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Copper in PDB 6qxd: Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site.

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site., PDB code: 6qxd was solved by B.Deri Zenaty, R.Gitto, Y.Pazy, A.Fishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.02 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.129, 78.263, 84.873, 90.00, 105.82, 90.00
R / Rfree (%) 19.9 / 24.8

Other elements in 6qxd:

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site. also contains other interesting chemical elements:

Fluorine (F) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site. (pdb code 6qxd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site., PDB code: 6qxd:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6qxd

Go back to Copper Binding Sites List in 6qxd
Copper binding site 1 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site.


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 with Jkb Inhibitor in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:48.4
occ:1.00
NE2 A:HIS231 2.0 42.3 1.0
C06 A:JKB303 2.0 53.9 0.9
NE2 A:HIS208 2.1 45.0 1.0
NE2 A:HIS204 2.1 40.8 1.0
C04 A:JKB303 2.3 52.6 0.9
F21 A:JKB303 2.5 57.3 0.9
CE1 A:HIS231 2.7 38.4 1.0
C05 A:JKB303 2.9 62.8 0.9
CE1 A:HIS208 3.0 49.3 1.0
CD2 A:HIS208 3.0 51.6 1.0
CE1 A:HIS204 3.0 42.9 1.0
CD2 A:HIS231 3.1 41.8 1.0
CD2 A:HIS204 3.1 36.9 1.0
C02 A:JKB303 3.3 51.5 0.9
CE2 A:PHE227 3.7 37.2 1.0
C03 A:JKB303 3.8 57.3 0.9
ND1 A:HIS231 3.9 35.8 1.0
C01 A:JKB303 3.9 58.6 0.9
CG A:HIS231 4.1 43.6 1.0
CU A:CU302 4.1 52.5 1.0
ND1 A:HIS208 4.1 50.8 1.0
CG A:HIS208 4.1 55.2 1.0
ND1 A:HIS204 4.2 43.9 1.0
NE2 A:HIS230 4.2 49.0 1.0
CD2 A:HIS230 4.2 42.4 1.0
CG A:HIS204 4.2 42.6 1.0
CD2 A:PHE227 4.4 38.0 1.0
NE2 A:HIS69 4.5 41.4 1.0
CZ A:PHE227 4.5 42.0 1.0
CE1 A:PHE65 4.8 39.7 1.0
CD2 A:HIS69 4.9 40.2 1.0

Copper binding site 2 out of 4 in 6qxd

Go back to Copper Binding Sites List in 6qxd
Copper binding site 2 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site.


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 with Jkb Inhibitor in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:52.5
occ:1.00
F21 A:JKB303 1.9 57.3 0.9
NE2 A:HIS42 2.0 48.3 1.0
NE2 A:HIS60 2.1 48.9 1.0
NE2 A:HIS69 2.1 41.4 1.0
C04 A:JKB303 2.3 52.6 0.9
CE1 A:HIS69 2.8 42.2 1.0
CD2 A:HIS42 2.8 42.3 1.0
CE1 A:HIS60 2.8 50.2 1.0
C06 A:JKB303 3.0 53.9 0.9
C02 A:JKB303 3.0 51.5 0.9
CE1 A:HIS42 3.2 39.8 1.0
CD2 A:HIS60 3.2 44.9 1.0
CD2 A:HIS69 3.3 40.2 1.0
ND1 A:HIS60 4.0 45.4 1.0
ND1 A:HIS69 4.1 39.7 1.0
CG A:HIS42 4.1 41.8 1.0
C05 A:JKB303 4.1 62.8 0.9
CU A:CU301 4.1 48.4 1.0
CZ A:PHE227 4.1 42.0 1.0
C01 A:JKB303 4.1 58.6 0.9
CG A:HIS60 4.2 47.4 1.0
ND1 A:HIS42 4.2 46.1 1.0
NE2 A:HIS231 4.2 42.3 1.0
CG A:HIS69 4.3 40.2 1.0
CE2 A:PHE227 4.3 37.2 1.0
CE1 A:HIS231 4.3 38.4 1.0
C03 A:JKB303 4.5 57.3 0.9
CZ3 A:TRP68 4.8 33.9 1.0
CB A:ALA59 4.8 44.1 1.0
O A:ALA59 4.8 38.9 1.0

Copper binding site 3 out of 4 in 6qxd

Go back to Copper Binding Sites List in 6qxd
Copper binding site 3 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site.


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 with Jkb Inhibitor in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:55.4
occ:1.00
NE2 B:HIS42 2.1 50.3 1.0
NE2 B:HIS69 2.1 49.5 1.0
NE2 B:HIS60 2.1 49.4 1.0
O B:HOH418 2.1 48.0 1.0
CE1 B:HIS60 2.8 56.9 1.0
CE1 B:HIS69 2.9 38.8 1.0
CD2 B:HIS42 2.9 38.0 1.0
CE1 B:HIS42 3.1 44.3 1.0
CD2 B:HIS69 3.2 43.5 1.0
CD2 B:HIS60 3.2 55.7 1.0
CZ B:PHE227 3.7 43.8 1.0
CU B:CU302 3.9 51.9 1.0
ND1 B:HIS60 4.0 56.4 1.0
ND1 B:HIS69 4.0 48.5 1.0
NE2 B:HIS231 4.1 47.4 1.0
CG B:HIS42 4.1 42.1 1.0
CE1 B:HIS231 4.1 43.8 1.0
CE2 B:PHE227 4.1 37.1 1.0
ND1 B:HIS42 4.2 43.5 1.0
CG B:HIS60 4.2 53.4 1.0
CG B:HIS69 4.2 48.1 1.0
CG1 B:VAL218 4.6 82.9 1.0
CZ3 B:TRP68 4.7 44.2 1.0
CE1 B:PHE227 4.9 40.7 1.0
O B:ALA59 4.9 45.1 1.0
CB B:ALA59 5.0 42.4 1.0

Copper binding site 4 out of 4 in 6qxd

Go back to Copper Binding Sites List in 6qxd
Copper binding site 4 out of 4 in the Crystal Structure of Tyrosinase From Bacillus Megaterium with Jkb Inhibitor in the Active Site.


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 with Jkb Inhibitor in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:51.9
occ:1.00
NE2 B:HIS231 1.9 47.4 1.0
NE2 B:HIS208 2.0 45.5 1.0
NE2 B:HIS204 2.1 55.1 1.0
O B:HOH418 2.2 48.0 1.0
CE1 B:HIS231 2.6 43.8 1.0
CE1 B:HIS208 2.9 44.4 1.0
CD2 B:HIS208 3.0 46.0 1.0
CE1 B:HIS204 3.0 47.0 1.0
CD2 B:HIS231 3.1 40.3 1.0
CD2 B:HIS204 3.2 53.0 1.0
ND1 B:HIS231 3.8 43.7 1.0
CE2 B:PHE227 3.8 37.1 1.0
CU B:CU301 3.9 55.4 1.0
ND1 B:HIS208 4.0 42.7 1.0
CG B:HIS208 4.1 45.2 1.0
CG B:HIS231 4.1 42.6 1.0
ND1 B:HIS204 4.2 53.9 1.0
CD2 B:HIS230 4.2 51.9 1.0
NE2 B:HIS230 4.2 53.7 1.0
CG B:HIS204 4.3 54.8 1.0
CZ B:PHE227 4.3 43.8 1.0
NE2 B:HIS69 4.5 49.5 1.0
CD2 B:PHE227 4.6 38.6 1.0
NE2 B:HIS60 4.8 49.4 1.0
CD2 B:HIS69 4.9 43.5 1.0

Reference:

L.Ielo, B.Deri, M.P.Germano, S.Vittorio, S.Mirabile, R.Gitto, A.Rapisarda, S.Ronsisvalle, S.Floris, Y.Pazy, A.Fais, A.Fishman, L.De Luca. Exploiting the 1-(4-Fluorobenzyl)Piperazine Fragment For the Development of Novel Tyrosinase Inhibitors As Anti-Melanogenic Agents: Design, Synthesis, Structural Insights and Biological Profile. Eur.J.Med.Chem. V. 178 380 2019.
ISSN: ISSN 0223-5234
PubMed: 31202126
DOI: 10.1016/J.EJMECH.2019.06.019
Page generated: Sun Dec 13 11:25:11 2020

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