Zinc in PDB 3lvz: New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum

The structure of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum, PDB code: 3lvz was solved by J.D.Docquier, M.Benvenuti, V.Calderone, M.Stoczko, G.M.Rossolini, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.24 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.501, 44.773, 76.966, 78.92, 89.51, 61.91
R / Rfree (%)	16.2 / 19.3

The binding sites of Zinc atom in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum (pdb code 3lvz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum, PDB code: 3lvz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn295 b:10.6 occ:1.00 O A:HOH302 1.9 9.5 1.0 NE2 A:HIS177 2.0 8.1 1.0 NE2 A:HIS101 2.1 5.8 1.0 ND1 A:HIS103 2.1 7.1 1.0 CD2 A:HIS177 2.9 7.5 1.0 CD2 A:HIS101 3.0 6.9 1.0 CE1 A:HIS101 3.0 7.9 1.0 CE1 A:HIS103 3.0 7.2 1.0 CE1 A:HIS177 3.1 7.4 1.0 CG A:HIS103 3.1 7.0 1.0 O A:HOH299 3.3 7.3 1.0 O A:HOH444 3.3 19.1 1.0 ZN A:ZN296 3.4 7.9 1.0 CB A:HIS103 3.5 6.8 1.0 OD1 A:ASP105 4.1 8.1 1.0 ND1 A:HIS101 4.1 10.8 1.0 CG A:HIS101 4.1 7.5 1.0 CG A:HIS177 4.1 6.8 1.0 CD2 A:HIS106 4.2 7.3 1.0 NE2 A:HIS103 4.2 8.8 1.0 NE2 A:HIS106 4.2 6.9 1.0 ND1 A:HIS177 4.2 9.8 1.0 CD2 A:HIS103 4.2 7.8 1.0 O A:HOH382 4.6 16.4 1.0 OD2 A:ASP105 4.7 8.3 1.0 CG A:ASP105 4.9 7.5 1.0 CA A:HIS103 4.9 6.8 1.0

Zinc binding site 2 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn296 b:7.9 occ:1.00 NE2 A:HIS242 2.0 7.3 1.0 OD2 A:ASP105 2.1 8.3 1.0 O A:HOH302 2.1 9.5 1.0 NE2 A:HIS106 2.1 6.9 1.0 O A:HOH299 2.5 7.3 1.0 CE1 A:HIS106 3.0 8.1 1.0 CE1 A:HIS242 3.0 7.5 1.0 CG A:ASP105 3.0 7.5 1.0 CD2 A:HIS242 3.1 6.4 1.0 CD2 A:HIS106 3.1 7.3 1.0 OD1 A:ASP105 3.3 8.1 1.0 ZN A:ZN295 3.4 10.6 1.0 NE2 A:HIS101 4.0 5.8 1.0 O A:HOH444 4.1 19.1 1.0 CE1 A:HIS101 4.1 7.9 1.0 ND1 A:HIS106 4.1 6.2 1.0 ND1 A:HIS242 4.1 7.9 1.0 CG A:HIS242 4.2 7.9 1.0 CG A:HIS106 4.2 6.8 1.0 CB A:ASP105 4.3 6.5 1.0 CH2 A:TRP34 4.6 17.6 1.0 CZ2 A:TRP34 4.7 14.9 1.0 NE2 A:HIS177 4.8 8.1 1.0

Zinc binding site 3 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn297 b:16.5 occ:1.00 OE2 A:GLU158 2.0 12.3 1.0 NZ A:LYS229 2.0 13.1 1.0 ND1 A:HIS172 2.1 10.3 1.0 CD A:GLU158 2.8 10.9 1.0 OE1 A:GLU158 2.9 13.5 1.0 CE1 A:HIS172 2.9 11.6 1.0 CE A:LYS229 3.1 18.4 1.0 CG A:HIS172 3.2 9.9 1.0 CB A:HIS172 3.6 9.1 1.0 CE A:MET233 4.0 23.5 1.0 NE2 A:HIS172 4.1 12.0 1.0 CA A:HIS172 4.1 7.7 1.0 CG A:GLU158 4.2 9.2 1.0 O A:HOH429 4.2 31.9 1.0 CD2 A:HIS172 4.2 10.9 1.0 CD A:LYS229 4.5 16.3 1.0 O A:ALA171 4.9 9.3 1.0 N A:ALA173 4.9 9.2 1.0 C A:HIS172 5.0 8.4 1.0

Zinc binding site 4 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn295 b:8.1 occ:1.00 O B:HOH482 2.0 9.8 1.0 NE2 B:HIS242 2.1 7.7 1.0 NE2 B:HIS106 2.1 7.2 1.0 OD2 B:ASP105 2.1 9.2 1.0 O B:HOH298 2.4 6.7 1.0 CE1 B:HIS106 2.9 6.3 1.0 CE1 B:HIS242 3.0 8.2 1.0 CG B:ASP105 3.1 8.3 1.0 CD2 B:HIS242 3.1 8.2 1.0 CD2 B:HIS106 3.1 6.0 1.0 OD1 B:ASP105 3.3 7.8 1.0 ZN B:ZN296 3.4 9.0 1.0 NE2 B:HIS101 4.0 8.4 1.0 CE1 B:HIS101 4.0 8.0 1.0 O B:HOH393 4.1 20.3 1.0 ND1 B:HIS106 4.1 5.9 1.0 ND1 B:HIS242 4.2 7.7 1.0 CG B:HIS242 4.2 7.6 1.0 CG B:HIS106 4.2 7.2 1.0 CH2 B:TRP34 4.3 20.2 1.0 CB B:ASP105 4.3 6.4 1.0 CZ3 B:TRP34 4.7 23.2 1.0 NE2 B:HIS177 4.7 6.7 1.0

Zinc binding site 5 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn296 b:9.0 occ:1.00 NE2 B:HIS177 2.0 6.7 1.0 O B:HOH482 2.0 9.8 1.0 NE2 B:HIS101 2.1 8.4 1.0 ND1 B:HIS103 2.1 7.3 1.0 CD2 B:HIS177 2.9 6.7 1.0 CD2 B:HIS101 3.0 7.8 1.0 CE1 B:HIS177 3.0 6.7 1.0 CE1 B:HIS103 3.0 9.2 1.0 CE1 B:HIS101 3.1 8.0 1.0 CG B:HIS103 3.1 8.6 1.0 O B:HOH393 3.2 20.3 1.0 O B:HOH298 3.2 6.7 1.0 ZN B:ZN295 3.4 8.1 1.0 CB B:HIS103 3.5 6.9 1.0 CG B:HIS177 4.1 8.3 1.0 ND1 B:HIS101 4.1 10.0 1.0 ND1 B:HIS177 4.1 8.0 1.0 CG B:HIS101 4.1 7.9 1.0 OD1 B:ASP105 4.1 7.8 1.0 NE2 B:HIS106 4.2 7.2 1.0 NE2 B:HIS103 4.2 9.3 1.0 CD2 B:HIS106 4.2 6.0 1.0 CD2 B:HIS103 4.2 7.5 1.0 O B:HOH381 4.6 17.6 1.0 OD2 B:ASP105 4.7 9.2 1.0 CA B:HIS103 4.9 5.8 1.0 CG B:ASP105 4.9 8.3 1.0

Zinc binding site 6 out of 6 in the New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of New Refinement of the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn297 b:15.8 occ:1.00 OE2 B:GLU158 1.9 14.1 1.0 NZ B:LYS229 2.0 14.1 1.0 ND1 B:HIS172 2.1 13.2 1.0 CD B:GLU158 2.8 15.4 1.0 OE1 B:GLU158 2.9 14.1 1.0 CE1 B:HIS172 3.0 12.4 1.0 CE B:LYS229 3.1 19.7 1.0 CG B:HIS172 3.2 10.7 1.0 CB B:HIS172 3.6 9.5 1.0 CA B:HIS172 4.1 9.1 1.0 NE2 B:HIS172 4.2 14.9 1.0 CG B:GLU158 4.2 11.2 1.0 CD2 B:HIS172 4.3 12.5 1.0 CE B:MET233 4.3 25.6 1.0 CD B:LYS229 4.4 19.2 1.0 C B:HIS172 4.9 10.0 1.0 N B:ALA173 5.0 10.4 1.0 CG B:LYS229 5.0 16.1 1.0 O B:ALA171 5.0 8.7 1.0

J.D.Docquier, M.Benvenuti, V.Calderone, M.Stoczko, N.Menciassi, G.M.Rossolini, S.Mangani. High-Resolution Crystal Structure of the Subclass B3 Metallo-Beta-Lactamase Bjp-1: Rational Basis For Substrate Specificity and Interaction with Sulfonamides. Antimicrob.Agents Chemother. V. 54 4343 2010.
ISSN: ISSN 0066-4804
PubMed: 20696874
DOI: 10.1128/AAC.00409-10