Zinc in PDB 6r73: Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem

All present enzymatic activity of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem:
3.5.2.6;

The structure of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem, PDB code: 6r73 was solved by C.A.Softley, K.Zak, M.Kolonko, M.Sattler, G.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.04 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.979, 72.368, 61.194, 90.00, 108.47, 90.00
R / Rfree (%)	18.9 / 24.8

The binding sites of Zinc atom in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem (pdb code 6r73). 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 Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem, PDB code: 6r73:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:37.2 occ:1.00 O72 A:LMP301 1.7 39.9 1.0 NE2 A:HIS139 1.9 41.5 1.0 ND1 A:HIS79 2.1 29.0 1.0 NE2 A:HIS77 2.1 38.9 1.0 C7 A:LMP301 2.6 39.5 1.0 CE1 A:HIS139 2.8 36.3 1.0 O71 A:LMP301 2.8 33.9 1.0 CD2 A:HIS139 3.0 38.0 1.0 CG A:HIS79 3.0 37.2 1.0 CD2 A:HIS77 3.0 31.0 1.0 CE1 A:HIS77 3.1 33.9 1.0 CE1 A:HIS79 3.2 30.6 1.0 CB A:HIS79 3.2 38.5 1.0 OD1 A:ASP81 3.8 43.6 1.0 N4 A:LMP301 3.9 42.3 1.0 ND1 A:HIS139 3.9 35.1 1.0 SG A:CYS158 4.0 36.8 1.0 CG A:HIS139 4.0 37.0 1.0 CD2 A:HIS79 4.2 33.5 1.0 ZN A:ZN303 4.2 37.1 1.0 C6 A:LMP301 4.2 33.1 1.0 CG A:HIS77 4.2 30.2 1.0 CB A:CYS158 4.2 28.9 1.0 ND1 A:HIS77 4.2 31.7 1.0 NE2 A:HIS79 4.2 30.9 1.0 O62 A:LMP301 4.3 40.6 1.0 O32 A:LMP301 4.5 40.4 1.0 CG2 A:THR140 4.6 33.2 1.0 CA A:HIS79 4.6 34.7 1.0 C5 A:LMP301 4.6 43.1 1.0 C3 A:LMP301 4.7 41.3 1.0 C61 A:LMP301 4.7 35.6 1.0 CG A:ASP81 4.7 44.6 1.0 C31 A:LMP301 4.8 43.2 1.0 OD2 A:ASP81 4.8 55.8 1.0 N A:HIS79 4.9 34.5 1.0

Zinc binding site 2 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:37.1 occ:1.00 N4 A:LMP301 2.1 42.3 1.0 NE2 A:HIS197 2.2 46.0 1.0 SG A:CYS158 2.4 36.8 1.0 OD2 A:ASP81 2.4 55.8 1.0 O32 A:LMP301 2.7 40.4 1.0 C3 A:LMP301 2.8 41.3 1.0 CE1 A:HIS197 3.1 42.0 1.0 CD2 A:HIS197 3.2 35.7 1.0 C31 A:LMP301 3.2 43.2 1.0 C5 A:LMP301 3.2 43.1 1.0 CG A:ASP81 3.2 44.6 1.0 O72 A:LMP301 3.4 39.9 1.0 OD1 A:ASP81 3.6 43.6 1.0 CB A:CYS158 3.7 28.9 1.0 C7 A:LMP301 3.8 39.5 1.0 C6 A:LMP301 4.1 33.1 1.0 CB A:SER196 4.1 35.5 1.0 C2 A:LMP301 4.1 41.1 1.0 C1 A:LMP301 4.1 39.7 1.0 ZN A:ZN302 4.2 37.2 1.0 ND1 A:HIS197 4.2 33.8 1.0 OG A:SER196 4.2 36.4 1.0 CB A:ASP81 4.3 43.0 1.0 CG A:HIS197 4.3 40.5 1.0 O62 A:LMP301 4.3 40.6 1.0 O31 A:LMP301 4.5 38.5 1.0 O71 A:LMP301 4.6 33.9 1.0 CA A:CYS158 4.7 28.9 1.0 NE2 A:HIS139 4.7 41.5 1.0 CE1 A:HIS77 4.7 33.9 1.0 CD A:LYS33 4.8 30.6 1.0 CE1 A:HIS139 4.8 36.3 1.0 C4A A:LMP301 4.8 40.1 1.0 CE A:LYS33 4.9 31.2 1.0 C61 A:LMP301 4.9 35.6 1.0 NE2 A:HIS77 4.9 38.9 1.0

Zinc binding site 3 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:32.8 occ:1.00 NE2 B:HIS139 2.1 34.5 1.0 ND1 B:HIS79 2.1 30.4 1.0 NE2 B:HIS77 2.3 28.8 1.0 C61 B:LMP301 2.7 39.8 1.0 CE1 B:HIS139 2.8 39.7 1.0 C62 B:LMP301 2.9 30.1 1.0 CG B:HIS79 3.0 34.3 1.0 CE1 B:HIS79 3.2 34.5 1.0 CB B:HIS79 3.2 33.3 1.0 CD2 B:HIS77 3.2 29.2 1.0 CD2 B:HIS139 3.3 42.0 1.0 CE1 B:HIS77 3.4 28.2 1.0 C6 B:LMP301 3.5 47.0 1.0 O62 B:LMP301 3.7 58.5 1.0 ND1 B:HIS139 4.0 32.8 1.0 N4 B:LMP301 4.0 43.8 1.0 ZN B:ZN303 4.1 35.1 1.0 SG B:CYS158 4.1 34.0 1.0 OD1 B:ASP81 4.1 30.7 1.0 CD2 B:HIS79 4.2 39.1 1.0 NE2 B:HIS79 4.2 36.8 1.0 CG B:HIS139 4.3 37.5 1.0 CB B:CYS158 4.3 37.8 1.0 C5 B:LMP301 4.4 36.8 1.0 CG B:HIS77 4.4 30.9 1.0 ND1 B:HIS77 4.4 36.2 1.0 CG2 B:THR140 4.5 34.0 1.0 C7 B:LMP301 4.5 44.8 1.0 CA B:HIS79 4.6 36.9 1.0 O72 B:LMP301 4.7 46.2 1.0 N B:HIS79 4.9 31.7 1.0 C3 B:LMP301 4.9 40.2 1.0 CG B:ASP81 4.9 32.1 1.0 OD2 B:ASP81 5.0 39.2 1.0 C31 B:LMP301 5.0 38.4 1.0

Zinc binding site 4 out of 4 in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:35.1 occ:1.00 N4 B:LMP301 1.9 43.8 1.0 OD2 B:ASP81 2.1 39.2 1.0 NE2 B:HIS197 2.2 35.3 1.0 SG B:CYS158 2.3 34.0 1.0 C5 B:LMP301 2.7 36.8 1.0 CE1 B:HIS197 2.9 33.4 1.0 C3 B:LMP301 3.0 40.2 1.0 CG B:ASP81 3.1 32.1 1.0 C6 B:LMP301 3.1 47.0 1.0 CD2 B:HIS197 3.4 34.8 1.0 OD1 B:ASP81 3.4 30.7 1.0 CB B:CYS158 3.6 37.8 1.0 O31 B:LMP301 3.8 47.8 1.0 C31 B:LMP301 3.8 38.4 1.0 C1 B:LMP301 3.9 39.9 1.0 C61 B:LMP301 4.1 39.8 1.0 ZN B:ZN302 4.1 32.8 1.0 C2 B:LMP301 4.1 44.4 1.0 ND1 B:HIS197 4.1 31.3 1.0 CB B:SER196 4.2 33.4 1.0 OG B:SER196 4.3 35.8 1.0 CG B:HIS197 4.4 36.3 1.0 C7 B:LMP301 4.4 44.8 1.0 C62 B:LMP301 4.4 30.1 1.0 CB B:ASP81 4.4 30.1 1.0 O72 B:LMP301 4.6 46.2 1.0 CA B:CYS158 4.6 33.1 1.0 CD B:LYS33 4.7 32.1 1.0 CE1 B:HIS139 4.8 39.7 1.0 NE2 B:HIS139 4.8 34.5 1.0 NZ B:LYS161 4.8 39.0 1.0 CE B:LYS33 4.9 28.0 1.0 NE2 B:HIS77 4.9 28.8 1.0 C4A B:LMP301 4.9 44.9 1.0 CE1 B:HIS77 4.9 28.2 1.0 O32 B:LMP301 5.0 43.0 1.0

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