Zinc in PDB 1vgn: Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1)

All present enzymatic activity of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1):
3.5.2.6;

The structure of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1), PDB code: 1vgn was solved by H.Kurosaki, Y.Yamaguchi, T.Higashi, K.Soga, S.Matsueda, S.Misumi, Y.Yamagata, Y.Arakawa, M.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.55 / 2.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.987, 53.314, 196.344, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 24.3

The binding sites of Zinc atom in the Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1) (pdb code 1vgn). 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-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1), PDB code: 1vgn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.4 occ:1.00 ND1 A:HIS79 1.8 23.9 1.0 NE2 A:HIS77 2.0 23.1 1.0 NE2 A:HIS139 2.1 23.3 1.0 SW A:OPS1161 2.2 24.8 1.0 CG A:HIS79 2.8 24.6 1.0 CE1 A:HIS79 2.8 24.7 1.0 CD2 A:HIS77 2.9 22.0 1.0 CE1 A:HIS77 3.0 24.5 1.0 CD2 A:HIS139 3.0 20.5 1.0 CE1 A:HIS139 3.1 23.1 1.0 CV A:OPS1161 3.2 32.3 1.0 CB A:HIS79 3.2 22.8 1.0 ZN A:ZN302 3.8 28.6 1.0 NE2 A:HIS79 3.9 25.3 1.0 CD2 A:HIS79 3.9 24.9 1.0 OD1 A:ASP81 4.0 23.1 1.0 CB A:CYS158 4.0 28.5 1.0 ND1 A:HIS77 4.1 23.9 1.0 SG A:CYS158 4.1 29.2 1.0 CG A:HIS77 4.1 24.1 1.0 ND1 A:HIS139 4.2 23.6 1.0 CG A:HIS139 4.2 21.8 1.0 CG2 A:THR140 4.3 25.2 1.0 CA A:HIS79 4.6 24.3 1.0 CU A:OPS1161 4.6 34.2 1.0 CG A:ASP81 4.9 25.3 1.0 N A:HIS79 4.9 24.5 1.0

Zinc binding site 2 out of 4 in the Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.6 occ:1.00 NE2 A:HIS197 2.0 31.7 1.0 OD2 A:ASP81 2.2 24.3 1.0 SW A:OPS1161 2.3 24.8 1.0 SG A:CYS158 2.3 29.2 1.0 CE1 A:HIS197 2.9 31.1 1.0 CG A:ASP81 3.0 25.3 1.0 CD2 A:HIS197 3.1 30.7 1.0 OD1 A:ASP81 3.2 23.1 1.0 CV A:OPS1161 3.3 32.3 1.0 CB A:CYS158 3.5 28.5 1.0 CU A:OPS1161 3.6 34.2 1.0 ZN A:ZN301 3.8 23.4 1.0 ND1 A:HIS197 4.1 30.9 1.0 CE1 A:HIS77 4.2 24.5 1.0 CG A:HIS197 4.2 30.3 1.0 CS A:OPS1161 4.2 36.3 1.0 CE A:LYS33 4.3 29.7 1.0 CD A:LYS33 4.3 29.9 1.0 CB A:ASP81 4.4 22.2 1.0 CB A:SER196 4.4 22.2 1.0 SR A:OPS1161 4.4 36.9 1.0 NE2 A:HIS77 4.4 23.1 1.0 NE2 A:HIS139 4.6 23.3 1.0 CA A:CYS158 4.6 27.6 1.0 OG A:SER196 4.9 24.8 1.0

Zinc binding site 3 out of 4 in the Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:32.7 occ:1.00 ND1 B:HIS79 1.9 26.8 1.0 NE2 B:HIS77 2.0 34.0 1.0 NE2 B:HIS139 2.2 35.4 1.0 SW B:OPS1161 2.2 33.8 1.0 CD2 B:HIS77 2.8 34.5 1.0 CG B:HIS79 2.8 29.1 1.0 CE1 B:HIS79 2.9 25.9 1.0 CD2 B:HIS139 3.0 35.3 1.0 CE1 B:HIS77 3.2 35.2 1.0 CE1 B:HIS139 3.2 35.0 1.0 CB B:HIS79 3.2 31.4 1.0 CV B:OPS1161 3.6 38.8 1.0 ZN B:ZN304 3.7 38.1 1.0 CB B:CYS158 3.8 36.4 1.0 NE2 B:HIS79 3.9 27.2 1.0 CD2 B:HIS79 3.9 27.7 1.0 SG B:CYS158 4.0 34.7 1.0 OD1 B:ASP81 4.0 41.1 1.0 CG B:HIS77 4.0 35.4 1.0 ND1 B:HIS77 4.2 35.5 1.0 CG B:HIS139 4.2 35.9 1.0 ND1 B:HIS139 4.3 35.3 1.0 CG2 B:THR140 4.3 43.8 1.0 CU B:OPS1161 4.6 40.9 1.0 CA B:HIS79 4.7 34.3 1.0 OD2 B:ASP81 4.7 37.2 1.0 CG B:ASP81 4.8 38.6 1.0 N B:HIS79 5.0 36.3 1.0

Zinc binding site 4 out of 4 in the Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure-Based Design of the Irreversible Inhibitors to Metallo--Lactamase (Imp-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:38.1 occ:1.00 OD2 B:ASP81 2.0 37.2 1.0 NE2 B:HIS197 2.1 40.9 1.0 SG B:CYS158 2.2 34.7 1.0 SW B:OPS1161 2.4 33.8 1.0 CV B:OPS1161 2.7 38.8 1.0 CE1 B:HIS197 3.0 40.6 1.0 CG B:ASP81 3.0 38.6 1.0 CD2 B:HIS197 3.2 40.3 1.0 CB B:CYS158 3.2 36.4 1.0 OD1 B:ASP81 3.4 41.1 1.0 ZN B:ZN303 3.7 32.7 1.0 ND1 B:HIS197 4.1 40.3 1.0 CU B:OPS1161 4.1 40.9 1.0 CE1 B:HIS77 4.2 35.2 1.0 NE2 B:HIS77 4.2 34.0 1.0 CG B:HIS197 4.3 40.5 1.0 SR B:OPS1161 4.3 45.3 1.0 CE B:LYS33 4.3 35.5 1.0 CB B:SER196 4.3 40.3 1.0 CB B:ASP81 4.3 37.2 1.0 CD B:LYS33 4.3 37.1 1.0 CA B:CYS158 4.4 34.5 1.0 NE2 B:HIS139 4.4 35.4 1.0 CS B:OPS1161 4.5 42.8 1.0 OG B:SER196 4.8 40.9 1.0 CE1 B:HIS139 5.0 35.0 1.0

H.Kurosaki, Y.Yamaguchi, T.Higashi, K.Soga, S.Matsueda, H.Yumoto, S.Misumi, Y.Yamagata, Y.Arakawa, M.Goto. Irreversible Inhibition of Metallo-Beta-Lactamase (Imp-1) By 3-(3-Mercaptopropionylsulfanyl)Propionic Acid Pentafluorophenyl Ester Angew.Chem.Int.Ed.Engl. V. 44 3861 2005.
ISSN: ISSN 1433-7851
PubMed: 15892033
DOI: 10.1002/ANIE.200500835