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

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

The structure of Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Imipenem, PDB code: 6rzr 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)	45.50 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.207, 90.925, 120.811, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.8

The binding sites of Zinc atom in the Structure of Imp-13 Metallo-Beta-Lactamase Complexed with Hydrolysed Imipenem (pdb code 6rzr). 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 Imipenem, PDB code: 6rzr:
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 Imipenem


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 Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:36.3 occ:1.00 O72 A:8YF311 1.9 31.9 1.0 ND1 A:HIS79 2.0 34.9 1.0 NE2 A:HIS139 2.0 30.5 1.0 NE2 A:HIS77 2.1 37.6 1.0 C7 A:8YF311 2.7 37.5 1.0 O71 A:8YF311 2.8 38.8 1.0 CG A:HIS79 3.0 31.9 1.0 CD2 A:HIS139 3.0 33.8 1.0 CD2 A:HIS77 3.0 32.8 1.0 CE1 A:HIS79 3.0 32.9 1.0 CE1 A:HIS139 3.0 33.3 1.0 CB A:HIS79 3.2 31.9 1.0 CE1 A:HIS77 3.3 36.0 1.0 SG A:CYS158 4.0 33.8 1.0 N4 A:8YF311 4.1 44.3 1.0 C6 A:8YF311 4.1 36.8 1.0 ZN A:ZN302 4.1 36.2 1.0 CD2 A:HIS79 4.1 36.5 1.0 ND1 A:HIS139 4.1 28.6 1.0 CG A:HIS139 4.1 32.1 1.0 NE2 A:HIS79 4.1 36.2 1.0 CB A:CYS158 4.2 35.2 1.0 CG A:HIS77 4.2 31.1 1.0 OD1 A:ASP81 4.2 40.8 1.0 ND1 A:HIS77 4.3 34.0 1.0 O62 A:8YF311 4.4 38.4 1.0 CG2 A:THR140 4.5 34.6 1.0 CA A:HIS79 4.6 33.1 1.0 O31 A:8YF311 4.6 33.4 1.0 C61 A:8YF311 4.7 38.4 1.0 C5 A:8YF311 4.7 37.9 1.0 C3 A:8YF311 4.8 37.7 1.0 OD2 A:ASP81 4.8 28.9 1.0 CG A:ASP81 4.9 37.8 1.0 C31 A:8YF311 4.9 37.9 1.0 N A:HIS79 5.0 32.6 1.0

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


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 Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:36.2 occ:1.00 N4 A:8YF311 2.0 44.3 1.0 NE2 A:HIS197 2.0 33.0 1.0 OD2 A:ASP81 2.1 28.9 1.0 SG A:CYS158 2.3 33.8 1.0 O31 A:8YF311 2.5 33.4 1.0 C3 A:8YF311 2.8 37.7 1.0 CD2 A:HIS197 3.0 33.4 1.0 C31 A:8YF311 3.0 37.9 1.0 CE1 A:HIS197 3.1 29.1 1.0 C5 A:8YF311 3.2 37.9 1.0 CG A:ASP81 3.2 37.8 1.0 O72 A:8YF311 3.2 31.9 1.0 CB A:CYS158 3.5 35.2 1.0 OD1 A:ASP81 3.6 40.8 1.0 C7 A:8YF311 3.7 37.5 1.0 C2 A:8YF311 3.9 47.6 1.0 C6 A:8YF311 4.1 36.8 1.0 ZN A:ZN301 4.1 36.3 1.0 C1 A:8YF311 4.1 39.4 1.0 ND1 A:HIS197 4.2 31.2 1.0 CG A:HIS197 4.2 34.6 1.0 CB A:SER196 4.3 32.0 1.0 O32 A:8YF311 4.3 39.0 1.0 O71 A:8YF311 4.4 38.8 1.0 CB A:ASP81 4.5 32.0 1.0 CA A:CYS158 4.5 33.1 1.0 O62 A:8YF311 4.5 38.4 1.0 NE2 A:HIS139 4.5 30.5 1.0 OG A:SER196 4.6 35.2 1.0 CE1 A:HIS139 4.7 33.3 1.0 CE1 A:HIS77 4.8 36.0 1.0 NE2 A:HIS77 4.8 37.6 1.0 CD A:LYS33 4.8 32.3 1.0 C61 A:8YF311 4.9 38.4 1.0 NZ A:LYS161 4.9 33.5 1.0 CE A:LYS33 5.0 33.6 1.0

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


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 Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:39.8 occ:1.00 O72 B:8YF307 1.9 28.3 0.5 ND1 B:HIS79 2.0 33.1 1.0 NE2 B:HIS139 2.0 39.0 1.0 NE2 B:HIS77 2.1 39.9 1.0 O72 B:8YF307 2.5 61.6 0.2 O72 B:8YF307 2.7 51.9 0.2 C7 B:8YF307 2.7 34.4 0.5 O71 B:8YF307 2.8 66.3 0.2 CD2 B:HIS77 2.9 34.6 1.0 O71 B:8YF307 2.9 29.4 0.5 CG B:HIS79 2.9 36.0 1.0 CE1 B:HIS79 3.0 40.2 1.0 CD2 B:HIS139 3.0 40.1 1.0 C7 B:8YF307 3.0 63.3 0.2 CE1 B:HIS139 3.0 42.6 1.0 CE1 B:HIS77 3.2 42.5 1.0 CB B:HIS79 3.2 33.9 1.0 C7 B:8YF307 3.3 53.3 0.2 O71 B:8YF307 3.4 55.5 0.2 N4 B:8YF307 4.0 37.3 0.5 SG B:CYS158 4.1 37.9 1.0 CD2 B:HIS79 4.1 35.1 1.0 N4 B:8YF307 4.1 59.0 0.2 NE2 B:HIS79 4.1 36.1 1.0 O62 B:8YF307 4.1 54.6 0.2 ZN B:ZN302 4.1 42.7 1.0 CG B:HIS77 4.1 38.2 1.0 C6 B:8YF307 4.1 34.2 0.5 N4 B:8YF307 4.1 51.3 0.2 CG B:HIS139 4.1 39.9 1.0 ND1 B:HIS139 4.1 40.3 1.0 CB B:CYS158 4.2 35.4 1.0 ND1 B:HIS77 4.2 40.2 1.0 OD1 B:ASP81 4.3 41.3 1.0 O62 B:8YF307 4.3 33.6 0.5 CG2 B:THR140 4.5 39.1 1.0 C6 B:8YF307 4.5 61.6 0.2 O31 B:8YF307 4.5 42.7 0.5 C6 B:8YF307 4.6 53.2 0.2 C61 B:8YF307 4.6 38.0 0.5 O31 B:8YF307 4.6 51.2 0.2 C5 B:8YF307 4.6 38.5 0.5 CA B:HIS79 4.6 39.9 1.0 O62 B:8YF307 4.7 62.9 0.2 C3 B:8YF307 4.7 41.7 0.5 OD2 B:ASP81 4.8 42.5 1.0 C31 B:8YF307 4.8 41.6 0.5 C5 B:8YF307 4.8 60.6 0.2 CG B:ASP81 4.9 41.7 1.0 C61 B:8YF307 4.9 54.8 0.2 O31 B:8YF307 4.9 61.8 0.2 C31 B:8YF307 4.9 49.8 0.2 C5 B:8YF307 4.9 52.9 0.2 N B:HIS79 4.9 39.4 1.0 C3 B:8YF307 5.0 49.1 0.2 C3 B:8YF307 5.0 57.9 0.2

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


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 Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:42.7 occ:1.00 NE2 B:HIS197 2.0 42.2 1.0 N4 B:8YF307 2.1 37.3 0.5 OD2 B:ASP81 2.1 42.5 1.0 O31 B:8YF307 2.3 42.7 0.5 SG B:CYS158 2.4 37.9 1.0 N4 B:8YF307 2.5 59.0 0.2 N4 B:8YF307 2.5 51.3 0.2 O31 B:8YF307 2.6 51.2 0.2 O31 B:8YF307 2.7 61.8 0.2 C3 B:8YF307 2.8 41.7 0.5 C31 B:8YF307 2.9 41.6 0.5 O72 B:8YF307 3.0 51.9 0.2 CE1 B:HIS197 3.0 35.2 1.0 CD2 B:HIS197 3.0 44.8 1.0 O72 B:8YF307 3.1 28.3 0.5 C3 B:8YF307 3.1 49.1 0.2 C3 B:8YF307 3.1 57.9 0.2 CG B:ASP81 3.2 41.7 1.0 C5 B:8YF307 3.2 38.5 0.5 O72 B:8YF307 3.2 61.6 0.2 C31 B:8YF307 3.2 49.8 0.2 C31 B:8YF307 3.3 58.8 0.2 C5 B:8YF307 3.5 60.6 0.2 CB B:CYS158 3.5 35.4 1.0 C5 B:8YF307 3.5 52.9 0.2 OD1 B:ASP81 3.6 41.3 1.0 C7 B:8YF307 3.7 34.4 0.5 C2 B:8YF307 3.9 46.9 0.5 C7 B:8YF307 4.0 63.3 0.2 ZN B:ZN301 4.1 39.8 1.0 C1 B:8YF307 4.1 43.3 0.5 ND1 B:HIS197 4.1 39.9 1.0 C7 B:8YF307 4.2 53.3 0.2 CG B:HIS197 4.2 44.1 1.0 O32 B:8YF307 4.2 40.9 0.5 C6 B:8YF307 4.2 34.2 0.5 C2 B:8YF307 4.2 58.2 0.2 O62 B:8YF307 4.2 54.6 0.2 C2 B:8YF307 4.3 50.4 0.2 CB B:SER196 4.3 42.1 1.0 O71 B:8YF307 4.3 29.4 0.5 O62 B:8YF307 4.4 33.6 0.5 C6 B:8YF307 4.4 61.6 0.2 C1 B:8YF307 4.4 59.2 0.2 CB B:ASP81 4.5 40.1 1.0 C6 B:8YF307 4.5 53.2 0.2 C1 B:8YF307 4.5 51.3 0.2 O32 B:8YF307 4.5 50.5 0.2 CA B:CYS158 4.6 37.6 1.0 O32 B:8YF307 4.6 62.0 0.2 NE2 B:HIS139 4.6 39.0 1.0 OG B:SER196 4.6 41.8 1.0 O71 B:8YF307 4.7 66.3 0.2 O62 B:8YF307 4.7 62.9 0.2 CD B:LYS33 4.8 37.8 1.0 CE1 B:HIS77 4.8 42.5 1.0 CE1 B:HIS139 4.8 42.6 1.0 NE2 B:HIS77 4.8 39.9 1.0 C22 B:8YF307 4.9 46.9 0.5 CE B:LYS33 4.9 40.1 1.0 C61 B:8YF307 5.0 54.8 0.2 C61 B:8YF307 5.0 38.0 0.5

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.