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Copper in PDB 3npy: Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4, PDB code: 3npy was solved by M.Sendovski, 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) 50.00 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.550, 82.130, 146.720, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 27.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4 (pdb code 3npy). 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 Tyrosinase From Bacillus Megaterium Soaked in CUSO4, PDB code: 3npy:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3npy

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Copper binding site 1 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:34.4
occ:0.80
CU A:CU501 0.0 34.4 0.8
CU A:CU501 0.3 31.1 0.2
O A:HOH350 1.9 34.4 1.0
NE2 A:HIS208 2.0 30.4 1.0
NE2 A:HIS231 2.0 16.0 1.0
NE2 A:HIS204 2.1 25.4 1.0
CE1 A:HIS231 2.8 17.6 1.0
CE1 A:HIS208 2.9 31.1 1.0
CD2 A:HIS208 3.0 29.9 1.0
CE1 A:HIS204 3.0 25.1 1.0
CD2 A:HIS231 3.2 13.6 1.0
CD2 A:HIS204 3.2 20.5 1.0
CU A:CU502 3.4 34.4 0.6
CU A:CU502 3.6 31.4 0.4
O A:HOH347 3.7 34.4 1.0
O A:HOH348 3.7 34.4 1.0
CE2 A:PHE227 3.8 18.2 1.0
ND1 A:HIS231 4.0 15.7 1.0
ND1 A:HIS208 4.0 30.9 1.0
CG A:HIS208 4.1 29.4 1.0
NE2 A:HIS69 4.1 18.7 1.0
ND1 A:HIS204 4.1 25.0 1.0
CG A:HIS231 4.2 16.2 1.0
CZ A:PHE227 4.2 23.2 1.0
CG A:HIS204 4.3 24.7 1.0
CE1 A:PHE65 4.5 30.8 1.0
CD2 A:HIS69 4.6 20.4 1.0
CD2 A:PHE227 4.7 19.3 1.0
CE1 A:HIS69 4.7 18.9 1.0
ND1 A:HIS230 4.7 25.3 1.0
CE1 A:HIS230 4.7 23.7 1.0
O A:HOH337 4.8 35.6 1.0
CZ A:PHE65 4.8 30.6 1.0
CD2 A:HIS60 4.9 28.0 1.0
NE2 A:HIS60 5.0 27.0 1.0

Copper binding site 2 out of 8 in 3npy

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Copper binding site 2 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:31.1
occ:0.20
CU A:CU501 0.0 31.1 0.2
CU A:CU501 0.3 34.4 0.8
NE2 A:HIS231 1.8 16.0 1.0
NE2 A:HIS208 1.9 30.4 1.0
O A:HOH350 2.0 34.4 1.0
NE2 A:HIS204 2.3 25.4 1.0
CE1 A:HIS231 2.7 17.6 1.0
CE1 A:HIS208 2.8 31.1 1.0
CD2 A:HIS231 2.9 13.6 1.0
CD2 A:HIS208 3.0 29.9 1.0
CE1 A:HIS204 3.2 25.1 1.0
CD2 A:HIS204 3.3 20.5 1.0
CU A:CU502 3.6 34.4 0.6
CE2 A:PHE227 3.7 18.2 1.0
CU A:CU502 3.7 31.4 0.4
ND1 A:HIS231 3.8 15.7 1.0
O A:HOH348 3.8 34.4 1.0
O A:HOH347 3.9 34.4 1.0
CG A:HIS231 3.9 16.2 1.0
ND1 A:HIS208 4.0 30.9 1.0
CZ A:PHE227 4.0 23.2 1.0
CG A:HIS208 4.1 29.4 1.0
NE2 A:HIS69 4.1 18.7 1.0
ND1 A:HIS204 4.3 25.0 1.0
CG A:HIS204 4.4 24.7 1.0
CD2 A:PHE227 4.4 19.3 1.0
ND1 A:HIS230 4.5 25.3 1.0
CD2 A:HIS69 4.6 20.4 1.0
CE1 A:HIS230 4.6 23.7 1.0
CE1 A:PHE65 4.7 30.8 1.0
CE1 A:HIS69 4.8 18.9 1.0
CZ A:PHE65 5.0 30.6 1.0

Copper binding site 3 out of 8 in 3npy

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Copper binding site 3 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:34.4
occ:0.60
CU A:CU502 0.0 34.4 0.6
CU A:CU502 0.8 31.4 0.4
O A:HOH350 1.6 34.4 1.0
NE2 A:HIS42 2.0 22.8 1.0
NE2 A:HIS60 2.1 27.0 1.0
O A:HOH348 2.7 34.4 1.0
CD2 A:HIS60 3.0 28.0 1.0
CD2 A:HIS42 3.0 20.8 1.0
CE1 A:HIS42 3.0 26.4 1.0
CE1 A:HIS60 3.2 28.3 1.0
O A:HOH347 3.4 34.4 1.0
NE2 A:HIS69 3.4 18.7 1.0
CU A:CU501 3.4 34.4 0.8
CU A:CU501 3.6 31.1 0.2
CE2 A:PHE227 3.9 18.2 1.0
CE1 A:HIS69 4.0 18.9 1.0
CZ A:PHE227 4.1 23.2 1.0
ND1 A:HIS42 4.1 25.6 1.0
CG A:HIS42 4.2 25.5 1.0
CG A:HIS60 4.2 30.4 1.0
ND1 A:HIS60 4.3 28.1 1.0
NE2 A:HIS231 4.6 16.0 1.0
CD2 A:HIS69 4.6 20.4 1.0
NE2 A:HIS208 4.6 30.4 1.0
O A:HOH349 4.8 34.4 1.0
CG2 A:VAL218 4.8 35.6 1.0
CE1 A:HIS208 4.8 31.1 1.0

Copper binding site 4 out of 8 in 3npy

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Copper binding site 4 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:31.4
occ:0.40
CU A:CU502 0.0 31.4 0.4
CU A:CU502 0.8 34.4 0.6
O A:HOH350 1.8 34.4 1.0
O A:HOH348 2.0 34.4 1.0
NE2 A:HIS42 2.2 22.8 1.0
NE2 A:HIS60 2.4 27.0 1.0
O A:HOH347 2.8 34.4 1.0
CE1 A:HIS42 2.9 26.4 1.0
CD2 A:HIS60 3.1 28.0 1.0
CD2 A:HIS42 3.4 20.8 1.0
CE1 A:HIS60 3.5 28.3 1.0
CU A:CU501 3.6 34.4 0.8
CU A:CU501 3.7 31.1 0.2
O A:HOH349 4.0 34.4 1.0
CE2 A:PHE227 4.1 18.2 1.0
CG2 A:VAL218 4.1 35.6 1.0
ND1 A:HIS42 4.1 25.6 1.0
NE2 A:HIS69 4.2 18.7 1.0
CG A:HIS60 4.3 30.4 1.0
CG A:HIS42 4.4 25.5 1.0
NE2 A:HIS208 4.4 30.4 1.0
ND1 A:HIS60 4.4 28.1 1.0
CA A:VAL218 4.5 31.4 1.0
CZ A:PHE227 4.5 23.2 1.0
CG1 A:VAL218 4.6 35.6 1.0
CE1 A:HIS208 4.6 31.1 1.0
CB A:VAL218 4.6 37.9 1.0
CE1 A:HIS69 4.7 18.9 1.0
O A:VAL218 4.7 30.0 1.0
CB A:ALA221 4.8 21.8 1.0
NE2 A:HIS231 5.0 16.0 1.0

Copper binding site 5 out of 8 in 3npy

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Copper binding site 5 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Tyrosinase From Bacillus Megaterium Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:34.4
occ:0.80
CU B:CU501 0.0 34.4 0.8
CU B:CU501 1.0 30.0 0.2
NE2 B:HIS208 1.8 24.5 1.0
O B:HOH342 1.8 34.4 1.0
NE2 B:HIS231 2.1 23.0 1.0
NE2 B:HIS204 2.2 34.1 1.0
CE1 B:HIS208 2.5 25.2 1.0
CD2 B:HIS208 3.0 23.9 1.0
CE1 B:HIS231 3.1 24.6 1.0
CD2 B:HIS231 3.1 20.5 1.0
CE1 B:HIS204 3.1 33.7 1.0
CD2 B:HIS204 3.2 29.1 1.0
O B:HOH343 3.3 34.4 1.0
CU B:CU502 3.4 31.1 0.4
CU B:CU502 3.6 34.4 0.6
CE2 B:PHE227 3.6 21.4 1.0
ND1 B:HIS208 3.7 24.9 1.0
CG B:HIS208 4.0 23.5 1.0
CZ B:PHE227 4.1 26.4 1.0
ND1 B:HIS231 4.2 22.7 1.0
ND1 B:HIS204 4.2 33.7 1.0
CG B:HIS231 4.2 23.2 1.0
CG B:HIS204 4.3 33.4 1.0
O B:HOH341 4.3 34.4 1.0
NE2 B:HIS69 4.3 22.5 1.0
CD2 B:PHE227 4.3 22.4 1.0
ND1 B:HIS230 4.5 27.5 1.0
CE1 B:HIS230 4.6 25.9 1.0
CD2 B:HIS69 4.8 24.2 1.0
CE1 B:PHE65 5.0 28.1 1.0

Copper binding site 6 out of 8 in 3npy

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Copper binding site 6 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Tyrosinase From Bacillus Megaterium Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:30.0
occ:0.20
CU B:CU501 0.0 30.0 0.2
CU B:CU501 1.0 34.4 0.8
NE2 B:HIS204 1.7 34.1 1.0
NE2 B:HIS231 1.7 23.0 1.0
O B:HOH342 1.9 34.4 1.0
CE1 B:HIS231 2.3 24.6 1.0
NE2 B:HIS208 2.6 24.5 1.0
CE1 B:HIS204 2.7 33.7 1.0
CD2 B:HIS204 2.7 29.1 1.0
CD2 B:HIS231 3.0 20.5 1.0
CU B:CU502 3.4 31.1 0.4
CE1 B:HIS208 3.4 25.2 1.0
O B:HOH343 3.4 34.4 1.0
ND1 B:HIS231 3.6 22.7 1.0
CD2 B:HIS208 3.6 23.9 1.0
CU B:CU502 3.8 34.4 0.6
ND1 B:HIS204 3.8 33.7 1.0
NE2 B:HIS69 3.8 22.5 1.0
CG B:HIS204 3.8 33.4 1.0
CG B:HIS231 3.9 23.2 1.0
CE1 B:PHE65 4.1 28.1 1.0
CE2 B:PHE227 4.2 21.4 1.0
CD2 B:HIS69 4.3 24.2 1.0
CE1 B:HIS69 4.3 22.7 1.0
CZ B:PHE227 4.4 26.4 1.0
CZ B:PHE65 4.4 27.8 1.0
ND1 B:HIS208 4.6 24.9 1.0
CG B:HIS208 4.7 23.5 1.0
CE1 B:HIS230 4.8 25.9 1.0
CD2 B:HIS60 4.8 31.5 1.0
ND1 B:HIS230 4.9 27.5 1.0
O B:HOH341 4.9 34.4 1.0
NE2 B:HIS60 5.0 30.5 1.0

Copper binding site 7 out of 8 in 3npy

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Copper binding site 7 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Tyrosinase From Bacillus Megaterium Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:34.4
occ:0.60
CU B:CU502 0.0 34.4 0.6
CU B:CU502 0.8 31.1 0.4
O B:HOH342 1.9 34.4 1.0
NE2 B:HIS42 2.1 22.2 1.0
NE2 B:HIS60 2.4 30.5 1.0
CE1 B:HIS42 2.9 25.8 1.0
O B:HOH343 2.9 34.4 1.0
CD2 B:HIS60 3.0 31.5 1.0
CD2 B:HIS42 3.3 20.3 1.0
O B:HOH341 3.4 34.4 1.0
CE1 B:HIS60 3.5 31.8 1.0
CU B:CU501 3.6 34.4 0.8
CU B:CU501 3.8 30.0 0.2
NE2 B:HIS69 3.9 22.5 1.0
CE2 B:PHE227 4.0 21.4 1.0
ND1 B:HIS42 4.1 25.0 1.0
CG B:HIS60 4.2 33.9 1.0
CG B:HIS42 4.3 24.9 1.0
ND1 B:HIS60 4.4 31.7 1.0
CZ B:PHE227 4.4 26.4 1.0
CE1 B:HIS69 4.5 22.7 1.0
CG2 B:VAL218 4.6 39.5 1.0
NE2 B:HIS208 4.6 24.5 1.0
CG1 B:VAL218 4.6 39.5 1.0
CE1 B:HIS208 4.6 25.2 1.0
CA B:VAL218 4.7 38.5 1.0
O B:VAL218 4.8 37.1 1.0
NE2 B:HIS231 4.9 23.0 1.0
CB B:VAL218 4.9 41.8 1.0
CB B:ALA221 4.9 21.3 1.0
NE2 B:HIS204 4.9 34.1 1.0

Copper binding site 8 out of 8 in 3npy

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Copper binding site 8 out of 8 in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4


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 Tyrosinase From Bacillus Megaterium Soaked in CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:31.1
occ:0.40
CU B:CU502 0.0 31.1 0.4
CU B:CU502 0.8 34.4 0.6
O B:HOH342 1.6 34.4 1.0
NE2 B:HIS60 2.0 30.5 1.0
NE2 B:HIS42 2.3 22.2 1.0
CD2 B:HIS60 2.6 31.5 1.0
NE2 B:HIS69 3.1 22.5 1.0
O B:HOH343 3.2 34.4 1.0
CD2 B:HIS42 3.2 20.3 1.0
CE1 B:HIS60 3.3 31.8 1.0
CE1 B:HIS42 3.4 25.8 1.0
CU B:CU501 3.4 30.0 0.2
CU B:CU501 3.4 34.4 0.8
CE1 B:HIS69 3.6 22.7 1.0
CG B:HIS60 3.9 33.9 1.0
CE2 B:PHE227 4.0 21.4 1.0
O B:HOH341 4.1 34.4 1.0
ND1 B:HIS60 4.2 31.7 1.0
CZ B:PHE227 4.2 26.4 1.0
CD2 B:HIS69 4.3 24.2 1.0
CG B:HIS42 4.4 24.9 1.0
NE2 B:HIS231 4.4 23.0 1.0
ND1 B:HIS42 4.4 25.0 1.0
NE2 B:HIS204 4.6 34.1 1.0
NE2 B:HIS208 4.7 24.5 1.0
CE1 B:HIS204 4.8 33.7 1.0
CE1 B:HIS231 4.9 24.6 1.0
CE1 B:HIS208 4.9 25.2 1.0
ND1 B:HIS69 4.9 24.9 1.0

Reference:

M.Sendovski, M.Kanteev, V.Shuster Ben-Yosef, N.Adir, A.Fishman. First Structures of An Active Bacterial Tyrosinase Reveal Copper Plasticity. J.Mol.Biol. V. 405 227 2011.
ISSN: ISSN 0022-2836
PubMed: 21040728
DOI: 10.1016/J.JMB.2010.10.048
Page generated: Fri Sep 4 08:11:10 2020
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