Zinc in PDB 5njw: Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid

The structure of Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid, PDB code: 5njw was solved by C.Pozzi, F.Di Pisa, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.14 / 1.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.370, 44.620, 76.120, 78.80, 89.13, 61.79
R / Rfree (%)	13.2 / 16.2

The binding sites of Zinc atom in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid (pdb code 5njw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid, PDB code: 5njw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid


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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:6.2 occ:1.00 O A:OH309 1.9 6.6 1.0 NE2 A:HIS101 2.1 6.0 1.0 NE2 A:HIS177 2.1 5.9 1.0 ND1 A:HIS103 2.1 5.7 1.0 CD2 A:HIS177 3.0 5.6 1.0 CD2 A:HIS101 3.0 6.2 1.0 CE1 A:HIS101 3.0 6.5 1.0 CE1 A:HIS103 3.0 5.8 1.0 O1 A:BO3304 3.0 8.8 1.0 CE1 A:HIS177 3.1 6.1 1.0 CG A:HIS103 3.1 5.6 1.0 O A:HOH445 3.3 15.0 1.0 ZN A:ZN303 3.4 5.9 1.0 CB A:HIS103 3.5 5.4 1.0 B A:BO3304 3.7 11.9 1.0 ND1 A:HIS101 4.1 7.4 1.0 OD1 A:ASP105 4.1 6.0 1.0 CG A:HIS101 4.1 6.2 1.0 CD2 A:HIS106 4.1 5.2 1.0 NE2 A:HIS106 4.1 5.4 1.0 NE2 A:HIS103 4.1 6.1 1.0 CG A:HIS177 4.2 6.0 1.0 ND1 A:HIS177 4.2 6.1 1.0 O2 A:BO3304 4.2 22.2 1.0 CD2 A:HIS103 4.2 6.1 1.0 O A:HOH519 4.6 13.6 1.0 OD2 A:ASP105 4.7 6.0 1.0 O3 A:BO3304 4.8 14.0 1.0 CG A:ASP105 4.8 5.8 1.0 CA A:HIS103 4.9 5.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric 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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.6 occ:1.00 ND1 A:HIS172 2.0 8.8 1.0 OE2 A:GLU158 2.0 11.3 1.0 NZ A:LYS229 2.1 11.9 1.0 CD A:GLU158 2.8 11.0 1.0 OE1 A:GLU158 2.8 10.6 1.0 CE1 A:HIS172 2.9 9.5 1.0 CG A:HIS172 3.1 8.2 1.0 CE A:LYS229 3.2 11.3 1.0 CB A:HIS172 3.5 8.2 1.0 O A:HOH611 4.0 27.5 1.0 NE2 A:HIS172 4.1 10.8 1.0 CA A:HIS172 4.1 7.8 1.0 CD2 A:HIS172 4.2 9.6 1.0 CG A:GLU158 4.2 11.5 1.0 CD A:LYS229 4.5 11.0 1.0 N A:ALA173 5.0 7.9 1.0 O A:ALA171 5.0 8.4 1.0 C A:HIS172 5.0 7.8 1.0 CG A:LYS229 5.0 10.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric 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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:5.9 occ:1.00 O A:OH309 2.0 6.6 1.0 O1 A:BO3304 2.1 8.8 1.0 NE2 A:HIS106 2.1 5.4 1.0 OD2 A:ASP105 2.1 6.0 1.0 NE2 A:HIS242 2.1 5.2 1.0 CE1 A:HIS106 3.0 5.0 1.0 B A:BO3304 3.0 11.9 1.0 CG A:ASP105 3.0 5.8 1.0 CE1 A:HIS242 3.1 5.4 1.0 CD2 A:HIS106 3.1 5.2 1.0 CD2 A:HIS242 3.1 5.8 1.0 O2 A:BO3304 3.2 22.2 1.0 OD1 A:ASP105 3.3 6.0 1.0 ZN A:ZN301 3.4 6.2 1.0 NE2 A:HIS101 4.0 6.0 1.0 CE1 A:HIS101 4.0 6.5 1.0 ND1 A:HIS106 4.1 5.0 1.0 O A:HOH445 4.1 15.0 1.0 CG A:HIS106 4.2 5.0 1.0 ND1 A:HIS242 4.2 5.8 1.0 CG A:HIS242 4.3 5.8 1.0 CB A:ASP105 4.4 5.5 1.0 O3 A:BO3304 4.4 14.0 1.0 CH2 A:TRP34 4.6 13.5 1.0 NE2 A:HIS177 4.7 5.9 1.0 CZ3 A:TRP34 4.7 14.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric 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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:5.7 occ:1.00 O B:OH305 2.0 5.5 1.0 O1 B:BO3304 2.1 8.3 1.0 NE2 B:HIS106 2.1 5.2 1.0 OD2 B:ASP105 2.1 6.0 1.0 NE2 B:HIS242 2.1 5.2 1.0 CE1 B:HIS106 3.0 4.7 1.0 CG B:ASP105 3.0 5.1 1.0 CE1 B:HIS242 3.0 5.3 1.0 B B:BO3304 3.0 12.6 1.0 CD2 B:HIS106 3.1 4.9 1.0 CD2 B:HIS242 3.1 5.4 1.0 O3 B:BO3304 3.2 20.5 1.0 OD1 B:ASP105 3.3 5.7 1.0 ZN B:ZN302 3.4 6.0 1.0 NE2 B:HIS101 4.0 5.8 1.0 CE1 B:HIS101 4.0 6.2 1.0 O B:HOH446 4.1 16.9 1.0 ND1 B:HIS106 4.1 4.6 1.0 ND1 B:HIS242 4.2 5.5 1.0 CG B:HIS106 4.2 4.4 1.0 CG B:HIS242 4.2 5.4 1.0 CB B:ASP105 4.4 5.2 1.0 O2 B:BO3304 4.5 13.5 1.0 CZ3 B:TRP34 4.6 18.2 1.0 CH2 B:TRP34 4.6 18.1 1.0 NE2 B:HIS177 4.7 5.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric 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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:6.0 occ:1.00 O B:OH305 1.8 5.5 1.0 NE2 B:HIS177 2.0 5.8 1.0 NE2 B:HIS101 2.1 5.8 1.0 ND1 B:HIS103 2.1 5.5 1.0 CD2 B:HIS177 2.9 5.4 1.0 CD2 B:HIS101 3.0 6.0 1.0 CE1 B:HIS103 3.0 5.8 1.0 CE1 B:HIS101 3.0 6.2 1.0 O1 B:BO3304 3.0 8.3 1.0 CE1 B:HIS177 3.1 5.9 1.0 CG B:HIS103 3.1 5.3 1.0 O B:HOH446 3.3 16.9 1.0 ZN B:ZN301 3.4 5.7 1.0 CB B:HIS103 3.5 5.0 1.0 B B:BO3304 3.8 12.6 1.0 ND1 B:HIS101 4.1 7.0 1.0 CG B:HIS101 4.1 5.8 1.0 NE2 B:HIS103 4.1 6.2 1.0 OD1 B:ASP105 4.1 5.7 1.0 CG B:HIS177 4.1 5.7 1.0 CD2 B:HIS106 4.1 4.9 1.0 NE2 B:HIS106 4.2 5.2 1.0 ND1 B:HIS177 4.2 6.2 1.0 CD2 B:HIS103 4.2 5.8 1.0 O3 B:BO3304 4.2 20.5 1.0 O B:HOH505 4.6 13.1 1.0 OD2 B:ASP105 4.7 6.0 1.0 O2 B:BO3304 4.8 13.5 1.0 CG B:ASP105 4.8 5.1 1.0 CA B:HIS103 4.9 4.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Bjp-1 Metallo Beta-Lactamase in Complex with Boric 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 Bjp-1 Metallo Beta-Lactamase in Complex with Boric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:10.2 occ:1.00 OE2 B:GLU158 2.0 13.0 1.0 ND1 B:HIS172 2.0 8.9 1.0 NZ B:LYS229 2.1 11.6 1.0 CD B:GLU158 2.7 11.2 1.0 OE1 B:GLU158 2.8 10.0 1.0 CE1 B:HIS172 2.9 9.9 1.0 CG B:HIS172 3.1 8.2 1.0 CE B:LYS229 3.1 10.7 1.0 CB B:HIS172 3.5 7.9 1.0 O B:HOH608 4.0 27.8 1.0 NE2 B:HIS172 4.1 10.5 1.0 CA B:HIS172 4.1 7.2 1.0 CG B:GLU158 4.2 11.3 1.0 CD2 B:HIS172 4.2 9.4 1.0 CD B:LYS229 4.4 10.0 1.0 CG B:LYS229 5.0 9.1 1.0 O B:ALA171 5.0 7.9 1.0 N B:ALA173 5.0 7.3 1.0

F.Di Pisa, C.Pozzi, M.Benvenuti, J.-D.Docquier, F.De Luca, S.Mangani. Boric Acid and Acetate Anion Binding to Subclass B3 Metallo-Beta-Lactamase Bjp-1 Provides Clues For Mechanism of Action and Inhibitor Design Inorg.Chim.Acta. 2017.
ISSN: ISSN 0020-1693
DOI: 10.1016/J.ICA.2017.07.030