Zinc in PDB 7dyz: Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-4- Methyl-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-4- Methyl-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dyz was solved by Y.-H.Yan, G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.63 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.864, 45.977, 64.553, 90, 90, 90
R / Rfree (%)	17.5 / 22

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-4- Methyl-1H-Imidazole-2-Carboxylic Acid (pdb code 7dyz). 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)-4- Methyl-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dyz:
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)-4- Methyl-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)-4- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.3 occ:1.00 NE2 A:HIS240 2.1 24.9 1.0 OD2 A:ASP118 2.1 22.0 1.0 O A:HOH428 2.2 24.2 1.0 N13 A:HQR303 2.3 34.1 1.0 O12 A:HQR303 2.3 27.8 1.0 SG A:CYS198 2.4 26.9 1.0 C09 A:HQR303 3.0 33.1 1.0 CE1 A:HIS240 3.0 25.2 1.0 C10 A:HQR303 3.0 31.0 1.0 CD2 A:HIS240 3.2 26.1 1.0 CG A:ASP118 3.2 25.8 1.0 C02 A:HQR303 3.4 30.7 1.0 CB A:CYS198 3.6 25.1 1.0 OD1 A:ASP118 3.6 24.1 1.0 ZN A:ZN302 3.8 29.2 1.0 C01 A:HQR303 3.9 31.2 1.0 NH2 A:ARG119 4.0 25.4 1.0 ND1 A:HIS240 4.2 23.9 1.0 N04 A:HQR303 4.2 30.9 1.0 CE1 A:HIS179 4.3 30.7 1.0 O11 A:HQR303 4.3 30.7 1.0 CG A:HIS240 4.3 26.3 1.0 NE2 A:HIS179 4.3 27.7 1.0 C03 A:HQR303 4.4 33.2 1.0 O A:HOH444 4.5 29.1 1.0 CB A:ASP118 4.5 21.0 1.0 NE A:ARG119 4.5 21.9 1.0 CA A:CYS198 4.7 28.5 1.0 CZ A:ARG119 4.8 26.9 1.0 CE1 A:HIS114 4.8 23.7 1.0 NE2 A:HIS114 4.8 28.5 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)-4- Methyl-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)-4- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.2 occ:1.00 O A:HOH428 2.0 24.2 1.0 ND1 A:HIS116 2.0 24.0 1.0 NE2 A:HIS179 2.0 27.7 1.0 NE2 A:HIS114 2.1 28.5 1.0 CD2 A:HIS179 2.9 24.8 1.0 CE1 A:HIS116 2.9 30.3 1.0 CG A:HIS116 3.0 26.6 1.0 CE1 A:HIS114 3.0 23.7 1.0 CE1 A:HIS179 3.1 30.7 1.0 CD2 A:HIS114 3.1 23.5 1.0 CB A:HIS116 3.4 23.7 1.0 ZN A:ZN301 3.8 31.3 1.0 O A:HOH471 4.0 35.8 0.5 OD1 A:ASP118 4.0 24.1 1.0 NE2 A:HIS116 4.1 28.6 1.0 SG A:CYS198 4.1 26.9 1.0 CG A:HIS179 4.1 28.4 1.0 ND1 A:HIS179 4.1 24.9 1.0 CD2 A:HIS116 4.1 28.6 1.0 CB A:CYS198 4.1 25.1 1.0 ND1 A:HIS114 4.1 24.8 1.0 CG A:HIS114 4.2 25.1 1.0 O A:HOH509 4.2 43.1 1.0 O12 A:HQR303 4.5 27.8 1.0 N13 A:HQR303 4.5 34.1 1.0 OD2 A:ASP118 4.6 22.0 1.0 CG A:ASP118 4.7 25.8 1.0 CA A:HIS116 4.8 23.6 1.0 O A:HOH473 5.0 34.4 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