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

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Hexylthiazole-4-Carboxylic Acid, PDB code: 8hxv 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)	37.05 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.78, 90.356, 126.14, 90, 90, 90
R / Rfree (%)	17.7 / 25.4

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Hexylthiazole-4-Carboxylic Acid (pdb code 8hxv). 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- Hexylthiazole-4-Carboxylic Acid, PDB code: 8hxv:
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- Hexylthiazole-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- Hexylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.6 occ:1.00 NE2 A:HIS179 1.9 36.1 1.0 ND1 A:HIS116 2.0 43.0 1.0 NE2 A:HIS114 2.1 36.2 1.0 O A:HOH409 2.1 47.7 1.0 CE1 A:HIS116 2.8 30.6 1.0 CE1 A:HIS179 2.8 37.9 1.0 CD2 A:HIS114 3.0 40.8 1.0 CD2 A:HIS179 3.0 31.1 1.0 CE1 A:HIS114 3.1 35.5 1.0 CG A:HIS116 3.2 44.1 1.0 ZN A:ZN302 3.6 49.4 1.0 CB A:HIS116 3.7 39.1 1.0 ND1 A:HIS179 3.9 35.6 1.0 OD1 A:ASP118 3.9 39.9 1.0 NE2 A:HIS116 4.0 39.9 1.0 SG A:CYS198 4.0 25.9 1.0 CG A:HIS179 4.1 32.0 1.0 ND1 A:HIS114 4.1 32.7 1.0 CG A:HIS114 4.1 38.8 1.0 CD2 A:HIS116 4.2 44.4 1.0 CB A:CYS198 4.2 41.1 1.0 O07 A:5ZD303 4.3 49.2 1.0 OD2 A:ASP118 4.3 41.8 1.0 CG A:ASP118 4.5 47.6 1.0 N03 A:5ZD303 4.8 57.9 1.0 O A:PHE115 4.8 64.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Hexylthiazole-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- Hexylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:49.4 occ:1.00 O A:HOH409 1.9 47.7 1.0 OD2 A:ASP118 2.1 41.8 1.0 O07 A:5ZD303 2.2 49.2 1.0 NE2 A:HIS240 2.3 54.4 1.0 N03 A:5ZD303 2.3 57.9 1.0 SG A:CYS198 2.5 25.9 1.0 CE1 A:HIS240 3.0 47.4 1.0 C05 A:5ZD303 3.0 50.4 1.0 C04 A:5ZD303 3.0 62.7 1.0 CG A:ASP118 3.2 47.6 1.0 C02 A:5ZD303 3.3 50.8 1.0 CD2 A:HIS240 3.4 48.9 1.0 ZN A:ZN301 3.6 34.6 1.0 OD1 A:ASP118 3.8 39.9 1.0 N01 A:5ZD303 3.8 50.6 1.0 CB A:CYS198 3.8 41.1 1.0 NH2 A:ARG119 3.9 42.8 1.0 ND1 A:HIS240 4.2 36.3 1.0 O06 A:5ZD303 4.2 50.8 1.0 C08 A:5ZD303 4.3 55.1 1.0 NE A:ARG119 4.4 34.2 1.0 CE1 A:HIS179 4.4 37.9 1.0 CB A:ASP118 4.4 39.6 1.0 CG A:HIS240 4.4 43.6 1.0 NE2 A:HIS179 4.5 36.1 1.0 NE2 A:HIS114 4.6 36.2 1.0 CZ A:ARG119 4.6 30.9 1.0 S15 A:5ZD303 4.7 51.4 1.0 CE1 A:HIS114 4.7 35.5 1.0 O A:HOH427 4.8 39.8 1.0 CA A:CYS198 5.0 40.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Hexylthiazole-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- Hexylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.1 occ:1.00 ND1 B:HIS116 1.9 38.0 1.0 O B:HOH414 2.0 38.5 1.0 NE2 B:HIS179 2.0 39.2 1.0 NE2 B:HIS114 2.1 36.8 1.0 CD2 B:HIS179 2.9 40.5 1.0 CE1 B:HIS116 2.9 38.3 1.0 CE1 B:HIS179 3.0 38.0 1.0 CG B:HIS116 3.0 38.3 1.0 CD2 B:HIS114 3.0 41.5 1.0 CE1 B:HIS114 3.0 42.1 1.0 CB B:HIS116 3.4 34.7 1.0 ZN B:ZN302 3.7 42.0 1.0 CG B:HIS179 4.0 32.2 1.0 ND1 B:HIS179 4.0 37.9 1.0 NE2 B:HIS116 4.0 33.9 1.0 OD1 B:ASP118 4.0 31.7 1.0 CD2 B:HIS116 4.1 36.2 1.0 ND1 B:HIS114 4.1 32.4 1.0 CG B:HIS114 4.1 34.2 1.0 SG B:CYS198 4.2 33.7 1.0 CB B:CYS198 4.3 36.9 1.0 OD2 B:ASP118 4.4 44.4 1.0 CG B:ASP118 4.6 38.4 1.0 O07 B:5ZD303 4.6 49.4 1.0 CA B:HIS116 4.8 37.5 1.0 N03 B:5ZD303 4.8 61.8 1.0 N B:HIS116 5.0 31.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Hexylthiazole-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- Hexylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:42.0 occ:1.00 NE2 B:HIS240 2.1 49.7 1.0 OD2 B:ASP118 2.1 44.4 1.0 O B:HOH414 2.2 38.5 1.0 N03 B:5ZD303 2.4 61.8 1.0 SG B:CYS198 2.4 33.7 1.0 O07 B:5ZD303 2.6 49.4 1.0 CE1 B:HIS240 2.9 46.3 1.0 C04 B:5ZD303 3.1 54.1 1.0 C05 B:5ZD303 3.2 52.1 1.0 CD2 B:HIS240 3.3 46.3 1.0 CG B:ASP118 3.3 38.4 1.0 C02 B:5ZD303 3.4 45.6 1.0 CB B:CYS198 3.7 36.9 1.0 ZN B:ZN301 3.7 37.1 1.0 OD1 B:ASP118 3.8 31.7 1.0 NH2 B:ARG119 3.9 40.5 1.0 N01 B:5ZD303 3.9 40.7 1.0 ND1 B:HIS240 4.1 48.2 1.0 CG B:HIS240 4.3 42.4 1.0 CE1 B:HIS179 4.3 38.0 1.0 O06 B:5ZD303 4.4 64.0 1.0 C08 B:5ZD303 4.4 63.9 1.0 NE B:ARG119 4.4 27.5 1.0 NE2 B:HIS179 4.4 39.2 1.0 CE1 B:HIS114 4.5 42.1 1.0 CB B:ASP118 4.5 33.2 1.0 NE2 B:HIS114 4.5 36.8 1.0 CZ B:ARG119 4.6 26.6 1.0 S15 B:5ZD303 4.8 46.0 1.0 CA B:CYS198 4.8 39.5 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