Zinc in PDB 7dux: Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dux 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)	41.19 / 1.98
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.134, 64.865, 91.476, 90, 90, 90
R / Rfree (%)	17.7 / 22

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid (pdb code 7dux). 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-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dux:
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-(But-3-En-1-Yl)-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-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.0 occ:1.00 O A:HOH445 1.9 20.9 1.0 ND1 A:HIS116 2.0 22.6 1.0 NE2 A:HIS179 2.0 24.0 1.0 NE2 A:HIS114 2.1 22.8 1.0 CE1 A:HIS116 2.9 26.9 1.0 CD2 A:HIS179 3.0 21.3 1.0 CE1 A:HIS179 3.0 27.0 1.0 CE1 A:HIS114 3.0 22.1 1.0 CG A:HIS116 3.0 25.4 1.0 CD2 A:HIS114 3.1 20.4 1.0 CB A:HIS116 3.4 21.1 1.0 ZN A:ZN302 3.6 30.7 1.0 O A:HOH529 3.7 27.3 0.5 OD1 A:ASP118 4.0 20.3 1.0 SG A:CYS198 4.0 23.6 1.0 NE2 A:HIS116 4.1 24.6 1.0 ND1 A:HIS179 4.1 24.6 1.0 CB A:CYS198 4.1 22.9 1.0 CG A:HIS179 4.1 25.1 1.0 ND1 A:HIS114 4.1 21.0 1.0 CD2 A:HIS116 4.2 22.0 1.0 CG A:HIS114 4.2 20.2 1.0 O07 A:HLF303 4.4 25.2 1.0 O A:HOH529 4.5 26.4 0.5 OD2 A:ASP118 4.5 17.7 1.0 CG A:ASP118 4.7 22.4 1.0 N05 A:HLF303 4.7 29.5 1.0 CA A:HIS116 4.8 20.4 1.0 C06 A:HLF303 4.9 26.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-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-(But-3-En-1-Yl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.7 occ:1.00 O A:HOH445 2.1 20.9 1.0 OD2 A:ASP118 2.1 17.7 1.0 NE2 A:HIS240 2.2 18.8 1.0 N05 A:HLF303 2.3 29.5 1.0 O07 A:HLF303 2.3 25.2 1.0 SG A:CYS198 2.5 23.6 1.0 C04 A:HLF303 3.0 26.8 1.0 CE1 A:HIS240 3.0 21.4 1.0 C06 A:HLF303 3.0 26.8 1.0 CG A:ASP118 3.2 22.4 1.0 CD2 A:HIS240 3.3 21.6 1.0 C01 A:HLF303 3.5 28.9 1.0 OD1 A:ASP118 3.5 20.3 1.0 ZN A:ZN301 3.6 24.0 1.0 CB A:CYS198 3.7 22.9 1.0 NH2 A:ARG119 3.9 21.1 1.0 ND1 A:HIS240 4.2 17.3 1.0 N03 A:HLF303 4.2 29.7 1.0 O08 A:HLF303 4.3 28.7 1.0 CG A:HIS240 4.3 22.6 1.0 CE1 A:HIS179 4.4 27.0 1.0 NE2 A:HIS179 4.4 24.0 1.0 NE A:ARG119 4.5 20.7 1.0 CB A:ASP118 4.5 15.6 1.0 C02 A:HLF303 4.5 31.0 1.0 O A:HOH467 4.5 26.6 1.0 O A:HOH529 4.6 27.3 0.5 CZ A:ARG119 4.7 21.3 1.0 CE1 A:HIS114 4.7 22.1 1.0 NE2 A:HIS114 4.8 22.8 1.0 CA A:CYS198 4.9 27.0 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