Zinc in PDB 6rzs: Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem

All present enzymatic activity of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem:
3.5.2.6;

The structure of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem, PDB code: 6rzs was solved by K.M.Zak, C.Softley, M.Kolonko, M.Sattler, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.82 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.688, 48.105, 92.574, 90.00, 105.73, 90.00
R / Rfree (%)	20 / 23.8

The binding sites of Zinc atom in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem (pdb code 6rzs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem, PDB code: 6rzs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:31.4 occ:1.00 NE2 A:HIS77 2.0 24.4 1.0 NE2 A:HIS139 2.0 26.9 1.0 ND1 A:HIS79 2.0 27.5 1.0 O6 A:LHT301 2.1 35.6 1.0 CD2 A:HIS77 2.8 25.3 1.0 CD2 A:HIS139 2.9 27.6 1.0 C20 A:LHT301 2.9 35.8 1.0 CG A:HIS79 3.0 27.1 1.0 O7 A:LHT301 3.1 40.4 1.0 CE1 A:HIS79 3.1 28.5 1.0 CE1 A:HIS139 3.2 27.0 1.0 CE1 A:HIS77 3.2 26.4 1.0 CB A:HIS79 3.2 27.4 1.0 SG A:CYS158 4.0 25.9 1.0 CG A:HIS77 4.0 24.4 1.0 CG A:HIS139 4.1 27.2 1.0 CD2 A:HIS79 4.1 28.3 1.0 CB A:CYS158 4.1 23.3 1.0 ND1 A:HIS77 4.2 23.9 1.0 NE2 A:HIS79 4.2 26.7 1.0 ND1 A:HIS139 4.2 27.4 1.0 ZN A:ZN303 4.2 28.2 1.0 N3 A:LHT301 4.3 29.9 1.0 OD1 A:ASP81 4.3 28.9 1.0 O8 A:LHT301 4.3 30.4 1.0 C19 A:LHT301 4.3 34.3 1.0 CG2 A:THR140 4.4 27.6 1.0 O4 A:LHT301 4.6 26.8 1.0 CA A:HIS79 4.6 27.6 1.0 C21 A:LHT301 4.8 35.0 1.0 C17 A:LHT301 4.8 30.8 1.0 OD2 A:ASP81 4.8 31.0 1.0 C16 A:LHT301 4.9 29.3 1.0 C18 A:LHT301 4.9 33.0 1.0 N A:HIS79 4.9 28.0 1.0 CG A:ASP81 4.9 29.2 1.0

Zinc binding site 2 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:28.2 occ:1.00 NE2 A:HIS197 2.0 33.9 1.0 SG A:CYS158 2.2 25.9 1.0 OD2 A:ASP81 2.2 31.0 1.0 N3 A:LHT301 2.2 29.9 1.0 O4 A:LHT301 2.4 26.8 1.0 C16 A:LHT301 3.0 29.3 1.0 CE1 A:HIS197 3.0 31.4 1.0 CD2 A:HIS197 3.0 30.2 1.0 C17 A:LHT301 3.1 30.8 1.0 C18 A:LHT301 3.2 33.0 1.0 CG A:ASP81 3.3 29.2 1.0 CB A:CYS158 3.3 23.3 1.0 O6 A:LHT301 3.3 35.6 1.0 OD1 A:ASP81 3.7 28.9 1.0 C20 A:LHT301 3.9 35.8 1.0 C3 A:LHT301 4.0 33.5 1.0 C2 A:LHT301 4.1 33.3 1.0 ND1 A:HIS197 4.1 29.1 1.0 CG A:HIS197 4.2 30.0 1.0 C19 A:LHT301 4.2 34.3 1.0 CB A:SER196 4.2 24.4 1.0 ZN A:ZN302 4.2 31.4 1.0 O5 A:LHT301 4.3 30.1 1.0 CA A:CYS158 4.3 22.9 1.0 O8 A:LHT301 4.4 30.4 1.0 OG A:SER196 4.4 22.7 1.0 CB A:ASP81 4.5 29.5 1.0 NE2 A:HIS139 4.6 26.9 1.0 O7 A:LHT301 4.7 40.4 1.0 CE1 A:HIS77 4.8 26.4 1.0 NE2 A:HIS77 4.8 24.4 1.0 C21 A:LHT301 4.9 35.0 1.0 CE1 A:HIS139 5.0 27.0 1.0

Zinc binding site 3 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:34.9 occ:1.00 NE2 B:HIS139 2.0 39.6 1.0 ND1 B:HIS79 2.1 30.4 1.0 O6 B:LHT301 2.1 40.7 1.0 NE2 B:HIS77 2.1 29.7 1.0 O7 B:LHT301 2.6 42.4 1.0 C20 B:LHT301 2.7 42.7 1.0 CD2 B:HIS77 3.0 31.0 1.0 CG B:HIS79 3.0 26.8 1.0 CD2 B:HIS139 3.0 37.9 1.0 CE1 B:HIS139 3.0 36.8 1.0 CE1 B:HIS79 3.1 32.8 1.0 CB B:HIS79 3.2 28.9 1.0 CE1 B:HIS77 3.3 32.8 1.0 ND1 B:HIS139 4.1 36.7 1.0 CG B:HIS139 4.1 37.0 1.0 CD2 B:HIS79 4.2 29.0 1.0 C19 B:LHT301 4.2 42.4 1.0 SG B:CYS158 4.2 31.4 1.0 CG B:HIS77 4.2 29.4 1.0 NE2 B:HIS79 4.2 30.1 1.0 ZN B:ZN303 4.2 40.3 1.0 CB B:CYS158 4.2 31.0 1.0 OD1 B:ASP81 4.3 35.5 1.0 ND1 B:HIS77 4.3 30.3 1.0 O8 B:LHT301 4.3 47.7 1.0 N3 B:LHT301 4.3 40.1 1.0 CG2 B:THR140 4.4 28.1 1.0 C21 B:LHT301 4.6 44.0 1.0 CA B:HIS79 4.7 30.8 1.0 C17 B:LHT301 4.8 45.8 1.0 C18 B:LHT301 4.9 43.2 1.0 C16 B:LHT301 4.9 44.6 1.0 O4 B:LHT301 4.9 45.1 1.0 N B:HIS79 5.0 30.0 1.0

Zinc binding site 4 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Ertapenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:40.3 occ:1.00 NE2 B:HIS197 2.0 43.4 1.0 N3 B:LHT301 2.2 40.1 1.0 SG B:CYS158 2.2 31.4 1.0 OD2 B:ASP81 2.3 41.1 1.0 O4 B:LHT301 2.8 45.1 1.0 CE1 B:HIS197 2.9 42.2 1.0 C16 B:LHT301 3.0 44.6 1.0 CD2 B:HIS197 3.2 41.7 1.0 C17 B:LHT301 3.2 45.8 1.0 O6 B:LHT301 3.3 40.7 1.0 CG B:ASP81 3.3 36.2 1.0 C18 B:LHT301 3.4 43.2 1.0 CB B:CYS158 3.4 31.0 1.0 OD1 B:ASP81 3.6 35.5 1.0 C20 B:LHT301 3.8 42.7 1.0 ND1 B:HIS197 4.0 39.6 1.0 C3 B:LHT301 4.1 45.9 1.0 CB B:SER196 4.1 36.2 1.0 C19 B:LHT301 4.2 42.4 1.0 CG B:HIS197 4.2 41.7 1.0 ZN B:ZN302 4.2 34.9 1.0 C2 B:LHT301 4.3 45.4 1.0 OG B:SER196 4.3 35.5 1.0 O5 B:LHT301 4.3 43.0 1.0 O7 B:LHT301 4.3 42.4 1.0 O8 B:LHT301 4.3 47.7 1.0 CA B:CYS158 4.4 31.4 1.0 CB B:ASP81 4.6 38.2 1.0 CE1 B:HIS77 4.8 32.8 1.0 NE2 B:HIS139 4.8 39.6 1.0 NE2 B:HIS77 4.9 29.7 1.0 CE B:LYS33 4.9 39.2 1.0 CE1 B:HIS139 4.9 36.8 1.0 CD B:LYS33 5.0 37.0 1.0 C21 B:LHT301 5.0 44.0 1.0

C.Softley, K.M.Zak, R.Fino, M.Kolonko, R.Mejdi-Nitiu, H.Meyer, M.Sattler, G.M.Popowicz. Structure and Molecular Recognition Mechanism of Imp-13 B-Lactamase To Be Published.