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Zinc in PDB 3nq1: Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid, PDB code: 3nq1 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) 42.09 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.380, 83.530, 146.160, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 29.4

Other elements in 3nq1:

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid (pdb code 3nq1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid, PDB code: 3nq1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 3nq1

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Zinc binding site 1 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:22.5
occ:1.00
ND1 A:HIS13 2.1 9.5 1.0
O A:HOH357 2.2 1.0 1.0
O A:HOH304 2.5 11.4 1.0
O A:HOH306 2.7 3.8 1.0
CE1 A:HIS13 2.9 11.1 1.0
CG A:HIS13 3.2 7.9 1.0
O A:HOH361 3.4 9.3 1.0
CB A:HIS13 3.6 8.0 1.0
N A:ASN10 4.0 10.7 1.0
NE2 A:HIS13 4.1 13.7 1.0
CD2 A:HIS13 4.2 13.2 1.0
CB A:ASN10 4.3 9.1 1.0
CB A:LYS9 4.4 12.2 1.0
CG A:LYS9 4.5 14.7 1.0
CA A:LYS9 4.5 19.0 1.0
OH A:TYR91 4.6 10.3 1.0
CA A:ASN10 4.8 12.2 1.0
C A:LYS9 4.8 13.6 1.0

Zinc binding site 2 out of 13 in 3nq1

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Zinc binding site 2 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:57.1
occ:1.00
OD1 A:ASP16 1.7 56.7 1.0
CG A:ASP16 2.5 45.0 1.0
OD2 A:ASP16 2.7 51.0 1.0
CB A:ASP16 4.0 27.6 1.0

Zinc binding site 3 out of 13 in 3nq1

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Zinc binding site 3 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:42.1
occ:1.00
OE2 A:GLU71 2.1 12.1 1.0
O A:HOH364 2.6 7.5 1.0
O A:HOH381 2.7 10.8 1.0
NH2 A:ARG75 3.0 17.0 1.0
CD A:GLU71 3.1 9.7 1.0
O A:HOH325 3.3 13.8 1.0
OE1 A:GLU71 3.4 12.8 1.0
NH1 A:ARG78 4.0 33.1 1.0
O A:HOH314 4.2 29.1 1.0
CZ A:ARG75 4.2 22.9 1.0
CG2 A:THR271 4.3 9.3 1.0
CG A:ARG75 4.4 20.7 1.0
CG A:GLU71 4.4 8.6 1.0
CB A:THR271 4.5 15.9 1.0
CD A:ARG75 4.7 16.1 1.0
NE A:ARG75 4.9 27.9 1.0

Zinc binding site 4 out of 13 in 3nq1

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Zinc binding site 4 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:27.9
occ:1.00
O A:HOH321 2.0 20.3 1.0
OE2 A:GLU95 2.5 24.3 1.0
CD A:GLU95 3.3 19.0 1.0
CG A:GLU95 3.4 28.0 1.0
O A:HOH386 3.8 26.1 1.0
CD A:ARG165 3.8 40.6 1.0
NH2 A:ARG236 4.0 16.0 1.0
NH1 A:ARG165 4.2 49.9 1.0
OE2 A:GLU93 4.3 21.4 1.0
CD A:GLU93 4.5 24.7 1.0
CB A:GLU95 4.5 23.0 1.0
OE1 A:GLU95 4.5 23.7 1.0
NH1 A:ARG236 4.6 15.5 1.0
CG A:GLU93 4.6 18.6 1.0
CG A:ARG165 4.7 40.1 1.0
CG1 A:VAL168 4.7 13.9 1.0
CZ A:ARG236 4.8 14.5 1.0
NE A:ARG165 4.8 30.8 1.0
CD1 A:ILE237 4.9 22.9 1.0
CZ A:ARG165 5.0 37.7 1.0

Zinc binding site 5 out of 13 in 3nq1

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Zinc binding site 5 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:49.0
occ:1.00
OD1 A:ASP112 2.1 39.9 1.0
CG A:ASP112 2.5 37.5 1.0
OD2 A:ASP112 2.6 53.4 1.0
CB A:ASP112 3.8 17.9 1.0
OG A:SER110 3.9 32.8 1.0
NZ A:LYS19 4.2 18.8 1.0
OD2 A:ASP16 4.3 51.0 1.0
CB A:SER110 4.6 21.5 1.0
CG A:ASP16 4.7 45.0 1.0
CD A:LYS19 4.8 17.6 1.0
CA A:ASP112 4.9 22.6 1.0
CE A:LYS19 4.9 16.5 1.0
C A:ASP112 5.0 22.1 1.0

Zinc binding site 6 out of 13 in 3nq1

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Zinc binding site 6 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:64.4
occ:1.00
OD1 A:ASP166 1.8 60.3 1.0
CG A:ASP166 2.6 37.2 1.0
OD2 A:ASP166 2.8 44.7 1.0
CB A:ASP166 4.1 24.0 1.0

Zinc binding site 7 out of 13 in 3nq1

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Zinc binding site 7 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:41.4
occ:1.00
ND1 A:HIS245 2.2 22.5 1.0
O A:HOH369 3.1 19.5 1.0
CE1 A:HIS245 3.1 20.3 1.0
CG A:HIS245 3.3 20.1 1.0
CB A:HIS245 3.7 20.9 1.0
CA A:HIS245 4.1 20.0 1.0
CG2 A:THR175 4.1 29.9 1.0
NE2 A:HIS245 4.2 19.3 1.0
CG A:GLN248 4.3 26.6 1.0
CD2 A:HIS245 4.4 17.1 1.0
O A:ILE244 4.6 20.5 1.0
NE2 A:GLN248 4.8 42.4 1.0
OG1 A:THR175 4.8 31.6 1.0
CB A:THR175 4.9 23.3 1.0
CA A:THR175 5.0 21.8 1.0

Zinc binding site 8 out of 13 in 3nq1

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Zinc binding site 8 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


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 in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:43.3
occ:1.00
NE2 A:HIS279 2.1 20.3 1.0
O A:HOH359 2.8 12.7 1.0
CE1 A:HIS279 3.1 24.4 1.0
CD2 A:HIS279 3.1 24.1 1.0
NH2 A:ARG280 3.8 48.2 1.0
ND1 A:HIS279 4.2 22.5 1.0
CB A:ALA239 4.2 12.3 1.0
CG A:HIS279 4.3 19.8 1.0
CG1 A:ILE243 4.3 30.6 1.0
O A:ALA239 4.5 11.0 1.0
CD1 A:ILE243 4.5 31.1 1.0
CZ A:ARG280 4.8 52.9 1.0
C A:ALA239 4.9 17.5 1.0

Zinc binding site 9 out of 13 in 3nq1

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Zinc binding site 9 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:18.7
occ:1.00
O B:HOH371 2.3 18.4 1.0
ND1 B:HIS13 2.4 18.1 1.0
O B:HOH363 2.5 8.8 1.0
CE1 B:HIS13 3.3 17.8 1.0
CG B:HIS13 3.4 15.7 1.0
O B:HOH366 3.4 10.9 1.0
O B:HOH313 3.5 7.3 1.0
CB B:HIS13 3.7 12.3 1.0
NE2 B:HIS13 4.4 16.4 1.0
CD2 B:HIS13 4.5 19.1 1.0
CG B:LYS9 4.5 18.1 1.0
CB B:LYS9 4.6 16.9 1.0
N B:ASN10 4.6 14.3 1.0
O B:HOH308 4.9 5.0 1.0
CA B:LYS9 4.9 12.9 1.0
CB B:ASN10 5.0 15.4 1.0
CD B:LYS9 5.0 10.9 1.0

Zinc binding site 10 out of 13 in 3nq1

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Zinc binding site 10 out of 13 in the Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Tyrosinase From Bacillus Megaterium in Complex with Inhibitor Kojic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:60.8
occ:1.00
NE2 B:HIS49 2.7 17.1 1.0
O A:HOH363 2.9 36.6 1.0
CE1 B:HIS49 3.4 17.1 1.0
CD2 B:HIS49 3.9 18.8 1.0
O A:GLN142 4.3 32.8 1.0
CA B:LYS47 4.5 20.6 1.0
O B:GLY46 4.5 13.7 1.0
OD1 A:ASN144 4.6 27.2 1.0
O B:HOH381 4.7 15.3 1.0
ND1 B:HIS49 4.7 13.9 1.0
O B:HOH344 4.8 35.3 1.0
CG B:HIS49 4.9 18.5 1.0
CG B:LYS47 4.9 27.6 1.0
O B:LYS47 5.0 18.0 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 Dec 16 04:39:13 2020

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