Zinc in PDB 4zej: Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime

The structure of Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime, PDB code: 4zej was solved by M.P.S.Booth, M.Kosmopoulou, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.88 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.397, 46.977, 183.758, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.9

The structure of Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Zinc atom in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime (pdb code 4zej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime, PDB code: 4zej:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime


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 Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.4 occ:1.00 OD2 A:ASP81 2.0 24.1 1.0 NE2 A:HIS200 2.2 21.6 1.0 SG A:CYS158 2.2 21.2 1.0 CL A:CL306 2.3 45.8 1.0 CL A:CL304 2.9 74.8 1.0 CG A:ASP81 3.0 24.6 1.0 CD2 A:HIS200 3.1 20.5 1.0 CE1 A:HIS200 3.1 21.5 1.0 CB A:CYS158 3.3 20.7 1.0 OD1 A:ASP81 3.4 25.6 1.0 NH2 A:ARG82 3.9 22.8 1.0 NE A:ARG82 4.0 20.6 1.0 CE1 A:HIS77 4.1 20.8 1.0 CG A:HIS200 4.2 20.2 1.0 ND1 A:HIS200 4.2 20.7 1.0 ZN A:ZN302 4.2 23.1 1.0 CZ A:ARG82 4.3 21.7 1.0 CB A:ASP81 4.3 24.5 1.0 CA A:CYS158 4.5 19.5 1.0 NE2 A:HIS77 4.6 21.3 1.0 O A:HOH479 4.8 40.8 1.0 NE2 A:HIS139 4.9 21.4 1.0 CD A:ARG82 4.9 20.1 1.0 O A:HOH442 5.0 32.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime


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 Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.1 occ:1.00 ND1 A:HIS79 2.0 24.7 1.0 NE2 A:HIS139 2.1 21.4 1.0 NE2 A:HIS77 2.2 21.3 1.0 CL A:CL306 2.3 45.8 1.0 O A:HOH479 2.5 40.8 1.0 CD2 A:HIS139 3.0 21.0 1.0 CE1 A:HIS79 3.0 26.0 1.0 CG A:HIS79 3.0 24.6 1.0 CE1 A:HIS77 3.1 20.8 1.0 CD2 A:HIS77 3.1 21.7 1.0 CE1 A:HIS139 3.1 21.3 1.0 CB A:HIS79 3.4 23.5 1.0 NE2 A:HIS79 4.1 26.7 1.0 CD2 A:HIS79 4.2 26.0 1.0 CG A:HIS139 4.2 20.9 1.0 ND1 A:HIS77 4.2 20.7 1.0 ND1 A:HIS139 4.2 21.0 1.0 OD1 A:ASP81 4.2 25.6 1.0 ZN A:ZN301 4.2 26.4 1.0 CG A:HIS77 4.2 21.2 1.0 CL A:CL304 4.4 74.8 1.0 CG2 A:THR140 4.6 24.4 1.0 CB A:CYS158 4.7 20.7 1.0 CA A:HIS79 4.8 23.7 1.0 SG A:CYS158 4.9 21.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime


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 Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.7 occ:1.00 O B:HOH463 2.0 42.9 1.0 NE2 B:HIS139 2.1 29.3 1.0 ND1 B:HIS79 2.2 34.5 1.0 NE2 B:HIS77 2.2 29.5 1.0 CD2 B:HIS139 3.0 28.4 1.0 CD2 B:HIS77 3.1 29.5 1.0 CG B:HIS79 3.1 35.3 1.0 CE1 B:HIS139 3.1 29.1 1.0 CE1 B:HIS79 3.1 34.8 1.0 CE1 B:HIS77 3.1 28.9 1.0 CB B:HIS79 3.4 35.1 1.0 CG B:HIS139 4.1 27.6 1.0 ND1 B:HIS139 4.2 28.1 1.0 ND1 B:HIS77 4.2 28.4 1.0 CG B:HIS77 4.2 28.4 1.0 NE2 B:HIS79 4.2 36.0 1.0 OD1 B:ASP81 4.2 39.0 1.0 CD2 B:HIS79 4.2 36.6 1.0 CL B:CL303 4.4 74.2 1.0 ZN B:ZN302 4.4 36.6 1.0 CG2 B:THR140 4.5 32.2 1.0 CA B:HIS79 4.8 36.0 1.0 CB B:CYS158 4.8 28.2 1.0 N B:HIS79 5.0 34.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime


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 Dim-1 Metallo-Beta-Lactamase Exposed to Ceftazidime within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:36.6 occ:1.00 OD2 B:ASP81 2.1 39.3 1.0 SG B:CYS158 2.1 29.1 1.0 NE2 B:HIS200 2.2 31.1 1.0 CL B:CL303 2.5 74.2 1.0 O B:HOH463 2.8 42.9 1.0 CE1 B:HIS200 3.1 30.9 1.0 CG B:ASP81 3.2 39.5 1.0 CD2 B:HIS200 3.2 29.8 1.0 CB B:CYS158 3.2 28.2 1.0 OD1 B:ASP81 3.6 39.0 1.0 NH2 B:ARG82 3.9 33.6 1.0 NE B:ARG82 4.0 31.6 1.0 ND1 B:HIS200 4.2 30.0 1.0 CE1 B:HIS77 4.2 28.9 1.0 CG B:HIS200 4.3 29.5 1.0 CZ B:ARG82 4.4 32.1 1.0 ZN B:ZN301 4.4 30.7 1.0 CB B:ASP81 4.4 40.9 1.0 CA B:CYS158 4.4 26.6 1.0 NE2 B:HIS77 4.7 29.5 1.0 NE2 B:HIS139 4.7 29.3 1.0 O B:HOH410 4.8 35.5 1.0

M.P.S.Booth, M.Kosmopoulou, L.Poirel, P.Nordmann, J.Spencer. Crystal Stricture of Dim-1 Metallo-Beta-Lactamase To Be Published.