Zinc in PDB 5ngg: Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion

The structure of Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion, PDB code: 5ngg 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)	34.68 / 1.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.310, 44.640, 75.910, 78.88, 89.41, 61.99
R / Rfree (%)	12.1 / 14.6

The binding sites of Zinc atom in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion (pdb code 5ngg). 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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion, PDB code: 5ngg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.3 occ:1.00 NE2 A:HIS106 2.1 6.9 1.0 O A:HOH488 2.1 7.1 1.0 NE2 A:HIS242 2.1 6.5 1.0 OD2 A:ASP105 2.1 7.5 1.0 OXT A:ACT304 2.2 9.0 1.0 CE1 A:HIS106 3.0 6.2 1.0 C A:ACT304 3.0 11.9 1.0 CG A:ASP105 3.0 6.5 1.0 CE1 A:HIS242 3.0 7.0 1.0 CD2 A:HIS106 3.1 6.4 1.0 CD2 A:HIS242 3.1 7.1 1.0 CH3 A:ACT304 3.1 16.4 1.0 OD1 A:ASP105 3.3 7.6 1.0 ZN A:ZN302 3.4 7.7 1.0 NE2 A:HIS101 4.0 7.5 1.0 CE1 A:HIS101 4.1 8.3 1.0 ND1 A:HIS106 4.1 6.0 1.0 O A:ACT304 4.2 13.6 1.0 CG A:HIS106 4.2 5.8 1.0 ND1 A:HIS242 4.2 7.1 1.0 O A:HOH658 4.2 24.9 1.0 CG A:HIS242 4.2 7.6 1.0 CB A:ASP105 4.3 6.4 1.0 CH2 A:TRP34 4.4 28.4 1.0 NE2 A:HIS177 4.7 7.5 1.0 CZ3 A:TRP34 4.9 30.5 1.0 CZ2 A:TRP34 4.9 24.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.7 occ:1.00 O A:HOH488 1.9 7.1 1.0 NE2 A:HIS101 2.1 7.5 1.0 NE2 A:HIS177 2.1 7.5 1.0 ND1 A:HIS103 2.1 7.3 1.0 CE1 A:HIS103 3.0 7.7 1.0 CD2 A:HIS177 3.0 7.4 1.0 CD2 A:HIS101 3.0 7.3 1.0 CE1 A:HIS101 3.0 8.3 1.0 CG A:HIS103 3.1 7.3 1.0 CE1 A:HIS177 3.1 7.9 1.0 OXT A:ACT304 3.1 9.0 1.0 O A:HOH658 3.3 24.9 1.0 ZN A:ZN301 3.4 7.3 1.0 CB A:HIS103 3.5 6.8 1.0 C A:ACT304 3.7 11.9 1.0 ND1 A:HIS101 4.1 9.4 1.0 OD1 A:ASP105 4.1 7.6 1.0 CD2 A:HIS106 4.1 6.4 1.0 CG A:HIS101 4.1 7.1 1.0 NE2 A:HIS106 4.1 6.9 1.0 NE2 A:HIS103 4.1 8.2 1.0 CH3 A:ACT304 4.1 16.4 1.0 CG A:HIS177 4.2 7.6 1.0 ND1 A:HIS177 4.2 7.8 1.0 CD2 A:HIS103 4.2 8.3 1.0 O A:ACT304 4.5 13.6 1.0 O A:HOH521 4.6 16.3 1.0 OD2 A:ASP105 4.7 7.5 1.0 CG A:ASP105 4.8 6.5 1.0 CA A:HIS103 4.9 6.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:13.0 occ:1.00 OE2 A:GLU158 2.0 14.9 1.0 ND1 A:HIS172 2.0 12.3 1.0 NZ A:LYS229 2.1 14.7 1.0 CD A:GLU158 2.7 14.2 1.0 OE1 A:GLU158 2.8 13.7 1.0 CE1 A:HIS172 2.9 13.8 1.0 CE A:LYS229 3.1 14.4 1.0 CG A:HIS172 3.1 10.9 1.0 CB A:HIS172 3.6 10.0 1.0 O A:HOH403 3.7 62.6 1.0 NE2 A:HIS172 4.1 14.6 1.0 CA A:HIS172 4.1 9.7 1.0 CG A:GLU158 4.1 14.9 1.0 CD2 A:HIS172 4.2 12.3 1.0 O A:HOH620 4.2 28.9 1.0 CD A:LYS229 4.4 13.4 1.0 N A:ALA173 5.0 10.3 1.0 CG A:LYS229 5.0 12.7 1.0 C A:HIS172 5.0 10.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:8.1 occ:1.00 O B:HOH507 2.0 9.0 1.0 NE2 B:HIS106 2.1 7.7 1.0 OD2 B:ASP105 2.1 8.4 1.0 NE2 B:HIS242 2.1 7.3 1.0 O B:ACT304 2.2 9.9 1.0 CE1 B:HIS106 3.0 7.1 1.0 C B:ACT304 3.0 12.2 1.0 CG B:ASP105 3.0 7.4 1.0 CE1 B:HIS242 3.1 8.3 1.0 CD2 B:HIS106 3.1 7.8 1.0 CD2 B:HIS242 3.1 7.7 1.0 CH3 B:ACT304 3.2 16.5 1.0 OD1 B:ASP105 3.3 8.5 1.0 ZN B:ZN302 3.4 8.5 1.0 NE2 B:HIS101 4.0 7.9 1.0 CE1 B:HIS101 4.1 9.1 1.0 ND1 B:HIS106 4.1 7.0 1.0 OXT B:ACT304 4.2 15.1 1.0 CG B:HIS106 4.2 7.0 1.0 ND1 B:HIS242 4.2 8.4 1.0 O B:HOH662 4.2 22.6 1.0 CG B:HIS242 4.3 8.0 1.0 CB B:ASP105 4.3 7.4 1.0 CH2 B:TRP34 4.6 23.2 1.0 CZ3 B:TRP34 4.7 22.4 1.0 NE2 B:HIS177 4.7 7.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:8.5 occ:1.00 O B:HOH507 1.9 9.0 1.0 NE2 B:HIS177 2.1 7.8 1.0 NE2 B:HIS101 2.1 7.9 1.0 ND1 B:HIS103 2.1 7.6 1.0 CD2 B:HIS177 3.0 8.5 1.0 CD2 B:HIS101 3.0 7.4 1.0 CE1 B:HIS103 3.0 9.0 1.0 CE1 B:HIS101 3.0 9.1 1.0 CE1 B:HIS177 3.1 8.3 1.0 CG B:HIS103 3.1 7.8 1.0 O B:ACT304 3.1 9.9 1.0 O B:HOH662 3.4 22.6 1.0 ZN B:ZN301 3.4 8.1 1.0 CB B:HIS103 3.5 7.9 1.0 C B:ACT304 3.7 12.2 1.0 ND1 B:HIS101 4.1 9.6 1.0 CG B:HIS101 4.1 7.8 1.0 CD2 B:HIS106 4.1 7.8 1.0 OD1 B:ASP105 4.1 8.5 1.0 NE2 B:HIS106 4.1 7.7 1.0 NE2 B:HIS103 4.1 9.5 1.0 CG B:HIS177 4.1 8.2 1.0 CH3 B:ACT304 4.2 16.5 1.0 ND1 B:HIS177 4.2 8.2 1.0 CD2 B:HIS103 4.2 8.8 1.0 OXT B:ACT304 4.6 15.1 1.0 O B:HOH505 4.7 17.6 1.0 OD2 B:ASP105 4.7 8.4 1.0 CG B:ASP105 4.8 7.4 1.0 CA B:HIS103 4.9 7.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion


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 the Subclass B3 Metallo-Beta-Lactamase Bjp-1 in Complex with Acetate Anion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:14.6 occ:1.00 O B:LYS294 2.0 17.1 1.0 C B:LYS294 2.9 19.3 1.0 OXT B:LYS294 3.0 23.3 1.0 CA B:LYS294 4.3 20.3 1.0 N B:LYS294 4.7 21.1 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