Zinc in PDB 7du1: Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-1H-Imidazole- 2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-1H-Imidazole- 2-Carboxylic Acid, PDB code: 7du1 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)	39.79 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.302, 79.58, 67.842, 90, 130.91, 90
R / Rfree (%)	21.4 / 26

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-1H-Imidazole- 2-Carboxylic Acid (pdb code 7du1). 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-Propyl-1H-Imidazole- 2-Carboxylic Acid, PDB code: 7du1:
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-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.3 occ:1.00 O1 A:FMT304 2.0 14.8 1.0 O2 A:FMT303 2.0 15.3 1.0 ND1 A:HIS251 2.1 13.4 1.0 O1 A:FMT303 2.3 19.8 1.0 C A:FMT303 2.4 21.4 1.0 C A:FMT304 2.9 17.5 1.0 CE1 A:HIS251 3.0 16.6 1.0 CG A:HIS251 3.1 16.8 1.0 O2 A:FMT304 3.4 22.8 1.0 CB A:HIS251 3.5 13.5 1.0 CA A:HIS251 3.8 13.8 1.0 NE2 A:HIS251 4.2 15.8 1.0 CD2 A:HIS251 4.2 14.1 1.0 CD2 A:LEU203 4.4 17.5 1.0 ND2 A:ASN254 4.4 18.2 1.0 O A:HIS251 4.6 16.4 1.0 C A:HIS251 4.7 15.8 1.0 N A:HIS251 4.9 13.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:15.2 occ:1.00 ND1 A:HIS116 2.0 11.2 1.0 O A:HOH420 2.1 18.4 1.0 NE2 A:HIS179 2.1 15.3 1.0 NE2 A:HIS114 2.1 10.8 1.0 CE1 A:HIS116 3.0 15.8 1.0 CD2 A:HIS179 3.0 11.0 1.0 CE1 A:HIS114 3.0 17.6 1.0 CG A:HIS116 3.0 15.8 1.0 CD2 A:HIS114 3.1 14.7 1.0 CE1 A:HIS179 3.1 15.6 1.0 CB A:HIS116 3.4 15.6 1.0 ZN A:ZN306 3.7 18.2 1.0 O08 A:HKR302 3.8 21.9 1.0 OD1 A:ASP118 4.1 13.3 1.0 NE2 A:HIS116 4.1 16.5 1.0 ND1 A:HIS114 4.1 11.7 1.0 CD2 A:HIS116 4.2 17.3 1.0 CG A:HIS179 4.2 14.0 1.0 CG A:HIS114 4.2 11.9 1.0 ND1 A:HIS179 4.2 15.1 1.0 SG A:CYS198 4.3 19.7 1.0 CB A:CYS198 4.3 11.6 1.0 OD2 A:ASP118 4.4 19.2 1.0 CG A:ASP118 4.7 17.0 1.0 C06 A:HKR302 4.7 23.2 1.0 CA A:HIS116 4.8 13.6 1.0 N05 A:HKR302 4.9 21.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:18.2 occ:1.00 OD2 A:ASP118 2.1 19.2 1.0 O A:HOH420 2.1 18.4 1.0 NE2 A:HIS240 2.1 19.2 1.0 O08 A:HKR302 2.2 21.9 1.0 N05 A:HKR302 2.2 21.2 1.0 C04 A:HKR302 2.8 25.1 1.0 C06 A:HKR302 2.8 23.2 1.0 CE1 A:HIS240 3.0 20.6 1.0 SG A:CYS198 3.1 19.7 1.0 CD2 A:HIS240 3.2 22.9 1.0 CG A:ASP118 3.2 17.0 1.0 C01 A:HKR302 3.3 24.5 1.0 ZN A:ZN305 3.7 15.2 1.0 OD1 A:ASP118 3.7 13.3 1.0 NH2 A:ARG119 3.9 21.6 1.0 N03 A:HKR302 4.0 27.7 1.0 O07 A:HKR302 4.1 27.5 1.0 ND1 A:HIS240 4.2 17.6 1.0 CG A:HIS240 4.3 20.7 1.0 C02 A:HKR302 4.3 24.0 1.0 CB A:CYS198 4.4 11.6 1.0 CB A:ASP118 4.4 15.8 1.0 NE2 A:HIS179 4.4 15.3 1.0 NE A:ARG119 4.5 13.7 1.0 CE1 A:HIS179 4.5 15.6 1.0 CZ A:ARG119 4.7 18.9 1.0 O A:HOH446 4.7 17.6 1.0 NE2 A:HIS114 4.8 10.8 1.0 CE1 A:HIS114 4.9 17.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.0 occ:1.00 O B:HOH428 1.9 16.3 1.0 ND1 B:HIS116 2.0 15.4 1.0 NE2 B:HIS179 2.1 15.3 1.0 NE2 B:HIS114 2.1 15.5 1.0 CE1 B:HIS116 2.9 15.6 1.0 CD2 B:HIS179 2.9 12.2 1.0 CG B:HIS116 3.0 17.9 1.0 CE1 B:HIS114 3.1 15.4 1.0 CD2 B:HIS114 3.1 18.4 1.0 CE1 B:HIS179 3.2 18.4 1.0 CB B:HIS116 3.4 16.4 1.0 ZN B:ZN302 3.7 22.9 1.0 OD1 B:ASP118 4.0 17.1 1.0 NE2 B:HIS116 4.1 19.9 1.0 SG B:CYS198 4.1 20.9 1.0 CD2 B:HIS116 4.1 20.6 1.0 CG B:HIS179 4.1 10.4 1.0 O07 B:HKR304 4.1 27.4 1.0 ND1 B:HIS114 4.2 15.0 1.0 CG B:HIS114 4.2 14.8 1.0 ND1 B:HIS179 4.2 12.3 1.0 CB B:CYS198 4.3 12.1 1.0 OD2 B:ASP118 4.3 19.7 1.0 CG B:ASP118 4.6 19.9 1.0 CA B:HIS116 4.8 17.4 1.0 C06 B:HKR304 4.8 26.9 1.0 N05 B:HKR304 4.9 25.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.9 occ:1.00 OD2 B:ASP118 2.1 19.7 1.0 O B:HOH428 2.2 16.3 1.0 NE2 B:HIS240 2.2 18.8 1.0 O07 B:HKR304 2.3 27.4 1.0 N05 B:HKR304 2.4 25.2 1.0 SG B:CYS198 2.7 20.9 1.0 C04 B:HKR304 2.8 28.9 1.0 C06 B:HKR304 2.9 26.9 1.0 CE1 B:HIS240 3.0 21.0 1.0 CG B:ASP118 3.2 19.9 1.0 CD2 B:HIS240 3.3 20.0 1.0 C01 B:HKR304 3.5 31.3 1.0 ZN B:ZN301 3.7 19.0 1.0 OD1 B:ASP118 3.7 17.1 1.0 N03 B:HKR304 4.0 29.7 1.0 CB B:CYS198 4.1 12.1 1.0 O08 B:HKR304 4.2 32.0 1.0 NH2 B:ARG119 4.2 20.9 1.0 ND1 B:HIS240 4.2 14.5 1.0 C02 B:HKR304 4.3 30.7 1.0 NE2 B:HIS179 4.4 15.3 1.0 CG B:HIS240 4.4 17.9 1.0 CB B:ASP118 4.4 23.2 1.0 NE B:ARG119 4.5 16.4 1.0 CE1 B:HIS179 4.6 18.4 1.0 NE2 B:HIS114 4.7 15.5 1.0 O B:HOH401 4.8 22.2 1.0 CE1 B:HIS114 4.8 15.4 1.0 CZ B:ARG119 4.8 14.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Propyl-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-Propyl-1H-Imidazole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:18.9 occ:1.00 O2 B:FMT306 2.1 16.5 1.0 ND1 B:HIS251 2.1 13.1 1.0 O1 B:FMT305 2.1 19.3 1.0 O1 B:FMT306 2.5 24.4 1.0 C B:FMT305 2.5 16.9 1.0 C B:FMT306 2.6 19.3 1.0 O2 B:FMT305 2.8 27.6 1.0 CE1 B:HIS251 3.0 15.4 1.0 CG B:HIS251 3.2 14.8 1.0 CB B:HIS251 3.5 14.8 1.0 CA B:HIS251 3.8 13.1 1.0 NE2 B:HIS251 4.2 14.0 1.0 CD2 B:HIS251 4.3 13.4 1.0 ND2 B:ASN254 4.4 14.2 1.0 O B:HIS251 4.5 17.0 1.0 C B:HIS251 4.6 13.2 1.0 CD2 B:LEU203 4.8 14.5 1.0 N B:HIS251 4.9 13.5 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