Zinc in PDB 5lcf: Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30), PDB code: 5lcf 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)	24.06 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.460, 65.637, 70.721, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 16.4

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) (pdb code 5lcf). 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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30), PDB code: 5lcf:
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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)


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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:9.8 occ:1.00 O A:HOH712 1.9 7.4 1.0 ND1 A:HIS116 2.0 7.2 1.0 NE2 A:HIS114 2.1 6.9 1.0 NE2 A:HIS179 2.1 8.0 1.0 CE1 A:HIS116 3.0 10.0 1.0 CD2 A:HIS179 3.0 10.1 1.0 CE1 A:HIS114 3.0 7.8 1.0 CG A:HIS116 3.0 7.3 1.0 CD2 A:HIS114 3.1 6.3 1.0 CE1 A:HIS179 3.1 7.0 1.0 CB A:HIS116 3.4 6.9 1.0 ZN A:ZN502 3.5 11.1 1.0 OD1 A:ASP118 3.9 10.3 1.0 CB A:CYS198 4.0 8.3 1.0 C19 A:6TJ504 4.0 17.7 1.0 NE2 A:HIS116 4.1 11.1 1.0 O12 A:6TJ504 4.1 11.6 1.0 ND1 A:HIS114 4.1 7.8 1.0 CD2 A:HIS116 4.2 9.4 1.0 CG A:HIS179 4.2 10.0 1.0 ND1 A:HIS179 4.2 7.0 1.0 CG A:HIS114 4.2 6.7 1.0 SG A:CYS198 4.3 7.3 1.0 C14 A:6TJ504 4.4 11.6 1.0 C18 A:6TJ504 4.5 22.9 1.0 OD2 A:ASP118 4.5 7.8 1.0 C11 A:6TJ504 4.6 10.2 1.0 CG A:ASP118 4.6 7.3 1.0 N10 A:6TJ504 4.7 12.6 1.0 CA A:HIS116 4.8 7.1 1.0

Zinc binding site 2 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)


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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.1 occ:1.00 O A:HOH712 2.0 7.4 1.0 OD2 A:ASP118 2.0 7.8 1.0 NE2 A:HIS240 2.1 7.2 1.0 SG A:CYS198 2.3 7.3 1.0 CG A:ASP118 3.0 7.3 1.0 CE1 A:HIS240 3.0 8.2 1.0 CD2 A:HIS240 3.0 6.2 1.0 OD1 A:ASP118 3.3 10.3 1.0 CB A:CYS198 3.4 8.3 1.0 ZN A:ZN501 3.5 9.8 1.0 NH2 A:ARG119 3.9 15.0 1.0 NE A:ARG119 3.9 10.3 1.0 ND1 A:HIS240 4.1 8.3 1.0 N10 A:6TJ504 4.1 12.6 1.0 CG A:HIS240 4.2 7.5 1.0 CE1 A:HIS114 4.2 7.8 1.0 CZ A:ARG119 4.2 11.0 1.0 C11 A:6TJ504 4.2 10.2 1.0 CB A:ASP118 4.3 11.3 1.0 NE2 A:HIS114 4.3 6.9 1.0 C09 A:6TJ504 4.3 12.4 1.0 C13 A:6TJ504 4.5 8.1 1.0 NE2 A:HIS179 4.5 8.0 1.0 C08 A:6TJ504 4.5 12.4 1.0 C14 A:6TJ504 4.6 11.6 1.0 O12 A:6TJ504 4.6 11.6 1.0 CA A:CYS198 4.6 6.4 1.0 O A:HOH665 4.7 7.9 1.0 CD A:ARG119 4.8 7.8 1.0 CE1 A:HIS179 4.9 7.0 1.0 OG A:SER69 5.0 11.6 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