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Copper in PDB 5zrd: Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition

Enzymatic activity of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition

All present enzymatic activity of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition:
1.14.18.1;

Protein crystallography data

The structure of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition, PDB code: 5zrd was solved by S.Lee, H.-F.Son, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.88 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.914, 142.914, 256.756, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.1

Copper Binding Sites:

The binding sites of Copper atom in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition (pdb code 5zrd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition, PDB code: 5zrd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5zrd

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Copper binding site 1 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu606

b:33.9
occ:1.00
NE2 A:HIS56 2.0 29.9 1.0
NE2 A:HIS84 2.1 30.8 1.0
NE2 A:HIS93 2.2 30.8 1.0
O A:O608 2.5 25.8 1.0
CE1 A:HIS56 2.9 27.6 1.0
CE1 A:HIS84 3.0 31.7 1.0
CD2 A:HIS56 3.0 28.5 1.0
CE1 A:HIS93 3.1 32.8 1.0
CD2 A:HIS84 3.1 32.8 1.0
CD2 A:HIS93 3.2 31.7 1.0
CB A:CYS82 3.6 28.4 1.0
SG A:CYS82 3.6 32.5 1.0
CZ A:PHE315 4.0 30.3 1.0
ND1 A:HIS56 4.1 28.3 1.0
CG A:HIS56 4.1 28.6 1.0
CU A:CU607 4.1 45.1 1.0
ND1 A:HIS84 4.1 31.0 1.0
ND1 A:HIS93 4.2 29.1 1.0
CG A:HIS84 4.2 29.1 1.0
ND2 A:ASN306 4.2 33.3 1.0
CE2 A:PHE315 4.2 27.9 1.0
NE2 A:HIS319 4.3 40.8 1.0
CG A:HIS93 4.3 27.9 1.0
CE1 A:HIS319 4.6 37.7 1.0
CZ3 A:TRP92 4.7 31.9 1.0
O A:ASN83 4.8 23.8 1.0
NE2 A:HIS276 4.9 26.9 1.0
CA A:CYS82 4.9 25.0 1.0
CG A:ASN306 4.9 34.0 1.0

Copper binding site 2 out of 8 in 5zrd

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Copper binding site 2 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu607

b:45.1
occ:1.00
NE2 A:HIS319 1.9 40.8 1.0
NE2 A:HIS280 2.0 34.2 1.0
NE2 A:HIS276 2.1 26.9 1.0
O A:O608 2.2 25.8 1.0
CD2 A:HIS319 2.8 36.5 1.0
CD2 A:HIS276 2.9 26.3 1.0
CE1 A:HIS319 2.9 37.7 1.0
CE1 A:HIS280 2.9 33.7 1.0
CD2 A:HIS280 3.0 33.5 1.0
CE1 A:HIS276 3.3 27.6 1.0
CE2 A:PHE315 3.6 27.9 1.0
CG A:HIS319 3.9 36.7 1.0
ND1 A:HIS319 3.9 32.5 1.0
ND1 A:HIS280 4.0 29.5 1.0
CZ A:PHE315 4.0 30.3 1.0
NE2 A:HIS318 4.1 32.3 1.0
CD2 A:HIS318 4.1 31.0 1.0
CG A:HIS276 4.1 27.6 1.0
CG A:HIS280 4.1 31.3 1.0
CU A:CU606 4.1 33.9 1.0
ND1 A:HIS276 4.2 28.0 1.0
CD2 A:PHE315 4.4 29.0 1.0
NE2 A:HIS93 4.6 30.8 1.0
CD2 A:HIS93 4.6 31.7 1.0
CD2 A:LEU466 4.9 27.6 1.0
NE2 A:HIS56 4.9 29.9 1.0
CE1 A:PHE89 5.0 28.7 1.0

Copper binding site 3 out of 8 in 5zrd

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Copper binding site 3 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu606

b:47.3
occ:1.00
CE1 B:HIS319 1.8 38.8 1.0
NE2 B:HIS280 1.9 34.3 1.0
O B:O608 2.1 25.4 1.0
NE2 B:HIS276 2.3 31.2 1.0
NE2 B:HIS319 2.7 38.4 1.0
CE1 B:HIS280 2.8 32.9 1.0
CD2 B:HIS276 2.9 29.4 1.0
ND1 B:HIS319 2.9 36.1 1.0
CD2 B:HIS280 3.0 37.1 1.0
CE1 B:HIS276 3.4 28.3 1.0
CE2 B:PHE315 3.6 28.9 1.0
CD2 B:HIS319 3.9 33.2 1.0
ND1 B:HIS280 3.9 33.8 1.0
CD2 B:HIS318 3.9 41.9 1.0
CZ B:PHE315 4.0 28.6 1.0
NE2 B:HIS318 4.0 44.0 1.0
CG B:HIS319 4.0 35.9 1.0
CG B:HIS280 4.0 34.1 1.0
CG B:HIS276 4.1 26.8 1.0
CU B:CU607 4.2 36.8 1.0
CD2 B:PHE315 4.3 32.1 1.0
ND1 B:HIS276 4.3 29.6 1.0
CE1 B:HIS93 4.7 30.9 1.0
CD2 B:LEU466 4.9 27.3 1.0
ND1 B:HIS93 4.9 37.7 1.0
CE1 B:PHE315 4.9 31.9 1.0
CE1 B:PHE89 5.0 34.1 1.0

Copper binding site 4 out of 8 in 5zrd

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Copper binding site 4 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu607

b:36.8
occ:1.00
CE1 B:HIS84 2.1 35.8 1.0
CE1 B:HIS56 2.1 38.3 1.0
CE1 B:HIS93 2.1 30.9 1.0
O B:O608 2.5 25.4 1.0
NE2 B:HIS93 2.7 27.1 1.0
NE2 B:HIS84 2.9 34.6 1.0
NE2 B:HIS56 2.9 35.1 1.0
ND1 B:HIS56 3.1 35.9 1.0
ND1 B:HIS84 3.2 37.7 1.0
ND1 B:HIS93 3.3 37.7 1.0
CB B:CYS82 3.6 36.4 1.0
SG B:CYS82 3.7 36.5 1.0
CZ B:PHE315 3.9 28.6 1.0
CD2 B:HIS93 4.0 30.2 1.0
CD2 B:HIS56 4.1 38.1 1.0
CD2 B:HIS84 4.1 36.2 1.0
CU B:CU606 4.2 47.3 1.0
CE2 B:PHE315 4.2 28.9 1.0
CG B:HIS56 4.2 36.9 1.0
CG B:HIS84 4.3 31.1 1.0
CG B:HIS93 4.3 31.2 1.0
NE2 B:HIS319 4.4 38.4 1.0
ND2 B:ASN306 4.4 42.1 1.0
CE1 B:HIS319 4.5 38.8 1.0
CZ3 B:TRP92 4.6 37.0 1.0
NE2 B:HIS276 4.9 31.2 1.0
CE1 B:PHE89 5.0 34.1 1.0

Copper binding site 5 out of 8 in 5zrd

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Copper binding site 5 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu604

b:55.0
occ:1.00
NE2 C:HIS280 2.0 44.6 1.0
CE1 C:HIS319 2.0 43.6 1.0
CE1 C:HIS276 2.1 34.4 1.0
O C:O606 2.2 28.3 1.0
NE2 C:HIS319 2.7 39.0 1.0
CE1 C:HIS280 2.9 45.8 1.0
CD2 C:HIS280 2.9 40.9 1.0
ND1 C:HIS276 2.9 33.7 1.0
ND1 C:HIS319 3.1 43.4 1.0
NE2 C:HIS276 3.2 35.2 1.0
CE2 C:PHE315 3.7 46.2 1.0
CD2 C:HIS319 3.9 38.2 1.0
CD2 C:HIS318 3.9 36.7 1.0
NE2 C:HIS318 4.0 40.9 1.0
ND1 C:HIS280 4.0 40.0 1.0
CG C:HIS280 4.0 38.4 1.0
CG C:HIS319 4.1 42.7 1.0
CU C:CU605 4.1 42.1 1.0
CZ C:PHE315 4.2 44.3 1.0
CG C:HIS276 4.2 32.1 1.0
CD2 C:HIS276 4.3 30.1 1.0
CD2 C:PHE315 4.3 39.2 1.0
NE2 C:HIS93 4.6 43.4 1.0
CD2 C:HIS93 4.8 42.4 1.0
CD2 C:LEU466 4.9 36.7 1.0
CE1 C:PHE89 5.0 38.8 1.0

Copper binding site 6 out of 8 in 5zrd

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Copper binding site 6 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu605

b:42.1
occ:1.00
NE2 C:HIS93 2.0 43.4 1.0
CE1 C:HIS56 2.0 36.8 1.0
NE2 C:HIS84 2.2 34.1 1.0
O C:O606 2.5 28.3 1.0
CE1 C:HIS93 2.9 45.1 1.0
NE2 C:HIS56 2.9 34.0 1.0
CD2 C:HIS84 3.0 29.9 1.0
ND1 C:HIS56 3.0 42.0 1.0
CD2 C:HIS93 3.1 42.4 1.0
CE1 C:HIS84 3.4 31.4 1.0
CB C:CYS82 3.6 37.2 1.0
SG C:CYS82 3.7 38.3 1.0
CZ C:PHE315 3.9 44.3 1.0
ND1 C:HIS93 4.0 44.4 1.0
CD2 C:HIS56 4.1 34.6 1.0
CU C:CU604 4.1 55.0 1.0
CE2 C:PHE315 4.1 46.2 1.0
CG C:HIS56 4.2 36.0 1.0
CG C:HIS93 4.2 42.4 1.0
CG C:HIS84 4.2 31.4 1.0
CE1 C:HIS319 4.3 43.6 1.0
NE2 C:HIS319 4.3 39.0 1.0
ND2 C:ASN306 4.3 40.3 1.0
ND1 C:HIS84 4.4 32.3 1.0
CE1 C:PHE89 4.8 38.8 1.0
CZ3 C:TRP92 4.8 40.7 1.0
CE1 C:HIS276 4.9 34.4 1.0
O C:ASN83 5.0 35.6 1.0

Copper binding site 7 out of 8 in 5zrd

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Copper binding site 7 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu606

b:40.8
occ:1.00
CE1 D:HIS84 2.0 29.7 1.0
CE1 D:HIS56 2.0 33.0 1.0
NE2 D:HIS93 2.0 46.2 1.0
O D:O608 2.5 34.4 1.0
NE2 D:HIS84 2.6 33.0 1.0
NE2 D:HIS56 2.9 32.8 1.0
CE1 D:HIS93 3.0 45.1 1.0
ND1 D:HIS56 3.0 38.5 1.0
CD2 D:HIS93 3.1 36.5 1.0
ND1 D:HIS84 3.2 32.6 1.0
SG D:CYS82 3.6 37.5 1.0
CB D:CYS82 3.6 39.1 1.0
CZ D:PHE315 3.8 35.5 1.0
CD2 D:HIS84 3.9 30.8 1.0
ND1 D:HIS93 4.1 39.3 1.0
CD2 D:HIS56 4.1 33.6 1.0
CG D:HIS56 4.1 35.0 1.0
CE2 D:PHE315 4.2 40.8 1.0
ND2 D:ASN306 4.2 42.9 1.0
CG D:HIS84 4.2 28.9 1.0
CG D:HIS93 4.2 39.8 1.0
CU D:CU607 4.2 51.1 1.0
NE2 D:HIS319 4.3 45.8 1.0
CE1 D:HIS319 4.3 45.8 1.0
CZ3 D:TRP92 4.7 37.3 1.0
CE1 D:PHE89 4.9 46.2 1.0
O D:ASN83 4.9 31.9 1.0
CG D:ASN306 5.0 41.0 1.0
CA D:CYS82 5.0 38.8 1.0

Copper binding site 8 out of 8 in 5zrd

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Copper binding site 8 out of 8 in the Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Tyrosinase From Burkholderia Thailandensis (Bttyr) at Low pH Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu607

b:51.1
occ:1.00
NE2 D:HIS280 1.9 35.6 1.0
CE1 D:HIS319 1.9 45.8 1.0
CE1 D:HIS276 2.1 34.1 1.0
O D:O608 2.3 34.4 1.0
NE2 D:HIS319 2.5 45.8 1.0
CE1 D:HIS280 2.9 36.2 1.0
CD2 D:HIS280 2.9 32.2 1.0
ND1 D:HIS276 3.0 30.9 1.0
NE2 D:HIS276 3.0 31.9 1.0
ND1 D:HIS319 3.1 42.5 1.0
CD2 D:HIS319 3.8 35.7 1.0
CE2 D:PHE315 3.9 40.8 1.0
NE2 D:HIS318 3.9 42.8 1.0
ND1 D:HIS280 4.0 35.1 1.0
CD2 D:HIS318 4.0 37.4 1.0
CG D:HIS280 4.0 34.6 1.0
CG D:HIS319 4.0 41.2 1.0
CD2 D:HIS276 4.2 31.4 1.0
CG D:HIS276 4.2 31.8 1.0
CZ D:PHE315 4.2 35.5 1.0
CU D:CU606 4.2 40.8 1.0
CD2 D:PHE315 4.5 36.4 1.0
NE2 D:HIS93 4.7 46.2 1.0
CD2 D:LEU466 4.8 30.4 1.0
CD2 D:HIS93 4.9 36.5 1.0

Reference:

H.F.Son, S.H.Lee, S.H.Lee, H.Kim, H.Hong, U.J.Lee, P.G.Lee, B.G.Kim, K.J.Kim. Structural Basis For Highly Efficient Production of Catechol Derivatives at Acidic pH By Tyrosinase From Burkholderia Thailandensis Acs Catalysis V. 8 10375 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B02635
Page generated: Sun Dec 13 11:21:55 2020

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