Zinc in PDB 7dv1: Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dv1 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)	39.73 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.946, 79.457, 68.04, 90, 130.56, 90
R / Rfree (%)	18.1 / 23.6

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid (pdb code 7dv1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dv1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.2 occ:1.00 O A:HOH444 2.0 14.2 1.0 ND1 A:HIS116 2.0 16.2 1.0 NE2 A:HIS179 2.1 17.9 1.0 NE2 A:HIS114 2.1 12.8 1.0 CE1 A:HIS116 3.0 20.5 1.0 CE1 A:HIS114 3.0 16.1 1.0 CD2 A:HIS179 3.0 16.7 1.0 CE1 A:HIS179 3.0 17.7 1.0 CG A:HIS116 3.0 12.6 1.0 CD2 A:HIS114 3.1 12.8 1.0 CB A:HIS116 3.4 11.6 1.0 O A:HOH501 3.6 26.9 1.0 ZN A:ZN302 3.7 21.8 1.0 OD1 A:ASP118 4.0 16.7 1.0 NE2 A:HIS116 4.1 20.4 1.0 ND1 A:HIS114 4.1 12.0 1.0 ND1 A:HIS179 4.1 20.3 1.0 CD2 A:HIS116 4.1 13.3 1.0 CG A:HIS179 4.2 16.6 1.0 O15 A:HN9304 4.2 20.1 1.0 CG A:HIS114 4.2 12.3 1.0 SG A:CYS198 4.2 21.1 1.0 CB A:CYS198 4.3 14.8 1.0 OD2 A:ASP118 4.4 13.9 1.0 CG A:ASP118 4.7 16.6 1.0 N01 A:HN9304 4.8 18.1 1.0 CA A:HIS116 4.8 13.3 1.0 C14 A:HN9304 5.0 24.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.8 occ:1.00 O A:HOH444 2.0 14.2 1.0 OD2 A:ASP118 2.1 13.9 1.0 NE2 A:HIS240 2.1 16.8 1.0 O15 A:HN9304 2.2 20.1 1.0 N01 A:HN9304 2.2 18.1 1.0 C02 A:HN9304 2.8 21.6 1.0 C14 A:HN9304 2.9 24.2 1.0 SG A:CYS198 3.0 21.1 1.0 CE1 A:HIS240 3.0 19.2 1.0 CG A:ASP118 3.2 16.6 1.0 CD2 A:HIS240 3.2 17.9 1.0 C05 A:HN9304 3.4 22.3 1.0 OD1 A:ASP118 3.6 16.7 1.0 ZN A:ZN301 3.7 16.2 1.0 NH2 A:ARG119 4.0 18.4 1.0 N03 A:HN9304 4.1 23.6 1.0 O A:HOH501 4.1 26.9 1.0 CB A:CYS198 4.1 14.8 1.0 O16 A:HN9304 4.1 28.8 1.0 ND1 A:HIS240 4.2 17.9 1.0 CG A:HIS240 4.3 19.5 1.0 C04 A:HN9304 4.4 23.3 1.0 CE1 A:HIS179 4.4 17.7 1.0 NE2 A:HIS179 4.4 17.9 1.0 CB A:ASP118 4.5 12.5 1.0 NE A:ARG119 4.5 15.7 1.0 O A:HOH466 4.6 23.6 1.0 CZ A:ARG119 4.7 18.3 1.0 NE2 A:HIS114 4.9 12.8 1.0 CE1 A:HIS114 4.9 16.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:23.3 occ:1.00 O2 A:FMT306 2.0 26.0 1.0 O1 A:FMT306 2.1 27.4 1.0 ND1 A:HIS251 2.1 17.3 1.0 C A:FMT306 2.3 28.2 1.0 O1 A:FMT305 2.3 31.6 1.0 O2 A:FMT305 2.6 31.4 1.0 C A:FMT305 2.8 22.6 1.0 CE1 A:HIS251 3.0 18.8 1.0 CG A:HIS251 3.2 18.6 1.0 CB A:HIS251 3.5 19.4 1.0 CA A:HIS251 3.9 19.0 1.0 NE2 A:HIS251 4.2 18.4 1.0 CD2 A:HIS251 4.3 14.9 1.0 O A:HIS251 4.5 16.7 1.0 C A:HIS251 4.6 18.4 1.0 ND2 A:ASN254 4.7 24.4 1.0 O A:LEU203 4.9 25.0 1.0 CD2 A:LEU203 4.9 18.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.1 occ:1.00 O B:HOH484 1.8 13.9 1.0 ND1 B:HIS116 1.9 13.5 1.0 NE2 B:HIS114 2.1 14.3 1.0 NE2 B:HIS179 2.1 19.8 1.0 CE1 B:HIS116 2.9 16.2 1.0 CD2 B:HIS179 3.0 14.4 1.0 CG B:HIS116 3.0 12.7 1.0 CE1 B:HIS114 3.0 15.9 1.0 CD2 B:HIS114 3.1 13.2 1.0 CE1 B:HIS179 3.1 20.8 1.0 CB B:HIS116 3.4 14.7 1.0 O B:HOH494 3.6 28.1 1.0 ZN B:ZN302 3.7 21.9 1.0 NE2 B:HIS116 4.0 15.9 1.0 OD1 B:ASP118 4.0 17.5 1.0 CD2 B:HIS116 4.1 16.2 1.0 ND1 B:HIS114 4.1 15.8 1.0 CG B:HIS179 4.1 18.2 1.0 CG B:HIS114 4.2 12.9 1.0 ND1 B:HIS179 4.2 17.1 1.0 O16 B:HN9304 4.2 20.8 1.0 SG B:CYS198 4.3 21.7 1.0 CB B:CYS198 4.3 16.0 1.0 ND2 B:ASN210 4.4 36.1 1.0 OD2 B:ASP118 4.6 15.3 1.0 N01 B:HN9304 4.7 17.9 1.0 CG B:ASP118 4.8 17.9 1.0 CA B:HIS116 4.8 17.1 1.0 C14 B:HN9304 5.0 20.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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 5 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:21.9 occ:1.00 NE2 B:HIS240 2.1 15.6 1.0 OD2 B:ASP118 2.1 15.3 1.0 N01 B:HN9304 2.2 17.9 1.0 O B:HOH484 2.2 13.9 1.0 O16 B:HN9304 2.3 20.8 1.0 C02 B:HN9304 2.8 21.4 1.0 CE1 B:HIS240 2.9 19.8 1.0 C14 B:HN9304 2.9 20.2 1.0 SG B:CYS198 2.9 21.7 1.0 CG B:ASP118 3.2 17.9 1.0 CD2 B:HIS240 3.3 14.7 1.0 C05 B:HN9304 3.3 21.1 1.0 OD1 B:ASP118 3.5 17.5 1.0 ZN B:ZN301 3.7 19.1 1.0 NH2 B:ARG119 3.9 18.7 1.0 CB B:CYS198 4.0 16.0 1.0 N03 B:HN9304 4.1 24.7 1.0 ND1 B:HIS240 4.1 19.1 1.0 O B:HOH494 4.1 28.1 1.0 O15 B:HN9304 4.2 25.2 1.0 CG B:HIS240 4.3 21.0 1.0 C04 B:HN9304 4.3 21.4 1.0 NE B:ARG119 4.4 14.3 1.0 O B:HOH443 4.4 22.4 1.0 NE2 B:HIS179 4.4 19.8 1.0 CE1 B:HIS179 4.5 20.8 1.0 CB B:ASP118 4.5 14.6 1.0 CZ B:ARG119 4.6 18.0 1.0 ND2 B:ASN210 4.6 36.1 1.0 NE2 B:HIS114 4.8 14.3 1.0 CE1 B:HIS114 4.8 15.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-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 6 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-Hydroxybenzyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:25.4 occ:1.00 O1 B:FMT306 1.8 33.5 1.0 NE2 B:HIS153 2.0 19.5 1.0 O1 B:FMT305 2.0 24.6 1.0 O2 B:FMT305 2.1 29.4 1.0 C B:FMT305 2.4 14.3 1.0 C B:FMT306 2.6 30.6 1.0 O2 B:FMT306 2.7 34.1 1.0 CE1 B:HIS153 2.9 23.4 1.0 CD2 B:HIS153 3.1 18.2 1.0 ND1 B:HIS153 4.0 22.1 1.0 CG B:HIS153 4.2 18.8 1.0 CB B:ALA132 4.2 17.2 1.0 CG2 B:THR152 4.7 22.7 1.0 CA B:ALA132 5.0 15.8 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