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

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-Carboxylic Acid, PDB code: 8hxo 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)	40.97 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.452, 45.938, 90.576, 90, 90.17, 90
R / Rfree (%)	16.6 / 21.7

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-Carboxylic Acid (pdb code 8hxo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-Carboxylic Acid, PDB code: 8hxo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-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- Isobutylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.2 occ:1.00 ND1 A:HIS116 1.9 12.2 1.0 O A:HOH506 2.0 15.4 1.0 NE2 A:HIS179 2.0 12.2 1.0 NE2 A:HIS114 2.1 14.9 1.0 CE1 A:HIS179 2.9 17.4 1.0 CE1 A:HIS116 2.9 22.9 1.0 CG A:HIS116 3.0 14.2 1.0 CE1 A:HIS114 3.1 12.6 1.0 CD2 A:HIS179 3.1 12.7 1.0 CD2 A:HIS114 3.1 16.1 1.0 CB A:HIS116 3.4 15.8 1.0 ZN A:ZN302 3.6 21.8 1.0 ND2 A:ASN210 3.9 37.2 1.0 OD1 A:ASP118 3.9 15.7 1.0 NE2 A:HIS116 4.0 15.5 1.0 ND1 A:HIS179 4.0 14.1 1.0 CD2 A:HIS116 4.1 18.2 1.0 SG A:CYS198 4.1 17.4 1.0 CB A:CYS198 4.2 18.4 1.0 CG A:HIS179 4.2 13.8 1.0 ND1 A:HIS114 4.2 15.0 1.0 CG A:HIS114 4.3 12.6 1.0 O07 A:5IY303 4.3 19.2 1.0 OD2 A:ASP118 4.6 13.1 1.0 CG A:ASP118 4.7 17.2 1.0 N03 A:5IY303 4.8 24.7 1.0 CA A:HIS116 4.8 13.5 1.0 C05 A:5IY303 4.9 19.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-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- Isobutylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.8 occ:1.00 O A:HOH506 1.9 15.4 1.0 NE2 A:HIS240 2.2 17.1 1.0 OD2 A:ASP118 2.2 13.1 1.0 N03 A:5IY303 2.3 24.7 1.0 O07 A:5IY303 2.3 19.2 1.0 SG A:CYS198 2.5 17.4 1.0 C05 A:5IY303 3.0 19.7 1.0 C04 A:5IY303 3.0 22.0 1.0 CE1 A:HIS240 3.1 14.8 1.0 CD2 A:HIS240 3.2 19.3 1.0 CG A:ASP118 3.2 17.2 1.0 C02 A:5IY303 3.3 28.9 1.0 OD1 A:ASP118 3.6 15.7 1.0 ZN A:ZN301 3.6 17.2 1.0 CB A:CYS198 3.6 18.4 1.0 N01 A:5IY303 3.7 26.2 1.0 NH2 A:ARG119 4.1 18.8 1.0 ND1 A:HIS240 4.2 13.3 1.0 CE1 A:HIS179 4.2 17.4 1.0 O06 A:5IY303 4.2 20.8 1.0 CG A:HIS240 4.3 19.2 1.0 NE2 A:HIS179 4.3 12.2 1.0 C08 A:5IY303 4.4 21.8 1.0 O A:HOH425 4.5 18.6 1.0 CB A:ASP118 4.5 11.9 1.0 NE A:ARG119 4.5 13.7 1.0 ND2 A:ASN210 4.7 37.2 1.0 CE1 A:HIS114 4.7 12.6 1.0 S13 A:5IY303 4.7 24.6 1.0 NE2 A:HIS114 4.7 14.9 1.0 CZ A:ARG119 4.8 11.0 1.0 CA A:CYS198 4.8 20.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-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 B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.6 occ:1.00 ND1 B:HIS116 2.0 13.4 1.0 O B:HOH500 2.0 12.9 1.0 NE2 B:HIS179 2.0 13.6 1.0 NE2 B:HIS114 2.1 14.7 1.0 CE1 B:HIS179 2.9 15.3 1.0 CE1 B:HIS116 2.9 21.5 1.0 CG B:HIS116 3.0 19.1 1.0 CE1 B:HIS114 3.1 14.8 1.0 CD2 B:HIS179 3.1 13.4 1.0 CD2 B:HIS114 3.1 19.6 1.0 CB B:HIS116 3.4 12.3 1.0 ZN B:ZN302 3.6 20.7 1.0 OD1 B:ASP118 3.9 17.1 1.0 O B:HOH417 4.0 37.3 1.0 ND1 B:HIS179 4.1 14.2 1.0 NE2 B:HIS116 4.1 17.9 1.0 OD1 B:ASN210 4.1 33.0 1.0 SG B:CYS198 4.1 16.7 1.0 CD2 B:HIS116 4.1 17.8 1.0 CB B:CYS198 4.1 16.1 1.0 CG B:HIS179 4.2 13.3 1.0 ND1 B:HIS114 4.2 18.8 1.0 CG B:HIS114 4.3 12.4 1.0 O06 B:5IY303 4.3 20.5 1.0 OD2 B:ASP118 4.5 12.0 1.0 CG B:ASP118 4.6 15.4 1.0 N03 B:5IY303 4.7 27.2 1.0 CA B:HIS116 4.8 15.8 1.0 C05 B:5IY303 5.0 19.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-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 B1 Vim-2 Mbl in Complex with 2-Amino-5- Isobutylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.7 occ:1.00 O B:HOH500 2.1 12.9 1.0 NE2 B:HIS240 2.2 16.6 1.0 OD2 B:ASP118 2.2 12.0 1.0 N03 B:5IY303 2.3 27.2 1.0 O06 B:5IY303 2.4 20.5 1.0 SG B:CYS198 2.4 16.7 1.0 C04 B:5IY303 3.0 20.2 1.0 C05 B:5IY303 3.1 19.3 1.0 CE1 B:HIS240 3.1 14.5 1.0 CD2 B:HIS240 3.2 17.8 1.0 CG B:ASP118 3.2 15.4 1.0 C02 B:5IY303 3.3 27.6 1.0 ZN B:ZN301 3.6 16.6 1.0 CB B:CYS198 3.6 16.1 1.0 OD1 B:ASP118 3.6 17.1 1.0 N01 B:5IY303 3.7 25.1 1.0 NH2 B:ARG119 4.1 18.1 1.0 ND1 B:HIS240 4.2 14.8 1.0 CE1 B:HIS179 4.2 15.3 1.0 O07 B:5IY303 4.3 21.1 1.0 NE2 B:HIS179 4.3 13.6 1.0 CG B:HIS240 4.3 20.8 1.0 C08 B:5IY303 4.4 21.6 1.0 O B:HOH437 4.4 17.1 1.0 CB B:ASP118 4.5 10.2 1.0 NE B:ARG119 4.5 14.5 1.0 O B:HOH417 4.6 37.3 1.0 CE1 B:HIS114 4.7 14.8 1.0 OD1 B:ASN210 4.7 33.0 1.0 S13 B:5IY303 4.7 24.7 1.0 NE2 B:HIS114 4.7 14.7 1.0 CA B:CYS198 4.8 17.6 1.0 CZ B:ARG119 4.8 15.4 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