Zinc in PDB 7due: Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7due 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)	39.80 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.974, 79.599, 67.251, 90, 129.88, 90
R / Rfree (%)	16.8 / 20.6

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid (pdb code 7due). 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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid, PDB code: 7due:
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 (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.6 occ:1.00 ND1 A:HIS116 1.9 11.0 1.0 NE2 A:HIS179 2.0 14.2 1.0 NE2 A:HIS114 2.1 10.1 1.0 O A:HOH409 2.1 13.5 1.0 CG A:HIS116 2.9 14.4 1.0 CE1 A:HIS116 2.9 15.3 1.0 CE1 A:HIS114 3.0 14.2 1.0 CD2 A:HIS179 3.0 14.5 1.0 CE1 A:HIS179 3.0 13.0 1.0 CD2 A:HIS114 3.1 11.9 1.0 CB A:HIS116 3.2 15.3 1.0 ZN A:ZN302 3.6 19.7 1.0 OD1 A:ASP118 4.0 17.4 1.0 O A:HOH527 4.0 19.0 0.5 NE2 A:HIS116 4.0 17.9 1.0 CD2 A:HIS116 4.0 12.6 1.0 SG A:CYS198 4.0 17.1 1.0 ND1 A:HIS114 4.1 11.1 1.0 ND1 A:HIS179 4.1 13.9 1.0 CG A:HIS179 4.1 9.0 1.0 O07 A:HL3304 4.1 17.0 1.0 CB A:CYS198 4.2 12.4 1.0 CG A:HIS114 4.2 10.0 1.0 OD2 A:ASP118 4.4 17.3 1.0 CG A:ASP118 4.6 17.8 1.0 O A:HOH527 4.7 18.8 0.5 CA A:HIS116 4.7 13.8 1.0 N05 A:HL3304 4.8 16.0 1.0 C06 A:HL3304 4.8 22.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.7 occ:1.00 O A:HOH409 1.9 13.5 1.0 OD2 A:ASP118 2.1 17.3 1.0 N05 A:HL3304 2.2 16.0 1.0 NE2 A:HIS240 2.3 18.7 1.0 O07 A:HL3304 2.3 17.0 1.0 SG A:CYS198 2.5 17.1 1.0 C04 A:HL3304 2.8 21.0 1.0 C06 A:HL3304 2.9 22.5 1.0 CE1 A:HIS240 3.1 15.3 1.0 CG A:ASP118 3.2 17.8 1.0 C01 A:HL3304 3.3 23.9 1.0 CD2 A:HIS240 3.4 11.8 1.0 ZN A:ZN301 3.6 16.6 1.0 OD1 A:ASP118 3.6 17.4 1.0 CB A:CYS198 3.7 12.4 1.0 N03 A:HL3304 4.1 23.5 1.0 NH2 A:ARG119 4.1 21.8 1.0 O A:HOH527 4.1 19.0 0.5 O08 A:HL3304 4.2 20.6 1.0 ND1 A:HIS240 4.3 16.7 1.0 C02 A:HL3304 4.3 19.6 1.0 NE2 A:HIS179 4.4 14.2 1.0 NE A:ARG119 4.4 13.0 1.0 CB A:ASP118 4.4 16.6 1.0 CG A:HIS240 4.5 15.4 1.0 CE1 A:HIS179 4.5 13.0 1.0 O A:HOH461 4.5 18.2 1.0 CE1 A:HIS114 4.7 14.2 1.0 CZ A:ARG119 4.7 17.6 1.0 NE2 A:HIS114 4.8 10.1 1.0 CA A:CYS198 4.9 12.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:19.0 occ:1.00 O1 A:FMT306 1.5 14.5 1.0 ND1 A:HIS251 2.1 14.0 1.0 O2 A:FMT305 2.3 23.4 1.0 O1 A:FMT305 2.4 28.7 1.0 C A:FMT306 2.6 25.7 1.0 C A:FMT305 2.7 24.7 1.0 CE1 A:HIS251 2.9 16.2 1.0 O2 A:FMT306 3.1 29.3 1.0 CG A:HIS251 3.2 14.3 1.0 CB A:HIS251 3.6 12.8 1.0 CA A:HIS251 4.0 13.3 1.0 NE2 A:HIS251 4.1 18.4 1.0 CD2 A:HIS251 4.2 12.8 1.0 O A:HIS251 4.6 11.6 1.0 ND2 A:ASN254 4.7 27.0 1.0 C A:HIS251 4.7 14.0 1.0 CD2 A:LEU203 4.8 16.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.3 occ:1.00 ND1 B:HIS116 1.9 14.1 1.0 O B:HOH471 2.0 13.3 1.0 NE2 B:HIS114 2.1 12.5 1.0 NE2 B:HIS179 2.1 9.7 1.0 CE1 B:HIS116 2.9 17.0 1.0 CG B:HIS116 2.9 13.2 1.0 CE1 B:HIS114 3.0 13.5 1.0 CD2 B:HIS179 3.0 11.7 1.0 CD2 B:HIS114 3.1 10.8 1.0 CE1 B:HIS179 3.1 15.0 1.0 CB B:HIS116 3.3 10.5 1.0 O B:HOH406 3.6 23.6 0.5 ZN B:ZN302 3.7 20.0 1.0 OD1 B:ASP118 4.0 15.8 1.0 NE2 B:HIS116 4.0 16.6 1.0 CD2 B:HIS116 4.0 13.5 1.0 ND1 B:HIS114 4.1 11.0 1.0 SG B:CYS198 4.1 16.1 1.0 ND1 B:HIS179 4.2 10.0 1.0 CG B:HIS114 4.2 9.0 1.0 CG B:HIS179 4.2 10.0 1.0 O08 B:HL3304 4.2 18.6 1.0 CB B:CYS198 4.2 12.4 1.0 O B:HOH406 4.4 24.3 0.5 OD2 B:ASP118 4.6 17.4 1.0 ND2 B:ASN210 4.7 40.0 1.0 CG B:ASP118 4.7 18.1 1.0 CA B:HIS116 4.7 14.6 1.0 N05 B:HL3304 4.8 19.1 1.0 C06 B:HL3304 4.9 25.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.0 occ:1.00 OD2 B:ASP118 2.1 17.4 1.0 N05 B:HL3304 2.2 19.1 1.0 O B:HOH471 2.2 13.3 1.0 NE2 B:HIS240 2.3 17.6 1.0 O08 B:HL3304 2.3 18.6 1.0 SG B:CYS198 2.4 16.1 1.0 C04 B:HL3304 2.8 19.9 1.0 C06 B:HL3304 2.9 25.9 1.0 CE1 B:HIS240 3.1 14.6 1.0 CG B:ASP118 3.2 18.1 1.0 C01 B:HL3304 3.3 20.5 1.0 CD2 B:HIS240 3.4 16.1 1.0 OD1 B:ASP118 3.6 15.8 1.0 CB B:CYS198 3.7 12.4 1.0 ZN B:ZN301 3.7 15.3 1.0 NH2 B:ARG119 4.0 21.5 1.0 N03 B:HL3304 4.0 22.4 1.0 O07 B:HL3304 4.2 23.0 1.0 O B:HOH406 4.2 23.6 0.5 ND1 B:HIS240 4.3 15.4 1.0 C02 B:HL3304 4.3 22.0 1.0 NE2 B:HIS179 4.4 9.7 1.0 O B:HOH454 4.4 18.3 1.0 NE B:ARG119 4.4 12.4 1.0 CG B:HIS240 4.4 16.4 1.0 CE1 B:HIS179 4.5 15.0 1.0 CB B:ASP118 4.5 18.0 1.0 CE1 B:HIS114 4.7 13.5 1.0 CZ B:ARG119 4.7 15.7 1.0 NE2 B:HIS114 4.7 12.5 1.0 CA B:CYS198 4.9 13.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with (R)-1-(Sec-Butyl)-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 (R)-1-(Sec-Butyl)-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:17.3 occ:1.00 O2 B:FMT306 1.9 27.0 1.0 NE2 B:HIS153 2.0 14.6 1.0 O2 B:FMT305 2.1 19.3 1.0 O1 B:FMT305 2.1 23.6 1.0 O1 B:FMT306 2.2 26.3 1.0 C B:FMT306 2.3 18.7 1.0 C B:FMT305 2.4 19.5 1.0 CE1 B:HIS153 2.8 13.6 1.0 CD2 B:HIS153 3.2 13.5 1.0 ND1 B:HIS153 4.0 13.8 1.0 CG B:HIS153 4.2 11.2 1.0 CB B:ALA132 4.3 11.8 1.0 O B:HOH407 4.5 30.8 1.0 CG2 B:THR152 4.9 12.6 1.0 CA B:ALA132 5.0 10.4 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