Zinc in PDB 7dub: Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dub 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.909, 79.454, 67.394, 90, 129.9, 90
R / Rfree (%)	16.5 / 20

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-1H- Imidazole-2-Carboxylic Acid (pdb code 7dub). 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-Isopropyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7dub:
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-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.2 occ:1.00 O A:HOH425 1.9 13.6 1.0 ND1 A:HIS116 2.0 14.6 1.0 NE2 A:HIS179 2.0 6.6 1.0 NE2 A:HIS114 2.0 7.3 1.0 CE1 A:HIS114 2.9 7.5 1.0 CE1 A:HIS116 3.0 9.2 1.0 CD2 A:HIS179 3.0 8.2 1.0 CG A:HIS116 3.0 11.1 1.0 CE1 A:HIS179 3.0 13.9 1.0 CD2 A:HIS114 3.1 8.3 1.0 CB A:HIS116 3.3 10.8 1.0 ZN A:ZN302 3.7 18.7 1.0 O A:HOH554 3.7 20.8 1.0 OD1 A:ASP118 4.0 14.3 1.0 O07 A:HKU304 4.0 15.6 1.0 ND1 A:HIS114 4.1 7.7 1.0 NE2 A:HIS116 4.1 14.3 1.0 ND1 A:HIS179 4.1 8.7 1.0 CD2 A:HIS116 4.1 11.2 1.0 CG A:HIS179 4.1 8.0 1.0 CG A:HIS114 4.2 7.1 1.0 SG A:CYS198 4.2 14.2 1.0 CB A:CYS198 4.3 8.5 1.0 OD2 A:ASP118 4.6 12.0 1.0 CA A:HIS116 4.7 11.8 1.0 CG A:ASP118 4.8 13.0 1.0 C06 A:HKU304 4.8 22.4 1.0 N05 A:HKU304 4.9 12.3 1.0 ND2 A:ASN210 5.0 24.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.7 occ:1.00 N05 A:HKU304 2.0 12.3 1.0 OD2 A:ASP118 2.1 12.0 1.0 O07 A:HKU304 2.2 15.6 1.0 O A:HOH425 2.3 13.6 1.0 SG A:CYS198 2.4 14.2 1.0 NE2 A:HIS240 2.4 17.4 1.0 C04 A:HKU304 2.8 17.4 1.0 C06 A:HKU304 2.9 22.4 1.0 CG A:ASP118 3.1 13.0 1.0 C01 A:HKU304 3.2 15.0 1.0 CE1 A:HIS240 3.2 14.2 1.0 OD1 A:ASP118 3.5 14.3 1.0 CD2 A:HIS240 3.6 13.4 1.0 CB A:CYS198 3.7 8.5 1.0 ZN A:ZN301 3.7 13.2 1.0 N03 A:HKU304 4.0 17.6 1.0 O08 A:HKU304 4.1 19.3 1.0 C02 A:HKU304 4.2 18.6 1.0 O A:HOH554 4.2 20.8 1.0 NE2 A:HIS179 4.3 6.6 1.0 NH2 A:ARG119 4.4 19.1 1.0 CE1 A:HIS179 4.4 13.9 1.0 CB A:ASP118 4.4 16.9 1.0 ND1 A:HIS240 4.4 10.8 1.0 NE A:ARG119 4.5 10.1 1.0 CE1 A:HIS114 4.6 7.5 1.0 O A:HOH558 4.6 16.3 1.0 CG A:HIS240 4.6 12.1 1.0 NE2 A:HIS114 4.7 7.3 1.0 CZ A:ARG119 4.8 10.9 1.0 CA A:CYS198 4.9 7.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.1 occ:1.00 O2 A:FMT306 1.8 28.2 1.0 O2 A:FMT305 2.0 24.7 1.0 ND1 A:HIS251 2.1 7.3 1.0 O1 A:FMT306 2.2 20.8 1.0 C A:FMT306 2.2 8.9 1.0 O1 A:FMT305 2.4 25.4 1.0 C A:FMT305 2.4 13.2 1.0 CE1 A:HIS251 2.9 10.2 1.0 CG A:HIS251 3.2 10.9 1.0 CB A:HIS251 3.6 8.8 1.0 CA A:HIS251 4.0 7.9 1.0 NE2 A:HIS251 4.1 9.8 1.0 CD2 A:HIS251 4.2 9.3 1.0 O A:HIS251 4.4 8.9 1.0 O A:HOH413 4.6 24.6 1.0 C A:HIS251 4.6 10.7 1.0 O A:HOH501 5.0 22.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.8 occ:1.00 ND1 B:HIS116 2.0 15.2 1.0 NE2 B:HIS179 2.0 10.4 1.0 NE2 B:HIS114 2.1 8.3 1.0 O B:HOH416 2.3 15.4 1.0 CE1 B:HIS114 2.9 8.2 1.0 CD2 B:HIS179 2.9 11.1 1.0 CE1 B:HIS116 3.0 9.4 1.0 CG B:HIS116 3.0 11.1 1.0 CE1 B:HIS179 3.0 12.9 1.0 CD2 B:HIS114 3.1 10.4 1.0 CB B:HIS116 3.3 12.2 1.0 O B:HOH449 3.7 21.7 1.0 ZN B:ZN302 3.8 18.3 1.0 OD1 B:ASP118 4.0 14.0 1.0 ND1 B:HIS114 4.1 8.2 1.0 NE2 B:HIS116 4.1 16.1 1.0 CG B:HIS179 4.1 7.5 1.0 ND1 B:HIS179 4.1 9.2 1.0 CD2 B:HIS116 4.1 14.2 1.0 SG B:CYS198 4.2 13.7 1.0 CG B:HIS114 4.2 8.4 1.0 CB B:CYS198 4.2 8.1 1.0 O08 B:HKU304 4.2 11.6 1.0 OD2 B:ASP118 4.6 11.0 1.0 CA B:HIS116 4.7 10.5 1.0 CG B:ASP118 4.8 14.1 1.0 N05 B:HKU304 4.8 11.3 1.0 C06 B:HKU304 4.8 17.7 1.0 O B:HOH617 4.9 28.1 1.0 ND2 B:ASN210 5.0 28.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.3 occ:1.00 O B:HOH416 1.9 15.4 1.0 OD2 B:ASP118 2.1 11.0 1.0 N05 B:HKU304 2.1 11.3 1.0 NE2 B:HIS240 2.2 14.8 1.0 O08 B:HKU304 2.3 11.6 1.0 SG B:CYS198 2.4 13.7 1.0 C04 B:HKU304 2.8 17.5 1.0 C06 B:HKU304 2.9 17.7 1.0 CE1 B:HIS240 3.1 12.4 1.0 CG B:ASP118 3.2 14.1 1.0 C01 B:HKU304 3.2 16.1 1.0 CD2 B:HIS240 3.3 11.6 1.0 OD1 B:ASP118 3.6 14.0 1.0 CB B:CYS198 3.7 8.1 1.0 ZN B:ZN301 3.8 14.8 1.0 N03 B:HKU304 4.0 21.2 1.0 NH2 B:ARG119 4.1 17.9 1.0 O07 B:HKU304 4.2 17.8 1.0 C02 B:HKU304 4.2 17.9 1.0 ND1 B:HIS240 4.3 10.9 1.0 CG B:HIS240 4.4 11.3 1.0 NE B:ARG119 4.4 10.3 1.0 CB B:ASP118 4.4 13.3 1.0 NE2 B:HIS179 4.5 10.4 1.0 O B:HOH449 4.5 21.7 1.0 CE1 B:HIS179 4.5 12.9 1.0 O B:HOH537 4.5 12.5 1.0 CE1 B:HIS114 4.7 8.2 1.0 CZ B:ARG119 4.7 14.3 1.0 CA B:CYS198 4.8 8.0 1.0 NE2 B:HIS114 4.9 8.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Isopropyl-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-Isopropyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:12.5 occ:1.00 O1 B:FMT306 1.8 26.9 1.0 NE2 B:HIS153 2.1 12.8 1.0 O2 B:FMT305 2.2 22.8 1.0 O1 B:FMT305 2.4 24.3 1.0 C B:FMT306 2.4 19.9 1.0 O2 B:FMT306 2.5 25.0 1.0 C B:FMT305 2.6 19.9 1.0 CE1 B:HIS153 2.7 17.6 1.0 CD2 B:HIS153 3.3 17.4 1.0 ND1 B:HIS153 4.0 21.4 1.0 CG B:HIS153 4.3 17.5 1.0 CB B:ALA132 4.3 11.8 1.0 O B:HOH403 4.6 27.9 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