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Zinc in PDB 3nm8: Crystal Structure of Tyrosinase From Bacillus Megaterium

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium

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

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium, PDB code: 3nm8 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.210, 84.490, 146.310, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.3

Other elements in 3nm8:

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

Copper (Cu) 4 atoms
Chlorine (Cl) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium (pdb code 3nm8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium, PDB code: 3nm8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3nm8

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Zinc binding site 1 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:31.2
occ:1.00
 OD2 A:ASP287 1.5 39.3 1.0
ND1 A:HIS13 2.0 18.4 1.0
CL A:CL506 2.2 30.0 0.9
CL A:CL507 2.3 30.0 0.9
CG A:ASP287 2.6 39.3 1.0
CE1 A:HIS13 2.9 17.4 1.0
CG A:HIS13 3.1 17.8 1.0
CB A:ASP287 3.3 39.3 1.0
CB A:HIS13 3.5 18.2 1.0
OD1 A:ASP287 3.7 39.3 1.0
O A:ASP287 3.9 38.2 1.0
NE2 A:HIS13 4.1 18.5 1.0
CD2 A:HIS13 4.2 19.7 1.0
CD1 A:ILE288 4.3 20.0 1.0
N A:ASN10 4.4 22.3 1.0
CB A:LYS9 4.5 29.6 1.0
CB A:ASN10 4.6 18.2 1.0
CA A:ASP287 4.6 38.2 1.0
C A:ASP287 4.6 38.2 1.0
CG A:LYS9 4.6 30.2 1.0
CG1 A:ILE288 4.8 20.0 1.0
CA A:LYS9 4.9 21.8 1.0

Zinc binding site 2 out of 7 in 3nm8

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Zinc binding site 2 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:31.2
occ:0.70
 NE2 A:HIS279 1.9 37.1 1.0
O A:HOH332 2.1 30.0 1.0
O A:HOH333 2.2 30.0 1.0
O A:HOH329 2.3 31.2 1.0
CE1 A:HIS279 2.8 38.4 1.0
CD2 A:HIS279 3.0 37.0 1.0
O A:HOH331 3.2 30.0 1.0
O A:HOH363 3.3 22.1 1.0
ND1 A:HIS279 3.9 36.1 1.0
CG1 A:ILE243 4.0 79.0 1.0
CG A:HIS279 4.1 36.9 1.0
CB A:ALA239 4.1 19.0 1.0
O A:ALA239 4.2 24.0 1.0
CD1 A:ILE243 4.4 47.6 1.0
O A:HOH443 4.5 52.5 1.0
O A:HOH316 4.5 41.2 1.0
C A:ALA239 4.7 22.8 1.0
CA A:ALA239 4.8 22.9 1.0

Zinc binding site 3 out of 7 in 3nm8

Go back to Zinc Binding Sites List in 3nm8
Zinc binding site 3 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:30.0
occ:1.00
 ND1 A:HIS245 2.5 38.4 1.0
CG A:HIS245 3.4 38.3 1.0
CE1 A:HIS245 3.5 38.4 1.0
CB A:HIS245 3.5 39.1 1.0
O A:HOH460 3.6 28.4 1.0
CG2 A:THR175 3.7 59.4 1.0
CG A:GLN248 3.8 53.5 1.0
CA A:HIS245 4.1 31.9 1.0
O A:THR175 4.3 42.7 1.0
CA A:THR175 4.3 41.7 1.0
CB A:THR175 4.4 57.5 1.0
OG1 A:THR175 4.4 58.3 1.0
CD2 A:HIS245 4.5 38.1 1.0
NE2 A:HIS245 4.6 40.3 1.0
NE2 A:GLN248 4.6 56.7 1.0
CD A:GLN248 4.6 55.9 1.0
C A:THR175 4.8 40.3 1.0

Zinc binding site 4 out of 7 in 3nm8

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Zinc binding site 4 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:30.0
occ:0.50
 NE2 A:HIS49 2.2 25.8 1.0
CD2 A:HIS49 3.2 24.7 1.0
CE1 A:HIS49 3.2 24.9 1.0
OD1 B:ASN144 3.8 58.0 1.0
O B:GLN142 4.3 55.3 1.0
ND1 A:HIS49 4.3 22.7 1.0
CG A:HIS49 4.3 22.4 1.0
CG B:ASN144 4.7 56.0 1.0
O A:LYS47 4.7 26.4 1.0
CA A:LYS47 4.8 29.0 1.0
O B:HOH420 4.9 44.5 1.0
ND2 B:ASN144 4.9 57.9 1.0

Zinc binding site 5 out of 7 in 3nm8

Go back to Zinc Binding Sites List in 3nm8
Zinc binding site 5 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:31.2
occ:1.00
 ND1 B:HIS13 2.0 19.2 1.0
CL B:CL508 2.1 30.0 0.9
OD2 B:ASP287 2.2 25.7 1.0
CL B:CL507 2.3 30.0 0.8
CE1 B:HIS13 2.9 21.1 1.0
CG B:ASP287 3.0 25.7 1.0
CG B:HIS13 3.1 22.5 1.0
CB B:ASP287 3.2 25.7 1.0
CB B:HIS13 3.6 21.3 1.0
OD1 B:ASP287 4.0 25.7 1.0
NE2 B:HIS13 4.1 19.5 1.0
CD2 B:HIS13 4.2 19.0 1.0
N B:ASN10 4.4 21.2 1.0
CB B:LYS9 4.6 20.4 1.0
CA B:ASP287 4.6 31.1 1.0
CB B:ASN10 4.7 20.3 1.0
CG B:LYS9 4.8 21.8 1.0
CA B:LYS9 4.9 20.5 1.0
CG1 B:ILE288 4.9 20.0 1.0

Zinc binding site 6 out of 7 in 3nm8

Go back to Zinc Binding Sites List in 3nm8
Zinc binding site 6 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:31.2
occ:0.80
 NE2 B:HIS279 2.0 26.6 1.0
CL B:CL510 2.1 30.0 0.5
CL B:CL509 2.2 30.0 0.5
O B:HOH330 2.5 31.2 1.0
CE1 B:HIS279 2.8 27.2 1.0
CD2 B:HIS279 3.1 26.3 1.0
O B:HOH343 3.3 28.8 1.0
ND1 B:HIS279 4.0 26.2 1.0
CG B:HIS279 4.1 25.7 1.0
CG1 B:ILE243 4.2 53.9 1.0
CD1 B:ILE243 4.2 43.5 1.0
CB B:ALA239 4.3 22.4 1.0
O B:ALA239 4.4 23.0 1.0
NE B:ARG280 4.5 70.4 1.0
O B:HOH368 4.8 35.4 1.0
C B:ALA239 4.8 23.9 1.0
CA B:ALA239 5.0 22.6 1.0

Zinc binding site 7 out of 7 in 3nm8

Go back to Zinc Binding Sites List in 3nm8
Zinc binding site 7 out of 7 in the Crystal Structure of Tyrosinase From Bacillus Megaterium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:30.0
occ:1.00
 O B:HOH359 2.3 48.6 1.0
OE2 B:GLU71 2.4 35.3 1.0
O B:HOH309 2.5 29.8 1.0
CD B:GLU71 2.7 37.4 1.0
OE1 B:GLU71 2.8 42.1 1.0
OG1 B:THR271 3.5 26.7 1.0
NH2 B:ARG75 3.7 35.5 1.0
CG B:GLU71 4.0 37.6 1.0
NH1 B:ARG78 4.1 45.0 1.0
CG2 B:THR271 4.2 22.2 1.0
CB B:THR271 4.5 24.4 1.0
CG B:ARG75 4.6 26.8 1.0
CZ B:ARG75 4.6 35.9 1.0
CD B:ARG75 4.7 31.2 1.0
CD2 B:LEU74 4.8 25.3 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: Sat Oct 26 10:30:34 2024

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