Zinc in PDB 7duy: Crystal Structure of Vim-2 Mbl in Complex with 1-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7duy 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)	41.13 / 2.00
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.038, 64.223, 91.554, 90, 90, 90
R / Rfree (%)	18.6 / 21.7

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid (pdb code 7duy). 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-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7duy:
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-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-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-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:28.8 occ:1.00 O A:HOH446 2.0 26.6 1.0 NE2 A:HIS179 2.0 24.9 1.0 ND1 A:HIS116 2.0 26.7 1.0 NE2 A:HIS114 2.1 23.6 1.0 CD2 A:HIS179 2.9 21.7 1.0 CE1 A:HIS116 3.0 27.0 1.0 CD2 A:HIS114 3.0 22.5 1.0 CE1 A:HIS179 3.0 25.0 1.0 CG A:HIS116 3.1 24.7 1.0 CE1 A:HIS114 3.1 22.3 1.0 CB A:HIS116 3.4 19.3 1.0 ZN A:ZN302 3.9 26.8 1.0 O A:HOH539 4.0 39.7 1.0 OD1 A:ASP118 4.0 20.5 1.0 SG A:CYS198 4.0 22.9 1.0 CG A:HIS179 4.0 23.9 1.0 ND1 A:HIS179 4.1 22.6 1.0 NE2 A:HIS116 4.1 28.6 1.0 ND1 A:HIS114 4.1 23.4 1.0 CG A:HIS114 4.1 24.5 1.0 CB A:CYS198 4.1 25.1 1.0 CD2 A:HIS116 4.2 20.4 1.0 OD2 A:ASP118 4.5 20.2 1.0 O A:HOH523 4.6 45.2 1.0 N05 A:HLL303 4.6 28.2 1.0 O08 A:HLL303 4.7 29.8 1.0 CG A:ASP118 4.7 22.5 1.0 CA A:HIS116 4.8 20.7 1.0 N A:HIS116 5.0 21.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-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-(2-(1H-1,2,3-Triazol- 1-Yl)Ethyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.8 occ:1.00 NE2 A:HIS240 2.1 18.1 1.0 OD2 A:ASP118 2.1 20.2 1.0 N05 A:HLL303 2.2 28.2 1.0 O08 A:HLL303 2.4 29.8 1.0 O A:HOH446 2.4 26.6 1.0 SG A:CYS198 2.5 22.9 1.0 CE1 A:HIS240 2.9 18.1 1.0 C04 A:HLL303 3.0 23.9 1.0 C06 A:HLL303 3.1 27.9 1.0 CG A:ASP118 3.2 22.5 1.0 CD2 A:HIS240 3.2 23.4 1.0 C01 A:HLL303 3.4 25.1 1.0 OD1 A:ASP118 3.6 20.5 1.0 CB A:CYS198 3.7 25.1 1.0 ZN A:ZN301 3.9 28.8 1.0 NH2 A:ARG119 4.0 19.7 1.0 ND1 A:HIS240 4.1 18.1 1.0 N03 A:HLL303 4.2 29.0 1.0 CG A:HIS240 4.3 21.4 1.0 CE1 A:HIS179 4.3 25.0 1.0 O07 A:HLL303 4.3 30.0 1.0 NE2 A:HIS179 4.4 24.9 1.0 C02 A:HLL303 4.4 27.7 1.0 O A:HOH445 4.4 25.3 1.0 CB A:ASP118 4.5 15.2 1.0 NE A:ARG119 4.5 19.9 1.0 CZ A:ARG119 4.7 22.8 1.0 CA A:CYS198 4.8 28.9 1.0 NE2 A:HIS114 4.8 23.6 1.0 CE1 A:HIS114 4.8 22.3 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