Zinc in PDB 4ub9: Structural and Catalytic Characterization of Molinate Hydrolase

The structure of Structural and Catalytic Characterization of Molinate Hydrolase, PDB code: 4ub9 was solved by J.P.Leite, M.Duarte, A.Paiva, F.Ferreira-Da-Silva, P.M.Matias, O.Nunes, L.Gales, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	123.72 / 2.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	367.696, 99.079, 131.337, 90.00, 109.61, 90.00
R / Rfree (%)	20.1 / 22.9

The binding sites of Zinc atom in the Structural and Catalytic Characterization of Molinate Hydrolase (pdb code 4ub9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural and Catalytic Characterization of Molinate Hydrolase, PDB code: 4ub9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:48.5 occ:0.40 O A:HOH662 1.9 42.5 1.0 O A:HOH661 2.2 32.9 1.0 NE2 A:HIS302 2.4 45.0 1.0 ND1 A:HIS282 2.5 36.9 1.0 CE1 A:HIS282 2.7 33.1 1.0 O A:HOH677 2.9 36.5 1.0 CE1 A:HIS302 3.3 39.9 1.0 CD2 A:HIS302 3.4 46.0 1.0 CG A:HIS282 3.8 30.0 1.0 NE2 A:HIS282 4.0 33.9 1.0 CD2 A:HIS246 4.1 42.1 1.0 NZ A:LYS240 4.2 39.2 1.0 NE2 A:HIS246 4.3 41.1 1.0 ND1 A:HIS302 4.5 38.8 1.0 CG A:HIS302 4.5 40.1 1.0 CD2 A:HIS282 4.5 30.5 1.0 CB A:HIS282 4.6 31.0 1.0 OD2 A:ASP373 4.7 42.5 1.0 O A:HOH636 5.0 34.5 1.0

Zinc binding site 2 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:55.4 occ:0.40 O B:HOH656 2.1 37.2 1.0 O B:HOH650 2.1 49.1 1.0 NE2 B:HIS302 2.3 39.4 1.0 ND1 B:HIS282 2.5 33.0 1.0 O B:HOH669 2.5 58.0 1.0 CE1 B:HIS282 2.9 30.1 1.0 CE1 B:HIS302 3.3 39.7 1.0 CD2 B:HIS302 3.3 35.5 1.0 CG B:HIS282 3.7 27.8 1.0 NZ B:LYS240 3.9 43.6 1.0 NE2 B:HIS282 4.2 33.7 1.0 CD2 B:HIS246 4.2 35.5 1.0 CB B:HIS282 4.4 32.9 1.0 ND1 B:HIS302 4.4 33.0 1.0 CG B:HIS302 4.5 37.1 1.0 NE2 B:HIS246 4.5 37.5 1.0 CD2 B:HIS282 4.6 31.7 1.0 OD2 B:ASP373 4.7 41.7 1.0 O B:HOH640 4.8 37.8 1.0 CG2 B:ILE301 4.9 33.5 1.0

Zinc binding site 3 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:65.7 occ:0.40 O C:HOH645 1.8 48.6 1.0 O C:HOH644 1.8 59.7 1.0 ND1 C:HIS282 2.5 37.9 1.0 NE2 C:HIS302 2.5 44.2 1.0 O C:HOH643 2.7 41.3 1.0 CE1 C:HIS282 3.2 37.8 1.0 CE1 C:HIS302 3.4 45.2 1.0 CD2 C:HIS302 3.5 42.7 1.0 NZ C:LYS240 3.5 50.9 1.0 CG C:HIS282 3.6 39.8 1.0 CB C:HIS282 4.1 42.3 1.0 NE2 C:HIS282 4.4 43.8 1.0 CD2 C:HIS246 4.4 38.8 1.0 ND1 C:HIS302 4.6 40.0 1.0 CG C:HIS302 4.6 41.8 1.0 CD2 C:HIS282 4.6 39.9 1.0 CE C:LYS240 4.6 42.9 1.0 CG2 C:ILE301 4.7 44.4 1.0 NE2 C:HIS246 4.7 37.8 1.0 CD1 C:LEU174 4.8 52.3 1.0 OD2 C:ASP373 4.8 43.9 1.0 CA C:HIS282 4.9 39.3 1.0 OD1 C:ASP373 5.0 48.8 1.0

Zinc binding site 4 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:56.1 occ:0.40 O D:HOH649 1.9 45.7 1.0 O D:HOH650 2.0 45.3 1.0 NE2 D:HIS302 2.2 51.9 1.0 ND1 D:HIS282 2.5 37.8 1.0 O D:HOH655 2.6 46.7 1.0 CE1 D:HIS282 3.0 34.8 1.0 CE1 D:HIS302 3.2 50.2 1.0 CD2 D:HIS302 3.3 49.3 1.0 CG D:HIS282 3.7 36.6 1.0 NZ D:LYS240 3.8 45.9 1.0 CB D:HIS282 4.3 35.3 1.0 NE2 D:HIS282 4.3 38.7 1.0 ND1 D:HIS302 4.3 45.2 1.0 CG D:HIS302 4.4 45.0 1.0 CD2 D:HIS246 4.4 45.1 1.0 CD2 D:HIS282 4.6 38.2 1.0 NE2 D:HIS246 4.7 44.1 1.0 CG2 D:ILE301 4.7 40.2 1.0 OD2 D:ASP373 4.8 47.8 1.0 CA D:HIS282 5.0 32.7 1.0 CE D:LYS240 5.0 46.2 1.0

Zinc binding site 5 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:60.1 occ:0.40 O E:HOH649 1.8 53.4 1.0 O E:HOH650 2.4 40.3 1.0 O E:HOH648 2.6 47.9 1.0 NE2 E:HIS302 2.7 42.4 1.0 ND1 E:HIS282 2.9 43.0 1.0 O E:HOH667 3.1 30.0 1.0 CE1 E:HIS282 3.1 39.5 1.0 CD2 E:HIS302 3.5 39.5 1.0 CE1 E:HIS302 3.7 44.4 1.0 CD2 E:HIS246 3.9 45.5 1.0 NE2 E:HIS246 4.0 42.7 1.0 CG E:HIS282 4.2 37.1 1.0 NZ E:LYS240 4.3 42.2 1.0 OD2 E:ASP373 4.4 44.7 1.0 NE2 E:HIS282 4.4 44.3 1.0 O E:HOH629 4.5 46.3 1.0 CG E:HIS302 4.7 41.2 1.0 ND1 E:HIS302 4.8 43.4 1.0 OD1 E:ASP373 4.8 44.5 1.0 CD2 E:HIS282 4.9 36.6 1.0 CB E:HIS282 4.9 33.7 1.0

Zinc binding site 6 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:63.3 occ:0.40 O F:HOH640 2.3 48.0 1.0 O F:HOH638 2.4 46.8 1.0 NE2 F:HIS302 2.6 53.7 1.0 O F:HOH639 2.7 50.0 1.0 ND1 F:HIS282 2.7 50.4 1.0 CE1 F:HIS282 2.8 47.3 1.0 CE1 F:HIS302 3.5 59.6 1.0 CD2 F:HIS302 3.6 54.0 1.0 CD2 F:HIS246 3.7 50.6 1.0 NE2 F:HIS246 3.9 48.2 1.0 CG F:HIS282 4.0 46.6 1.0 NE2 F:HIS282 4.1 49.2 1.0 O F:HOH634 4.2 41.7 1.0 NZ F:LYS240 4.5 49.5 1.0 OD2 F:ASP373 4.6 58.3 1.0 ND1 F:HIS302 4.7 51.8 1.0 CD2 F:HIS282 4.7 46.4 1.0 CG F:HIS302 4.7 53.4 1.0 CB F:HIS282 4.8 44.3 1.0

Zinc binding site 7 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn501 b:55.6 occ:0.40 O G:HOH636 2.5 41.2 1.0 NE2 G:HIS302 2.6 45.6 1.0 O G:HOH641 2.7 59.7 1.0 O G:HOH637 2.8 58.2 1.0 ND1 G:HIS282 2.8 38.7 1.0 CE1 G:HIS282 2.8 39.9 1.0 CE1 G:HIS302 3.5 50.5 1.0 CD2 G:HIS302 3.6 46.5 1.0 CD2 G:HIS246 3.6 54.2 1.0 NE2 G:HIS246 3.8 55.5 1.0 O G:HOH615 3.9 34.2 1.0 NE2 G:HIS282 4.1 47.3 1.0 CG G:HIS282 4.2 38.4 1.0 O G:HOH653 4.5 30.0 1.0 ND1 G:HIS302 4.7 45.5 1.0 OD2 G:ASP373 4.7 54.3 1.0 CG G:HIS302 4.7 43.6 1.0 NZ G:LYS240 4.7 47.2 1.0 CD2 G:HIS282 4.8 36.7 1.0 CG G:HIS246 4.9 50.1 1.0

Zinc binding site 8 out of 8 in the Structural and Catalytic Characterization of Molinate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural and Catalytic Characterization of Molinate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn501 b:67.2 occ:0.40 O H:HOH633 1.8 52.9 1.0 O H:HOH634 2.2 44.7 1.0 O H:HOH639 2.7 48.1 1.0 ND1 H:HIS282 2.9 65.7 1.0 NE2 H:HIS302 3.0 59.4 1.0 O H:HOH635 3.1 51.3 1.0 CE1 H:HIS282 3.3 57.0 1.0 CD2 H:HIS246 3.8 63.6 1.0 O H:HOH631 3.8 40.1 1.0 CD2 H:HIS302 3.9 53.0 1.0 NE2 H:HIS246 3.9 60.4 1.0 CE1 H:HIS302 4.0 56.2 1.0 NZ H:LYS240 4.1 53.8 1.0 CG H:HIS282 4.2 60.4 1.0 OD2 H:ASP373 4.5 54.6 1.0 NE2 H:HIS282 4.6 59.9 1.0 OD1 H:ASP373 4.8 47.7 1.0 CB H:HIS282 4.8 55.6 1.0 CD1 H:LEU174 4.9 67.9 1.0

J.P.Leite, M.Duarte, A.M.Paiva, F.Ferreira-Da-Silva, P.M.Matias, O.C.Nunes, L.Gales. Structure-Guided Engineering of Molinate Hydrolase For the Degradation of Thiocarbamate Pesticides. Plos One V. 10 23430 2015.
ISSN: ESSN 1932-6203
PubMed: 25905461
DOI: 10.1371/JOURNAL.PONE.0123430