Zinc in PDB 7dz0: Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dz0 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)	73.19 / 3.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.804, 90.128, 125.43, 90, 90, 90
R / Rfree (%)	19.4 / 29

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid (pdb code 7dz0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dz0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- 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)-5- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.9 occ:1.00 O A:HOH401 1.4 17.8 1.0 NE2 A:HIS179 1.9 14.0 1.0 ND1 A:HIS116 1.9 23.8 1.0 NE2 A:HIS114 2.0 13.6 1.0 CE1 A:HIS179 2.8 19.5 1.0 CE1 A:HIS116 2.8 22.3 1.0 CD2 A:HIS114 2.9 16.3 1.0 CG A:HIS116 3.0 22.6 1.0 CE1 A:HIS114 3.0 15.4 1.0 CD2 A:HIS179 3.0 16.3 1.0 CB A:HIS116 3.4 25.7 1.0 ZN A:ZN302 3.6 24.3 1.0 SG A:CYS198 3.6 12.6 1.0 CB A:CYS198 3.9 11.5 1.0 ND1 A:HIS179 3.9 16.5 1.0 NE2 A:HIS116 4.0 24.1 1.0 OD1 A:ASP118 4.0 23.6 1.0 CD2 A:HIS116 4.1 16.9 1.0 CG A:HIS179 4.1 13.6 1.0 ND1 A:HIS114 4.1 15.7 1.0 CG A:HIS114 4.1 13.8 1.0 O03 A:HQ0303 4.2 16.4 1.0 N05 A:HQ0303 4.2 20.2 1.0 OD2 A:ASP118 4.3 14.0 1.0 CG A:ASP118 4.6 18.9 1.0 C02 A:HQ0303 4.7 18.0 1.0 CA A:HIS116 4.8 23.5 1.0 C04 A:HQ0303 4.8 18.2 1.0 N A:HIS116 4.9 19.9 1.0 O A:HOH404 5.0 16.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- 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)-5- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.3 occ:1.00 N05 A:HQ0303 2.0 20.2 1.0 OD2 A:ASP118 2.0 14.0 1.0 NE2 A:HIS240 2.0 24.5 1.0 SG A:CYS198 2.2 12.6 1.0 O A:HOH401 2.3 17.8 1.0 CE1 A:HIS240 2.4 20.1 1.0 O03 A:HQ0303 2.6 16.4 1.0 C04 A:HQ0303 2.9 18.2 1.0 C06 A:HQ0303 3.0 17.7 1.0 CG A:ASP118 3.1 18.9 1.0 C02 A:HQ0303 3.2 18.0 1.0 CD2 A:HIS240 3.4 22.2 1.0 NH2 A:ARG119 3.4 25.0 1.0 ZN A:ZN301 3.6 16.9 1.0 CB A:CYS198 3.6 11.5 1.0 OD1 A:ASP118 3.7 23.6 1.0 ND1 A:HIS240 3.7 15.1 1.0 N09 A:HQ0303 4.1 16.6 1.0 NE A:ARG119 4.1 17.9 1.0 C07 A:HQ0303 4.1 14.6 1.0 CZ A:ARG119 4.1 17.8 1.0 CG A:HIS240 4.2 15.0 1.0 CB A:ASP118 4.4 16.9 1.0 CE1 A:HIS179 4.4 19.5 1.0 O01 A:HQ0303 4.4 20.1 1.0 NE2 A:HIS179 4.5 14.0 1.0 NE2 A:HIS114 4.6 13.6 1.0 CE1 A:HIS114 4.6 15.4 1.0 CA A:CYS198 4.7 12.4 1.0 OG A:SER69 4.7 15.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- 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 3 of Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:22.1 occ:1.00 ND1 B:HIS116 1.8 20.1 1.0 O B:HOH402 1.8 16.8 1.0 NE2 B:HIS179 1.9 10.9 1.0 NE2 B:HIS114 2.0 15.1 1.0 CD2 B:HIS179 2.6 12.0 1.0 CE1 B:HIS116 2.7 20.7 1.0 CG B:HIS116 2.9 13.8 1.0 CD2 B:HIS114 3.0 12.1 1.0 CE1 B:HIS114 3.0 16.3 1.0 CE1 B:HIS179 3.0 17.9 1.0 CB B:HIS116 3.4 13.9 1.0 ZN B:ZN302 3.6 23.1 1.0 CG B:HIS179 3.8 14.8 1.0 NE2 B:HIS116 3.8 14.0 1.0 SG B:CYS198 3.9 10.4 1.0 CD2 B:HIS116 4.0 12.5 1.0 ND1 B:HIS179 4.0 17.1 1.0 OD1 B:ASP118 4.1 13.8 1.0 ND1 B:HIS114 4.1 9.8 1.0 CG B:HIS114 4.1 10.0 1.0 CB B:CYS198 4.1 10.3 1.0 OD2 B:ASP118 4.3 12.9 1.0 O03 B:HQ0303 4.4 14.1 1.0 CG B:ASP118 4.6 9.8 1.0 N05 B:HQ0303 4.7 12.9 1.0 CA B:HIS116 4.9 19.1 1.0 C02 B:HQ0303 4.9 16.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- 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 4 of Crystal Structure of Vim-2 Mbl in Complex with 1-(But-3-En-1-Yl)-5- Methyl-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:23.1 occ:1.00 NE2 B:HIS240 2.0 15.5 1.0 OD2 B:ASP118 2.0 12.9 1.0 O B:HOH402 2.1 16.8 1.0 N05 B:HQ0303 2.2 12.9 1.0 SG B:CYS198 2.3 10.4 1.0 O03 B:HQ0303 2.3 14.1 1.0 CE1 B:HIS240 2.9 13.2 1.0 C04 B:HQ0303 2.9 15.4 1.0 C02 B:HQ0303 3.0 16.0 1.0 CD2 B:HIS240 3.1 16.0 1.0 CG B:ASP118 3.2 9.8 1.0 C06 B:HQ0303 3.3 14.9 1.0 CB B:CYS198 3.4 10.3 1.0 NH2 B:ARG119 3.6 11.6 1.0 ZN B:ZN301 3.6 22.1 1.0 OD1 B:ASP118 3.7 13.8 1.0 ND1 B:HIS240 4.1 10.9 1.0 N09 B:HQ0303 4.2 22.7 1.0 CG B:HIS240 4.2 10.8 1.0 O01 B:HQ0303 4.2 24.0 1.0 NE2 B:HIS179 4.2 10.9 1.0 NE B:ARG119 4.3 10.0 1.0 CB B:ASP118 4.3 7.0 1.0 C07 B:HQ0303 4.4 13.3 1.0 CZ B:ARG119 4.4 10.9 1.0 CE1 B:HIS179 4.5 17.9 1.0 CA B:CYS198 4.7 10.1 1.0 NE2 B:HIS114 4.7 15.1 1.0 CE1 B:HIS114 4.8 16.3 1.0 CD2 B:HIS179 5.0 12.0 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