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Zinc 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

Other elements in 3npy:

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4 also contains other interesting chemical elements:

Copper (Cu) 8 atoms
Chlorine (Cl) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium Soaked in CUSO4, PDB code: 3npy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn505

b:34.4
occ:1.00
 CL A:CL511 1.8 31.4 0.7
CL A:CL510 2.2 34.4 1.0
OD1 A:ASP287 2.4 34.4 1.0
ND1 A:HIS13 2.7 29.3 1.0
CG A:ASP287 3.3 34.4 1.0
CB A:ASP287 3.4 34.4 1.0
CG A:HIS13 3.5 28.7 1.0
CB A:HIS13 3.6 29.0 1.0
CE1 A:HIS13 3.7 28.3 1.0
N A:ASN10 4.4 30.9 1.0
OD2 A:ASP287 4.5 34.4 1.0
CG A:LYS9 4.5 33.5 1.0
CB A:ASN10 4.6 29.4 1.0
CB A:LYS9 4.6 32.9 1.0
CD2 A:HIS13 4.7 30.6 1.0
NE2 A:HIS13 4.7 29.4 1.0
CA A:LYS9 4.8 42.5 1.0
CA A:ASP287 4.9 38.8 1.0

Zinc binding site 2 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn506

b:34.4
occ:0.50
 NE2 A:HIS49 2.1 41.2 1.0
CL B:CL512 2.4 31.1 0.5
CL A:CL513 2.6 31.1 0.5
CE1 A:HIS49 3.0 40.3 1.0
O B:GLN142 3.1 58.2 1.0
CD2 A:HIS49 3.2 40.1 1.0
OD1 B:ASN144 3.3 50.9 1.0
CG B:ASN144 4.1 51.2 1.0
ND1 A:HIS49 4.1 38.2 1.0
O A:LYS47 4.1 27.8 1.0
C B:GLN142 4.2 57.6 1.0
CG A:HIS49 4.3 37.8 1.0
ND2 B:ASN144 4.3 51.7 1.0
CA A:LYS47 4.4 30.5 1.0
C A:LYS47 4.6 28.5 1.0
C B:GLY143 4.7 50.0 1.0
CA B:GLY143 4.8 52.9 1.0
CB A:LYS47 4.9 53.7 1.0
O A:GLY46 4.9 30.3 1.0
N B:ASN144 4.9 34.5 1.0
O B:GLY143 4.9 47.5 1.0
N B:GLY143 5.0 57.4 1.0

Zinc binding site 3 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn507

b:30.0
occ:0.50
 O A:HOH357 2.3 34.4 1.0
OE2 A:GLU95 2.7 35.3 1.0
CG A:GLU95 3.1 35.0 1.0
NH1 A:ARG165 3.3 93.2 1.0
CD A:GLU95 3.3 34.9 1.0
CZ A:ARG165 3.4 90.3 1.0
CG A:ARG165 3.7 70.7 1.0
NH2 A:ARG165 3.8 92.5 1.0
O A:HOH352 3.8 34.4 1.0
CG1 A:VAL168 3.9 33.0 1.0
NE A:ARG165 4.0 87.0 1.0
CB A:GLU95 4.1 33.4 1.0
NH2 A:ARG236 4.2 33.4 1.0
CB A:VAL168 4.3 33.8 1.0
CD A:ARG165 4.4 78.3 1.0
CG2 A:VAL168 4.5 32.3 1.0
OE1 A:GLU95 4.6 35.8 1.0
NH1 A:ARG236 4.9 30.6 1.0
OE2 A:GLU93 5.0 45.8 1.0
CB A:ARG165 5.0 63.8 1.0

Zinc binding site 4 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn508

b:34.4
occ:0.50
 OD1 A:ASP166 1.9 64.9 1.0
O A:HOH384 2.1 31.4 1.0
CG A:ASP166 2.8 64.6 1.0
OD2 A:ASP166 3.2 65.4 1.0
CB A:ASP166 4.2 62.5 1.0

Zinc binding site 5 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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
A:Zn509

b:34.4
occ:0.70
 NE2 A:HIS279 1.7 27.5 1.0
O A:HOH386 2.2 31.4 1.0
O A:HOH385 2.4 31.4 1.0
CE1 A:HIS279 2.6 28.9 1.0
CD2 A:HIS279 2.8 27.5 1.0
ND1 A:HIS279 3.7 26.5 1.0
CG A:HIS279 3.9 27.3 1.0
CB A:ALA239 4.1 21.8 1.0
O A:ALA239 4.1 39.8 1.0
CG1 A:ILE243 4.4 51.7 1.0
CD1 A:ILE243 4.6 51.7 1.0
C A:ALA239 4.6 38.6 1.0
CA A:ALA239 4.8 38.7 1.0
O A:HOH361 4.9 34.4 1.0

Zinc binding site 6 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn505

b:34.4
occ:1.00
 ND1 B:HIS13 2.0 36.3 1.0
OD2 B:ASP287 2.1 68.1 1.0
CL B:CL508 2.1 34.4 1.0
CL B:CL509 2.1 34.4 1.0
CG B:ASP287 2.7 68.1 1.0
CG B:HIS13 2.9 35.7 1.0
CE1 B:HIS13 3.0 35.3 1.0
CB B:HIS13 3.2 36.0 1.0
CB B:ASP287 3.4 68.1 1.0
OD1 B:ASP287 3.5 68.1 1.0
CD2 B:HIS13 4.1 37.6 1.0
NE2 B:HIS13 4.1 36.4 1.0
N B:ASN10 4.4 34.0 1.0
CG B:LYS9 4.5 32.1 1.0
CB B:LYS9 4.6 31.5 1.0
CB B:ASN10 4.6 29.1 1.0
CA B:ASP287 4.6 96.7 1.0
CA B:HIS13 4.7 34.3 1.0
CA B:LYS9 4.8 33.3 1.0
CD B:LYS9 4.9 35.1 1.0

Zinc binding site 7 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn506

b:34.4
occ:0.50
 NE2 B:HIS49 1.8 34.3 1.0
O B:HOH376 2.2 31.4 1.0
O B:HOH388 2.7 30.0 1.0
CD2 B:HIS49 2.7 33.2 1.0
CE1 B:HIS49 2.8 33.4 1.0
OD1 A:ASN144 3.0 47.3 1.0
O A:GLN142 3.7 50.8 1.0
ND1 B:HIS49 3.8 31.3 1.0
CG B:HIS49 3.8 30.9 1.0
CG A:ASN144 4.0 47.7 1.0
O B:LYS47 4.3 31.9 1.0
ND2 A:ASN144 4.3 48.2 1.0
C A:GLN142 4.7 50.1 1.0
C A:GLY143 4.8 33.5 1.0
CA B:LYS47 4.8 34.6 1.0
O A:GLY143 4.8 31.0 1.0
C B:LYS47 4.9 32.6 1.0
O B:GLY46 4.9 48.5 1.0
N A:ASN144 4.9 52.0 1.0

Zinc binding site 8 out of 8 in 3npy

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Zinc 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 Zinc with other atoms in the Zn 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:Zn507

b:34.4
occ:0.50
 NE2 B:HIS279 1.9 34.7 1.0
O B:HOH380 1.9 31.4 1.0
O B:HOH377 2.4 31.4 1.0
CE1 B:HIS279 2.5 36.1 1.0
O B:HOH378 2.8 31.4 1.0
CD2 B:HIS279 3.1 34.7 1.0
CD1 B:ILE243 3.5 65.3 1.0
ND1 B:HIS279 3.8 33.7 1.0
CG B:HIS279 4.0 34.5 1.0
CB B:ALA239 4.3 23.0 1.0
O B:ALA239 4.4 32.5 1.0
O B:HOH379 4.7 31.4 1.0
CG1 B:ILE243 4.7 65.3 1.0
NE B:ARG280 4.9 83.0 1.0
C B:ALA239 4.9 31.4 1.0
CZ B:ARG280 5.0 84.4 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: Wed Aug 20 12:23:10 2025

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