Zinc in PDB 8hy2: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8hy2 was solved by Y.-H.Yan, K.-R.Zhu, G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.39 / 2.00
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.248, 64.446, 91.034, 90, 90, 90
R / Rfree (%)	15.3 / 20.6

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid (pdb code 8hy2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8hy2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-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 B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.5 occ:1.00 O A:HOH523 1.9 25.6 1.0 ND1 A:HIS116 2.0 24.4 1.0 NE2 A:HIS179 2.0 28.7 1.0 NE2 A:HIS114 2.1 23.8 1.0 CE1 A:HIS116 2.9 31.3 1.0 CD2 A:HIS179 3.0 21.8 1.0 CE1 A:HIS179 3.0 28.9 1.0 CG A:HIS116 3.0 24.9 1.0 CE1 A:HIS114 3.1 19.4 1.0 CD2 A:HIS114 3.1 23.3 1.0 CB A:HIS116 3.4 21.6 1.0 ZN A:ZN302 3.6 28.1 1.0 OD1 A:ASP118 3.9 23.7 1.0 SG A:CYS198 4.0 24.3 1.0 NE2 A:HIS116 4.1 28.4 1.0 ND1 A:HIS179 4.1 26.7 1.0 O A:HOH515 4.1 44.3 1.0 CG A:HIS179 4.1 23.4 1.0 CD2 A:HIS116 4.1 25.6 1.0 CB A:CYS198 4.1 25.6 1.0 ND1 A:HIS114 4.2 23.2 1.0 CG A:HIS114 4.2 21.1 1.0 O01 A:5ZX303 4.3 26.5 1.0 O1 A:FMT304 4.3 55.5 1.0 OD2 A:ASP118 4.5 22.6 1.0 CG A:ASP118 4.7 24.8 1.0 N17 A:5ZX303 4.8 34.5 1.0 CA A:HIS116 4.8 17.3 1.0 O2 A:FMT304 4.8 47.0 1.0 C A:FMT304 4.9 52.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-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 B1 Vim-2 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.1 occ:1.00 NE2 A:HIS240 2.1 22.2 1.0 O A:HOH523 2.2 25.6 1.0 OD2 A:ASP118 2.2 22.6 1.0 O01 A:5ZX303 2.4 26.5 1.0 N17 A:5ZX303 2.4 34.5 1.0 SG A:CYS198 2.5 24.3 1.0 CE1 A:HIS240 3.1 22.6 1.0 C04 A:5ZX303 3.1 36.5 1.0 C02 A:5ZX303 3.1 33.4 1.0 CD2 A:HIS240 3.2 24.2 1.0 CG A:ASP118 3.2 24.8 1.0 C15 A:5ZX303 3.3 41.2 1.0 OD1 A:ASP118 3.6 23.7 1.0 ZN A:ZN301 3.6 25.5 1.0 CB A:CYS198 3.6 25.6 1.0 N16 A:5ZX303 3.7 35.4 1.0 NH2 A:ARG119 4.0 23.9 1.0 ND1 A:HIS240 4.2 21.4 1.0 NE2 A:HIS179 4.2 28.7 1.0 CE1 A:HIS179 4.3 28.9 1.0 CG A:HIS240 4.3 27.7 1.0 O03 A:5ZX303 4.3 35.5 1.0 C05 A:5ZX303 4.4 45.9 1.0 O A:HOH475 4.5 26.6 1.0 CB A:ASP118 4.5 18.8 1.0 NE A:ARG119 4.5 20.7 1.0 NE2 A:HIS114 4.7 23.8 1.0 CE1 A:HIS114 4.7 19.4 1.0 S14 A:5ZX303 4.7 33.9 1.0 O A:HOH515 4.7 44.3 1.0 CZ A:ARG119 4.8 19.9 1.0 CA A:CYS198 4.8 25.0 1.0 O1 A:FMT304 5.0 55.5 1.0

Y.H.Yan, T.T.Zhang, R.Li, S.Y.Wang, L.L.Wei, X.Y.Wang, K.R.Zhu, S.R.Li, G.Q.Liang, Z.B.Yang, L.L.Yang, S.Qin, G.B.Li. Discovery of 2-Aminothiazole-4-Carboxylic Acids As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors By Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. V. 66 13746 2023.
ISSN: ISSN 0022-2623
PubMed: 37791640
DOI: 10.1021/ACS.JMEDCHEM.3C01189