
CZ3 C:TRP93 4.8 43.7 1.0
CE1 C:PHE90 4.8 38.9 1.0
OA1 C:0TR410 4.8 1.0 1.0
CE2 C:PHE292 4.9 47.0 1.0
CA C:CYS83 4.9 46.4 1.0

Copper binding site 6 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 6 out of 8 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 Copper with other atoms in the Cu binding site number 6 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:Cu401

b:42.1
occ:1.00
NE2 C:HIS296 2.1 50.7 1.0
NE2 C:HIS263 2.1 52.1 1.0
NE2 C:HIS259 2.1 49.7 1.0
CD2 C:HIS296 2.9 49.9 1.0
CD2 C:HIS263 3.0 51.2 1.0
CD2 C:HIS259 3.0 48.2 1.0
CE1 C:HIS263 3.1 51.8 1.0
CE1 C:HIS259 3.1 48.8 1.0
CE1 C:HIS296 3.2 49.5 1.0
OA2 C:0TR410 3.4 0.1 1.0
CE2 C:PHE292 3.8 47.0 1.0
CA2 C:0TR410 3.8 0.6 1.0
CD2 C:HIS295 4.0 47.2 1.0
OA1 C:0TR410 4.1 1.0 1.0
CG C:HIS263 4.1 51.1 1.0
CG C:HIS296 4.1 49.3 1.0
ND1 C:HIS263 4.2 51.6 1.0
CG C:HIS259 4.2 47.5 1.0
ND1 C:HIS259 4.2 48.0 1.0
ND1 C:HIS296 4.2 49.4 1.0
CA1 C:0TR410 4.2 0.8 1.0
NE2 C:HIS295 4.2 46.6 1.0
CU C:CU400 4.4 42.6 1.0
CZ C:PHE292 4.4 47.5 1.0
CA3 C:0TR410 4.5 0.8 1.0
CD2 C:PHE292 4.5 47.5 1.0
NE2 C:HIS61 5.0 50.9 1.0

Copper binding site 7 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 7 out of 8 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 Copper with other atoms in the Cu binding site number 7 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:Cu400

b:44.6
occ:1.00
NE2 D:HIS85 2.1 46.4 1.0
NE2 D:HIS94 2.1 45.5 1.0
NE2 D:HIS61 2.1 49.8 1.0
CE1 D:HIS94 3.0 43.5 1.0
CD2 D:HIS85 3.0 44.3 1.0
CE1 D:HIS61 3.1 49.3 1.0
CD2 D:HIS61 3.1 48.8 1.0
CE1 D:HIS85 3.1 45.1 1.0
CD2 D:HIS94 3.1 43.9 1.0
OA1 D:0TR410 3.3 73.6 1.0
SG D:CYS83 3.6 45.5 1.0
CB D:CYS83 3.8 45.2 1.0
CU D:CU401 4.1 42.9 1.0
ND1 D:HIS94 4.1 43.1 1.0
ND1 D:HIS85 4.2 44.7 1.0
ND1 D:HIS61 4.2 48.9 1.0
CG D:HIS85 4.2 43.6 1.0
CG D:HIS61 4.2 48.5 1.0
CG D:HIS94 4.2 42.9 1.0
OA2 D:0TR410 4.3 74.3 1.0
CZ D:PHE292 4.3 44.7 1.0
CE1 D:HIS296 4.4 46.9 1.0
CA1 D:0TR410 4.4 73.8 1.0
NE2 D:HIS296 4.5 47.9 1.0
CE2 D:PHE292 4.8 44.0 1.0
CE1 D:PHE90 4.8 37.6 1.0
CA2 D:0TR410 4.9 73.8 1.0

Copper binding site 8 out of 8 in 2y9x

Go back to Copper Binding Sites List in 2y9x
Copper binding site 8 out of 8 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 Copper with other atoms in the Cu binding site number 8 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:Cu401

b:42.9
occ:1.00
NE2 D:HIS259 2.1 46.7 1.0
NE2 D:HIS263 2.1 48.7 1.0
NE2 D:HIS296 2.1 47.9 1.0
OA1 D:0TR410 2.8 73.6 1.0
CE1 D:HIS296 2.9 46.9 1.0
CD2 D:HIS259 2.9 45.2 1.0
CE1 D:HIS263 3.0 48.3 1.0
CD2 D:HIS263 3.0 47.9 1.0
CE1 D:HIS259 3.1 45.9 1.0
CD2 D:HIS296 3.2 47.0 1.0
CA1 D:0TR410 3.4 73.8 1.0
OA2 D:0TR410 3.5 74.3 1.0
CA2 D:0TR410 3.8 73.8 1.0
CE2 D:PHE292 4.0 44.0 1.0
ND1 D:HIS296 4.0 46.8 1.0
ND1 D:HIS263 4.1 48.0 1.0
CG D:HIS263 4.1 47.4 1.0
CU D:CU400 4.1 44.6 1.0
CG D:HIS259 4.1 44.8 1.0
ND1 D:HIS259 4.2 45.4 1.0
CG D:HIS296 4.2 46.9 1.0
CZ D:PHE292 4.2 44.7 1.0
CD2 D:HIS295 4.3 44.5 1.0
CA6 D:0TR410 4.4 73.9 1.0
NE2 D:HIS295 4.4 43.7 1.0
CD2 D:PHE292 4.8 44.8 1.0
CA3 D:0TR410 4.9 73.8 1.0
NE2 D:HIS94 5.0 45.5 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 11:08:00 2020

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