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Zinc in PDB 4p6s: Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site

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

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site, PDB code: 4p6s 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) 47.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.880, 81.550, 84.060, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site (pdb code 4p6s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site, PDB code: 4p6s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4p6s

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Zinc binding site 1 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:36.9
occ:0.90
 O A:HOH539 1.5 54.9 1.0
NE2 A:HIS60 2.1 23.6 1.0
NE2 A:HIS42 2.3 22.9 1.0
OE2 A:DAH305 2.8 20.0 1.0
CE1 A:HIS60 3.0 22.7 1.0
CD2 A:HIS60 3.1 23.5 1.0
NE2 A:HIS69 3.1 15.9 1.0
ZN A:ZN302 3.2 21.9 1.0
CE1 A:HIS42 3.2 22.3 1.0
CD2 A:HIS42 3.3 21.1 1.0
OZ A:DAH305 3.6 20.0 1.0
CE1 A:HIS69 3.7 16.0 1.0
CZ A:PHE227 3.8 14.9 1.0
CE2 A:PHE227 3.9 16.0 1.0
CE2 A:DAH305 4.0 20.0 1.0
ND1 A:HIS60 4.1 22.7 1.0
CG A:HIS60 4.2 23.1 1.0
CZ A:DAH305 4.2 20.0 1.0
CD2 A:HIS69 4.3 15.9 1.0
NE2 A:HIS231 4.3 10.6 1.0
ND1 A:HIS42 4.4 22.7 1.0
CG A:HIS42 4.4 21.9 1.0
NE2 A:HIS208 4.6 18.8 1.0
NE2 A:HIS204 4.7 15.4 1.0
CE1 A:HIS231 4.8 10.4 1.0
CE1 A:HIS208 4.8 18.5 1.0
ND1 A:HIS69 4.9 15.9 1.0
CG1 A:VAL218 4.9 30.4 1.0
CE1 A:HIS204 5.0 15.9 1.0

Zinc binding site 2 out of 6 in 4p6s

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Zinc binding site 2 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:21.9
occ:1.00
 O A:HOH539 1.7 54.9 1.0
NE2 A:HIS231 2.0 10.6 1.0
NE2 A:HIS204 2.1 15.4 1.0
NE2 A:HIS208 2.2 18.8 1.0
CE1 A:HIS231 2.7 10.4 1.0
OE2 A:DAH305 3.0 20.0 1.0
CE1 A:HIS204 3.0 15.9 1.0
CE1 A:HIS208 3.1 18.5 1.0
CD2 A:HIS204 3.1 15.7 1.0
ZN A:ZN301 3.2 36.9 0.9
CD2 A:HIS231 3.2 10.7 1.0
CD2 A:HIS208 3.2 18.7 1.0
ND1 A:HIS231 3.9 10.1 1.0
CE2 A:PHE227 4.0 16.0 1.0
CE2 A:DAH305 4.0 20.0 1.0
NE2 A:HIS69 4.1 15.9 1.0
CZ A:PHE227 4.1 14.9 1.0
ND1 A:HIS204 4.2 16.0 1.0
CG A:HIS231 4.2 10.4 1.0
ND1 A:HIS208 4.2 18.8 1.0
CG A:HIS204 4.2 16.0 1.0
CG A:HIS208 4.3 19.1 1.0
OZ A:DAH305 4.4 20.0 1.0
CD2 A:HIS230 4.5 13.8 1.0
CE1 A:PHE65 4.5 15.7 1.0
NE2 A:HIS230 4.6 14.1 1.0
CZ A:DAH305 4.6 20.0 1.0
CE1 A:HIS69 4.6 16.0 1.0
CD2 A:HIS69 4.6 15.9 1.0
NE2 A:HIS60 4.7 23.6 1.0
CD2 A:DAH305 4.8 20.0 1.0
CD2 A:PHE227 4.8 16.0 1.0
CD2 A:HIS60 4.9 23.5 1.0
CZ A:PHE65 5.0 16.2 1.0

Zinc binding site 3 out of 6 in 4p6s

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Zinc binding site 3 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:44.0
occ:0.50
 OD1 A:ASP55 2.5 40.4 1.0
CG A:MET184 2.7 34.5 1.0
N A:MET184 3.0 32.8 1.0
CG A:ASP55 3.0 41.0 1.0
OD2 A:ASP55 3.1 41.5 1.0
CB A:ASP183 3.2 26.8 1.0
CB A:MET184 3.3 32.9 1.0
O A:MET61 3.4 22.7 1.0
O A:ASP55 3.4 37.4 1.0
CB A:MET61 3.4 22.0 1.0
CA A:MET184 3.7 33.6 1.0
C A:ASP55 3.8 37.9 1.0
CA A:ASP183 3.9 26.0 1.0
C A:ASP183 3.9 26.2 1.0
CG A:ASP183 4.0 28.6 1.0
SD A:MET184 4.1 35.6 1.0
CB A:ASP55 4.1 40.4 1.0
CG A:MET61 4.2 22.6 1.0
C A:MET61 4.2 22.1 1.0
CA A:MET61 4.2 21.8 1.0
N A:ARG56 4.2 22.4 1.0
SD A:MET61 4.3 23.4 1.0
OD1 A:ASP183 4.4 29.5 1.0
O A:HOH498 4.5 30.5 1.0
CA A:ARG56 4.5 21.7 1.0
CA A:ASP55 4.5 38.9 1.0
CG A:ARG56 4.6 22.3 1.0
OD2 A:ASP183 4.7 28.4 1.0
C A:MET184 4.9 34.4 1.0

Zinc binding site 4 out of 6 in 4p6s

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Zinc binding site 4 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:42.3
occ:0.80
 O B:HOH510 1.6 30.0 1.0
NE2 B:HIS42 2.1 24.3 1.0
NE2 B:HIS60 2.2 28.9 1.0
OZ B:DAH305 2.3 20.0 1.0
NE2 B:HIS69 2.5 18.5 1.0
CD2 B:HIS60 3.1 28.7 1.0
CD2 B:HIS42 3.1 23.2 1.0
CE1 B:HIS42 3.1 23.9 1.0
ZN B:ZN302 3.2 32.2 0.9
CE1 B:HIS69 3.2 18.2 1.0
CE1 B:HIS60 3.3 28.3 1.0
OE2 B:DAH305 3.3 20.0 1.0
CZ B:DAH305 3.5 20.0 1.0
CD2 B:HIS69 3.6 18.6 1.0
CE2 B:DAH305 3.8 20.0 1.0
CZ B:PHE227 3.9 19.8 1.0
CE2 B:PHE227 4.0 20.0 1.0
NE2 B:HIS231 4.2 15.9 1.0
ND1 B:HIS42 4.2 23.3 1.0
CG B:HIS60 4.3 28.8 1.0
CG B:HIS42 4.3 22.9 1.0
ND1 B:HIS60 4.3 27.9 1.0
ND1 B:HIS69 4.4 18.1 1.0
CE1 B:HIS231 4.6 16.2 1.0
CG B:HIS69 4.6 18.9 1.0
CE1 B:DAH305 4.6 20.0 1.0
NE2 B:HIS204 4.7 25.4 1.0
NE2 B:HIS208 4.9 27.4 1.0
CE1 B:PHE65 5.0 20.4 1.0

Zinc binding site 5 out of 6 in 4p6s

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Zinc binding site 5 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:32.2
occ:0.90
 O B:HOH510 1.7 30.0 1.0
NE2 B:HIS231 2.1 15.9 1.0
NE2 B:HIS208 2.1 27.4 1.0
NE2 B:HIS204 2.2 25.4 1.0
CE1 B:HIS231 2.9 16.2 1.0
CE1 B:HIS208 3.0 27.4 1.0
OZ B:DAH305 3.0 20.0 1.0
CE1 B:HIS204 3.1 25.7 1.0
CD2 B:HIS208 3.2 28.0 1.0
CD2 B:HIS231 3.2 15.6 1.0
ZN B:ZN301 3.2 42.3 0.8
CD2 B:HIS204 3.2 25.5 1.0
OE2 B:DAH305 3.3 20.0 1.0
CZ B:DAH305 3.4 20.0 1.0
CE2 B:DAH305 3.6 20.0 1.0
CE2 B:PHE227 3.8 20.0 1.0
ND1 B:HIS231 4.1 16.2 1.0
CZ B:PHE227 4.1 19.8 1.0
ND1 B:HIS208 4.1 27.3 1.0
NE2 B:HIS69 4.1 18.5 1.0
CG B:HIS208 4.2 28.2 1.0
CG B:HIS231 4.3 15.8 1.0
ND1 B:HIS204 4.3 25.7 1.0
CE1 B:DAH305 4.3 20.0 1.0
CG B:HIS204 4.4 26.2 1.0
CD2 B:HIS69 4.5 18.6 1.0
NE2 B:HIS230 4.5 20.4 1.0
CD2 B:PHE227 4.6 20.2 1.0
CD2 B:DAH305 4.6 20.0 1.0
CD2 B:HIS230 4.6 19.8 1.0
CE1 B:PHE65 4.7 20.4 1.0
CE1 B:HIS69 4.9 18.2 1.0
NE2 B:HIS42 4.9 24.3 1.0
NE2 B:HIS60 5.0 28.9 1.0

Zinc binding site 6 out of 6 in 4p6s

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Zinc binding site 6 out of 6 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Tyrosinase From Bacillus Megaterium with L-Dopa in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:0.5
occ:0.70
 O B:HOH488 2.3 39.0 1.0
CB B:HIS60 2.8 28.3 1.0
CE B:MET61 2.8 32.9 1.0
CG B:HIS60 3.0 28.8 1.0
ND1 B:HIS60 3.4 27.9 1.0
ND2 B:ASN57 3.4 26.0 1.0
CG2 B:VAL218 3.7 42.7 1.0
CG B:MET61 3.7 31.9 1.0
CD2 B:HIS60 3.8 28.7 1.0
SD B:MET61 4.0 33.2 1.0
CA B:HIS60 4.3 28.2 1.0
CE1 B:HIS60 4.3 28.3 1.0
O B:HOH461 4.4 29.3 1.0
CG1 B:VAL218 4.5 41.4 1.0
NE2 B:HIS60 4.5 28.9 1.0
CG B:ASN57 4.5 25.1 1.0
CB B:VAL218 4.6 41.9 1.0
C B:HIS60 4.6 28.4 1.0
OD1 B:ASN57 4.7 25.0 1.0
N B:MET61 4.8 31.0 1.0
OE2 B:DAH305 4.8 20.0 1.0
O B:HOH410 4.9 42.4 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 Oct 27 04:17:03 2024

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