Zinc in PDB 5le1: Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16), PDB code: 5le1 was solved by G.-B.Li, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 1.40
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.171, 60.720, 97.911, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 15.4

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) (pdb code 5le1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16), PDB code: 5le1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:15.5 occ:1.00 O A:HOH730 1.9 12.2 1.0 NE2 A:HIS240 2.1 11.5 1.0 O A:HOH621 2.3 16.5 1.0 OD2 A:ASP118 2.3 14.4 1.0 SG A:CYS198 2.3 12.5 1.0 CD2 A:HIS240 3.0 11.2 1.0 CE1 A:HIS240 3.1 11.2 1.0 CB A:CYS198 3.3 12.8 1.0 CG A:ASP118 3.4 12.3 1.0 ZN A:ZN502 3.4 12.6 1.0 OD1 A:ASP118 3.7 14.0 1.0 NH2 A:ARG119 4.0 15.0 1.0 C04 A:6UW503 4.0 15.8 1.0 C10 A:6UW503 4.1 16.6 1.0 C03 A:6UW503 4.1 15.8 1.0 NE A:ARG119 4.2 11.6 1.0 NE2 A:HIS179 4.2 13.3 1.0 CG A:HIS240 4.2 11.6 1.0 CE1 A:HIS114 4.2 10.9 1.0 ND1 A:HIS240 4.2 11.1 1.0 N12 A:6UW503 4.3 14.7 1.0 C13 A:6UW503 4.3 16.3 1.0 NE2 A:HIS114 4.3 11.4 1.0 O A:HOH753 4.4 14.3 1.0 CE1 A:HIS179 4.4 13.0 1.0 CZ A:ARG119 4.5 13.3 1.0 C05 A:6UW503 4.5 16.7 1.0 O11 A:6UW503 4.5 19.2 1.0 CA A:CYS198 4.6 12.3 1.0 O08 A:6UW503 4.6 21.7 1.0 CB A:ASP118 4.7 11.3 1.0 C02 A:6UW503 4.7 15.3 1.0

Zinc binding site 2 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:12.6 occ:1.00 O A:HOH730 1.9 12.2 1.0 NE2 A:HIS179 2.0 13.3 1.0 ND1 A:HIS116 2.0 13.1 1.0 NE2 A:HIS114 2.1 11.4 1.0 CE1 A:HIS116 3.0 15.0 1.0 CE1 A:HIS114 3.0 10.9 1.0 CD2 A:HIS179 3.0 12.3 1.0 CE1 A:HIS179 3.0 13.0 1.0 CG A:HIS116 3.0 12.4 1.0 CD2 A:HIS114 3.1 10.9 1.0 CB A:HIS116 3.4 12.5 1.0 ZN A:ZN501 3.4 15.5 1.0 O11 A:6UW503 3.8 19.2 1.0 O A:HOH621 3.8 16.5 1.0 OD1 A:ASP118 3.9 14.0 1.0 C14 A:6UW503 4.0 18.4 1.0 NE2 A:HIS116 4.1 15.7 1.0 ND1 A:HIS179 4.1 14.9 1.0 ND1 A:HIS114 4.1 11.3 1.0 CG A:HIS179 4.1 12.0 1.0 CD2 A:HIS116 4.1 13.7 1.0 CB A:CYS198 4.2 12.8 1.0 C10 A:6UW503 4.2 16.6 1.0 CG A:HIS114 4.2 10.7 1.0 N12 A:6UW503 4.3 14.7 1.0 SG A:CYS198 4.3 12.5 1.0 OD2 A:ASP118 4.5 14.4 1.0 CG A:ASP118 4.7 12.3 1.0 CA A:HIS116 4.8 11.4 1.0

G.B.Li, M.I.Abboud, J.Brem, H.Someya, C.T.Lohans, S.Y.Yang, J.Spencer, D.W.Wareham, M.A.Mcdonough, C.J.Schofield. uc(Nmr)-Filtered Virtual Screening Leads to Non-Metal Chelating Metallo-Beta-Lactamase Inhibitors. Chem Sci V. 8 928 2017.
ISSN: ISSN 2041-6520
PubMed: 28451231
DOI: 10.1039/C6SC04524C