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Copper in PDB 4p6t: Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site, PDB code: 4p6t was solved by M.Goldfeder, M.Kanteev, N.Adir, A.Fishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.23 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.690, 78.090, 84.280, 90.00, 105.96, 90.00
R / Rfree (%) 20.8 / 26.1

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site (pdb code 4p6t). 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 Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site, PDB code: 4p6t:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 4p6t

Go back to Copper Binding Sites List in 4p6t
Copper binding site 1 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site


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 Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:32.1
occ:1.00
O A:HOH490 1.6 56.2 1.0
H041 A:YRL301 1.9 49.1 1.0
NE2 A:HIS60 2.0 22.7 1.0
O07 A:YRL301 2.1 51.1 1.0
NE2 A:HIS42 2.1 17.2 1.0
C04 A:YRL301 2.5 49.1 1.0
NE2 A:HIS69 2.6 18.7 1.0
H071 A:YRL301 2.6 51.1 1.0
C06 A:YRL301 2.8 47.1 1.0
CD2 A:HIS60 2.8 20.3 1.0
CE1 A:HIS42 2.9 17.2 1.0
CE1 A:HIS60 3.2 21.0 1.0
CE1 A:HIS69 3.2 18.5 1.0
CD2 A:HIS42 3.3 14.9 1.0
CU A:CU303 3.3 15.2 1.0
CD2 A:HIS69 3.7 16.8 1.0
C02 A:YRL301 3.8 50.5 1.0
CZ A:PHE227 3.8 13.8 1.0
CE2 A:PHE227 4.0 14.6 1.0
CG A:HIS60 4.0 20.9 1.0
ND1 A:HIS42 4.1 16.9 1.0
C05 A:YRL301 4.1 51.0 1.0
ND1 A:HIS60 4.2 22.0 1.0
H021 A:YRL301 4.2 50.5 1.0
NE2 A:HIS231 4.3 14.5 1.0
CG A:HIS42 4.3 14.9 1.0
ND1 A:HIS69 4.4 15.5 1.0
H051 A:YRL301 4.6 51.0 1.0
CG A:HIS69 4.7 19.0 1.0
NE2 A:HIS208 4.8 22.4 1.0
CG1 A:VAL218 4.8 33.5 1.0
CE1 A:HIS231 4.8 11.8 1.0
NE2 A:HIS204 4.9 15.0 1.0
C01 A:YRL301 4.9 51.5 1.0
CE1 A:HIS208 4.9 22.4 1.0

Copper binding site 2 out of 4 in 4p6t

Go back to Copper Binding Sites List in 4p6t
Copper binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site


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 Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:15.2
occ:1.00
O A:HOH490 1.8 56.2 1.0
NE2 A:HIS208 2.0 22.4 1.0
H041 A:YRL301 2.1 49.1 1.0
NE2 A:HIS204 2.1 15.0 1.0
NE2 A:HIS231 2.1 14.5 1.0
C04 A:YRL301 2.6 49.1 1.0
H021 A:YRL301 2.7 50.5 1.0
CE1 A:HIS208 2.8 22.4 1.0
C02 A:YRL301 2.9 50.5 1.0
CD2 A:HIS231 3.0 13.6 1.0
CD2 A:HIS204 3.1 13.4 1.0
CE1 A:HIS204 3.1 15.5 1.0
CD2 A:HIS208 3.2 22.9 1.0
CE1 A:HIS231 3.2 11.8 1.0
CU A:CU302 3.3 32.1 1.0
C06 A:YRL301 3.5 47.1 1.0
CE2 A:PHE227 3.8 14.6 1.0
O07 A:YRL301 3.9 51.1 1.0
ND1 A:HIS208 3.9 22.9 1.0
H071 A:YRL301 4.0 51.1 1.0
C01 A:YRL301 4.1 51.5 1.0
NE2 A:HIS69 4.1 18.7 1.0
CZ A:PHE227 4.2 13.8 1.0
CG A:HIS208 4.2 23.8 1.0
ND1 A:HIS204 4.2 16.1 1.0
CG A:HIS231 4.2 11.3 1.0
CG A:HIS204 4.2 15.5 1.0
ND1 A:HIS231 4.2 9.9 1.0
CE1 A:HIS230 4.3 20.2 1.0
CD2 A:HIS69 4.4 16.8 1.0
C05 A:YRL301 4.5 51.0 1.0
ND1 A:HIS230 4.6 18.6 1.0
H082 A:YRL301 4.7 51.2 1.0
CD2 A:PHE227 4.7 13.9 1.0
CE1 A:PHE65 4.7 14.6 1.0
C03 A:YRL301 4.7 49.1 1.0
CE1 A:HIS69 4.8 18.5 1.0
CD2 A:HIS60 4.9 20.3 1.0
NE2 A:HIS60 4.9 22.7 1.0
C08 A:YRL301 5.0 51.2 1.0

Copper binding site 3 out of 4 in 4p6t

Go back to Copper Binding Sites List in 4p6t
Copper binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site


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 Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:36.2
occ:1.00
O B:HOH465 1.5 0.1 1.0
H071 B:YRL301 1.7 44.5 1.0
O07 B:YRL301 1.8 44.5 1.0
NE2 B:HIS60 1.9 24.7 1.0
NE2 B:HIS42 2.2 19.6 1.0
CE1 B:HIS60 2.7 20.9 1.0
CD2 B:HIS60 3.0 23.9 1.0
CE1 B:HIS42 3.0 17.4 1.0
NE2 B:HIS69 3.0 11.2 1.0
C06 B:YRL301 3.2 42.6 1.0
CD2 B:HIS42 3.2 15.4 1.0
CU B:CU303 3.2 20.5 1.0
H051 B:YRL301 3.6 45.1 1.0
CE1 B:HIS69 3.7 11.7 1.0
C05 B:YRL301 3.9 45.1 1.0
ND1 B:HIS60 3.9 24.2 1.0
CG B:HIS60 4.0 23.4 1.0
C04 B:YRL301 4.2 46.7 1.0
CE2 B:PHE227 4.2 13.9 1.0
H041 B:YRL301 4.2 46.7 1.0
ND1 B:HIS42 4.2 15.2 1.0
CD2 B:HIS69 4.2 9.2 1.0
CZ B:PHE227 4.2 12.2 1.0
NE2 B:HIS231 4.2 14.8 1.0
CG B:HIS42 4.3 16.1 1.0
NE2 B:HIS204 4.6 18.4 1.0
NE2 B:HIS208 4.7 10.5 1.0
CE1 B:HIS231 4.8 13.9 1.0
CE1 B:HIS204 4.9 22.2 1.0
ND1 B:HIS69 4.9 9.5 1.0

Copper binding site 4 out of 4 in 4p6t

Go back to Copper Binding Sites List in 4p6t
Copper binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site


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 Tyrosinase From Bacillus Megaterium with P- Tyrosol in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu303

b:20.5
occ:1.00
O B:HOH465 1.8 0.1 1.0
NE2 B:HIS231 2.0 14.8 1.0
NE2 B:HIS208 2.1 10.5 1.0
NE2 B:HIS204 2.2 18.4 1.0
CE1 B:HIS231 2.9 13.9 1.0
CD2 B:HIS208 3.0 12.8 1.0
CE1 B:HIS204 3.1 22.2 1.0
CD2 B:HIS231 3.1 13.8 1.0
CD2 B:HIS204 3.1 20.3 1.0
CE1 B:HIS208 3.1 12.4 1.0
CU B:CU302 3.2 36.2 1.0
O07 B:YRL301 3.3 44.5 1.0
H051 B:YRL301 3.5 45.1 1.0
C06 B:YRL301 3.8 42.6 1.0
C05 B:YRL301 3.8 45.1 1.0
CE2 B:PHE227 3.9 13.9 1.0
H071 B:YRL301 4.0 44.5 1.0
NE2 B:HIS69 4.0 11.2 1.0
ND1 B:HIS231 4.1 13.8 1.0
CG B:HIS208 4.1 15.3 1.0
CG B:HIS231 4.2 13.7 1.0
ND1 B:HIS208 4.2 14.2 1.0
CZ B:PHE227 4.2 12.2 1.0
ND1 B:HIS204 4.2 20.1 1.0
CG B:HIS204 4.3 20.7 1.0
CD2 B:HIS69 4.5 9.2 1.0
NE2 B:HIS60 4.6 24.7 1.0
CE1 B:HIS230 4.6 21.8 1.0
CD2 B:PHE227 4.7 13.2 1.0
ND1 B:HIS230 4.7 21.7 1.0
CE1 B:HIS69 4.8 11.7 1.0
C04 B:YRL301 4.9 46.7 1.0
CE1 B:PHE65 4.9 18.2 1.0
C03 B:YRL301 4.9 49.9 1.0

Reference:

M.Goldfeder, M.Kanteev, S.Isaschar-Ovdat, N.Adir, A.Fishman. Determination of Tyrosinase Substrate-Binding Modes Reveals Mechanistic Differences Between Type-3 Copper Proteins. Nat Commun V. 5 4505 2014.
ISSN: ESSN 2041-1723
PubMed: 25074014
DOI: 10.1038/NCOMMS5505
Page generated: Sun Dec 13 11:15:35 2020

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