Zinc in PDB 7dz1: Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dz1 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)	55.65 / 2.71
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.016, 79.112, 67.763, 90, 130.53, 90
R / Rfree (%)	17.2 / 26.1

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid (pdb code 7dz1). 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-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dz1:
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-Benzyl-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-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.9 occ:1.00 ND1 A:HIS116 1.9 11.8 1.0 NE2 A:HIS114 2.0 9.5 1.0 NE2 A:HIS179 2.0 24.3 1.0 O A:HOH403 2.1 15.3 1.0 CE1 A:HIS179 2.8 23.4 1.0 CG A:HIS116 2.9 6.6 1.0 CE1 A:HIS116 2.9 11.3 1.0 CE1 A:HIS114 3.0 5.3 1.0 CD2 A:HIS114 3.0 8.4 1.0 CD2 A:HIS179 3.1 22.6 1.0 CB A:HIS116 3.2 7.2 1.0 ZN A:ZN302 3.7 21.9 1.0 OD1 A:ASP118 3.8 9.8 1.0 NE2 A:HIS116 3.9 9.3 1.0 CD2 A:HIS116 4.0 5.1 1.0 ND1 A:HIS179 4.0 14.5 1.0 O A:HOH412 4.0 22.7 1.0 SG A:CYS198 4.0 18.9 1.0 ND1 A:HIS114 4.1 9.4 1.0 CG A:HIS114 4.1 4.7 1.0 CG A:HIS179 4.2 20.0 1.0 CB A:CYS198 4.2 12.9 1.0 OD2 A:ASP118 4.2 6.5 1.0 N05 A:HQ3303 4.3 16.8 1.0 O01 A:HQ3303 4.4 9.8 1.0 CG A:ASP118 4.5 12.3 1.0 CA A:HIS116 4.7 3.9 1.0 C02 A:HQ3303 4.9 17.9 1.0 C04 A:HQ3303 4.9 19.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-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-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.9 occ:1.00 N05 A:HQ3303 2.0 16.8 1.0 OD2 A:ASP118 2.0 6.5 1.0 NE2 A:HIS240 2.0 11.4 1.0 O A:HOH403 2.1 15.3 1.0 SG A:CYS198 2.3 18.9 1.0 O01 A:HQ3303 2.4 9.8 1.0 C04 A:HQ3303 2.8 19.8 1.0 C02 A:HQ3303 2.9 17.9 1.0 CE1 A:HIS240 3.0 15.3 1.0 CD2 A:HIS240 3.0 13.0 1.0 C06 A:HQ3303 3.1 9.5 1.0 CG A:ASP118 3.2 12.3 1.0 CB A:CYS198 3.5 12.9 1.0 ZN A:ZN301 3.7 21.9 1.0 OD1 A:ASP118 3.7 9.8 1.0 N09 A:HQ3303 3.9 10.5 1.0 ND1 A:HIS240 4.1 16.7 1.0 NH2 A:ARG119 4.1 10.6 1.0 C07 A:HQ3303 4.1 5.4 1.0 CG A:HIS240 4.1 16.7 1.0 O03 A:HQ3303 4.2 16.5 1.0 NE A:ARG119 4.3 7.7 1.0 CB A:ASP118 4.4 10.1 1.0 CE1 A:HIS114 4.5 5.3 1.0 NE2 A:HIS179 4.6 24.3 1.0 CE1 A:HIS179 4.6 23.4 1.0 NE2 A:HIS114 4.6 9.5 1.0 CA A:CYS198 4.6 12.6 1.0 CZ A:ARG119 4.7 10.7 1.0 O A:HOH412 4.9 22.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-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-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.6 occ:1.00 ND1 B:HIS116 1.9 9.8 1.0 O B:HOH402 1.9 16.6 1.0 NE2 B:HIS179 2.0 8.3 1.0 NE2 B:HIS114 2.1 9.2 1.0 CE1 B:HIS179 2.8 3.0 1.0 CE1 B:HIS116 2.9 8.0 1.0 CE1 B:HIS114 2.9 12.1 1.0 CG B:HIS116 3.0 8.0 1.0 CD2 B:HIS114 3.1 7.4 1.0 CD2 B:HIS179 3.2 6.2 1.0 CB B:HIS116 3.3 4.6 1.0 O B:HOH410 3.5 21.5 1.0 ZN B:ZN302 3.6 15.0 1.0 O01 B:HQ3303 3.7 20.3 1.0 OD1 B:ASP118 3.8 7.5 1.0 NE2 B:HIS116 4.0 9.6 1.0 ND1 B:HIS179 4.0 4.0 1.0 CD2 B:HIS116 4.1 9.8 1.0 ND1 B:HIS114 4.1 3.6 1.0 CG B:HIS114 4.2 8.3 1.0 SG B:CYS198 4.2 10.6 1.0 CG B:HIS179 4.2 5.1 1.0 CB B:CYS198 4.3 15.2 1.0 OD2 B:ASP118 4.4 8.7 1.0 C02 B:HQ3303 4.5 18.9 1.0 CG B:ASP118 4.5 14.9 1.0 N05 B:HQ3303 4.5 19.8 1.0 CA B:HIS116 4.8 3.3 1.0 C04 B:HQ3303 4.9 16.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Benzyl-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-Benzyl-5-Methyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:15.0 occ:1.00 O01 B:HQ3303 1.5 20.3 1.0 O B:HOH402 1.9 16.6 1.0 OD2 B:ASP118 1.9 8.7 1.0 NE2 B:HIS240 2.2 16.1 1.0 N05 B:HQ3303 2.2 19.8 1.0 SG B:CYS198 2.4 10.6 1.0 C02 B:HQ3303 2.5 18.9 1.0 C04 B:HQ3303 2.7 16.7 1.0 CE1 B:HIS240 2.9 17.8 1.0 CG B:ASP118 3.0 14.9 1.0 CD2 B:HIS240 3.3 9.2 1.0 C06 B:HQ3303 3.4 9.8 1.0 OD1 B:ASP118 3.4 7.5 1.0 CB B:CYS198 3.6 15.2 1.0 ZN B:ZN301 3.6 21.6 1.0 O03 B:HQ3303 3.6 18.4 1.0 N09 B:HQ3303 4.0 17.2 1.0 NH2 B:ARG119 4.1 22.4 1.0 ND1 B:HIS240 4.1 12.2 1.0 CB B:ASP118 4.3 7.6 1.0 C07 B:HQ3303 4.3 15.1 1.0 CG B:HIS240 4.3 7.0 1.0 NE2 B:HIS179 4.4 8.3 1.0 O B:HOH410 4.4 21.5 1.0 CE1 B:HIS114 4.5 12.1 1.0 CE1 B:HIS179 4.5 3.0 1.0 NE B:ARG119 4.5 15.6 1.0 NE2 B:HIS114 4.6 9.2 1.0 CZ B:ARG119 4.7 18.0 1.0 CA B:CYS198 4.8 6.4 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