Zinc in PDB 7dv0: Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dv0 was solved by G.-B.Li, Y.-H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.96 / 1.60
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.148, 64.535, 90.995, 90, 90, 90
R / Rfree (%)	18.1 / 21.2

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid (pdb code 7dv0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dv0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.5 occ:1.00 O A:HOH424 1.9 14.8 1.0 ND1 A:HIS116 2.0 14.7 1.0 NE2 A:HIS179 2.0 11.2 1.0 NE2 A:HIS114 2.1 11.8 1.0 CD2 A:HIS179 2.9 14.7 1.0 CE1 A:HIS116 2.9 14.7 1.0 CG A:HIS116 3.0 10.3 1.0 CE1 A:HIS114 3.0 12.2 1.0 CE1 A:HIS179 3.0 17.1 1.0 CD2 A:HIS114 3.1 11.9 1.0 CB A:HIS116 3.3 9.2 1.0 ZN A:ZN302 3.7 14.7 1.0 O A:HOH573 3.8 33.7 1.0 OD1 A:ASP118 3.9 12.4 1.0 O A:HOH572 4.0 28.5 1.0 NE2 A:HIS116 4.0 15.8 1.0 SG A:CYS198 4.1 16.9 1.0 CG A:HIS179 4.1 13.8 1.0 CD2 A:HIS116 4.1 17.4 1.0 ND1 A:HIS114 4.1 11.7 1.0 ND1 A:HIS179 4.1 15.1 1.0 CB A:CYS198 4.1 15.1 1.0 CG A:HIS114 4.2 10.4 1.0 O08 A:HML303 4.3 12.8 1.0 OD2 A:ASP118 4.5 11.2 1.0 CG A:ASP118 4.6 13.3 1.0 N05 A:HML303 4.7 17.8 1.0 CA A:HIS116 4.8 11.1 1.0 O A:HOH503 4.9 24.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.7 occ:1.00 OD2 A:ASP118 2.1 11.2 1.0 NE2 A:HIS240 2.1 12.6 1.0 O08 A:HML303 2.2 12.8 1.0 N05 A:HML303 2.2 17.8 1.0 O A:HOH424 2.3 14.8 1.0 SG A:CYS198 2.6 16.9 1.0 C04 A:HML303 2.9 16.7 1.0 C06 A:HML303 2.9 17.5 1.0 CE1 A:HIS240 3.1 11.1 1.0 CD2 A:HIS240 3.1 9.8 1.0 CG A:ASP118 3.2 13.3 1.0 C01 A:HML303 3.4 17.9 1.0 OD1 A:ASP118 3.6 12.4 1.0 ZN A:ZN301 3.7 15.5 1.0 CB A:CYS198 3.7 15.1 1.0 NH2 A:ARG119 4.0 14.0 1.0 N03 A:HML303 4.1 18.2 1.0 O07 A:HML303 4.1 18.8 1.0 ND1 A:HIS240 4.2 9.2 1.0 CG A:HIS240 4.3 10.8 1.0 CE1 A:HIS179 4.3 17.1 1.0 C02 A:HML303 4.3 17.4 1.0 NE2 A:HIS179 4.4 11.2 1.0 O A:HOH444 4.4 15.1 1.0 O A:HOH573 4.4 33.7 1.0 CB A:ASP118 4.5 10.4 1.0 NE A:ARG119 4.5 10.5 1.0 O A:HOH572 4.6 28.5 1.0 CZ A:ARG119 4.7 12.9 1.0 CE1 A:HIS114 4.8 12.2 1.0 NE2 A:HIS114 4.8 11.8 1.0 CA A:CYS198 4.9 12.4 1.0

Y.H.Yan, W.Li, W.Chen, C.Li, K.R.Zhu, J.Deng, Q.Q.Dai, L.L.Yang, Z.Wang, G.B.Li. Structure-Guided Optimization of 1H-Imidazole-2-Carboxylic Acid Derivatives Affording Potent Vim-Type Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 228 13965 2022.
ISSN: ISSN 0223-5234
PubMed: 34763944
DOI: 10.1016/J.EJMECH.2021.113965