Zinc in PDB 7dyy: Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dyy 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)	51.84 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.123, 45.08, 98.028, 90, 90.06, 90
R / Rfree (%)	23.2 / 29.8

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid (pdb code 7dyy). 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 Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dyy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-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-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.8 occ:1.00 OD2 A:ASP118 2.1 16.6 1.0 NE2 A:HIS240 2.1 26.8 1.0 N01 A:HQF303 2.3 22.9 1.0 O18 A:HQF303 2.4 24.8 1.0 SG A:CYS198 2.4 25.0 1.0 O A:HOH438 2.4 25.9 1.0 CE1 A:HIS240 2.9 27.1 1.0 C02 A:HQF303 3.1 26.1 1.0 CG A:ASP118 3.1 22.5 1.0 C17 A:HQF303 3.2 33.4 1.0 C05 A:HQF303 3.3 37.1 1.0 CD2 A:HIS240 3.3 29.3 1.0 OD1 A:ASP118 3.4 25.9 1.0 CB A:CYS198 3.6 29.0 1.0 ZN A:ZN302 3.7 25.0 1.0 ND1 A:HIS240 4.1 24.6 1.0 NH2 A:ARG119 4.2 28.2 1.0 NE2 A:HIS179 4.2 23.4 1.0 N03 A:HQF303 4.3 32.8 1.0 CG A:HIS240 4.3 19.2 1.0 C04 A:HQF303 4.4 23.0 1.0 NE2 A:HIS114 4.5 23.1 1.0 O19 A:HQF303 4.5 25.6 1.0 CB A:ASP118 4.5 25.4 1.0 NE A:ARG119 4.5 17.3 1.0 CE1 A:HIS114 4.5 25.1 1.0 O A:HOH418 4.7 24.3 1.0 CE1 A:HIS179 4.7 33.6 1.0 C1 A:PEG304 4.8 37.9 1.0 CA A:CYS198 4.8 24.6 1.0 CZ A:ARG119 4.8 21.3 1.0 CD2 A:HIS179 5.0 22.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-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-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:25.0 occ:1.00 ND1 A:HIS116 2.0 22.9 1.0 O A:HOH438 2.0 25.9 1.0 NE2 A:HIS179 2.1 23.4 1.0 NE2 A:HIS114 2.2 23.1 1.0 CD2 A:HIS179 2.8 22.2 1.0 CE1 A:HIS116 2.8 18.2 1.0 CD2 A:HIS114 3.0 23.8 1.0 CG A:HIS116 3.1 28.6 1.0 CE1 A:HIS114 3.3 25.1 1.0 CE1 A:HIS179 3.3 33.6 1.0 CB A:HIS116 3.6 33.1 1.0 ZN A:ZN301 3.7 33.8 1.0 OD1 A:ASP118 3.9 25.9 1.0 NE2 A:HIS116 4.0 27.2 1.0 CG A:HIS179 4.0 16.0 1.0 CD2 A:HIS116 4.2 29.8 1.0 CG A:HIS114 4.2 23.6 1.0 ND1 A:HIS179 4.2 28.9 1.0 SG A:CYS198 4.2 25.0 1.0 ND1 A:HIS114 4.3 24.4 1.0 CB A:CYS198 4.3 29.0 1.0 O18 A:HQF303 4.3 24.8 1.0 C1 A:PEG304 4.4 37.9 1.0 N01 A:HQF303 4.6 22.9 1.0 OD2 A:ASP118 4.7 16.6 1.0 CG A:ASP118 4.8 22.5 1.0 O2 A:PEG304 4.8 33.5 1.0 C17 A:HQF303 4.9 33.4 1.0 CA A:HIS116 5.0 25.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-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-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:28.7 occ:1.00 O B:HOH429 1.8 10.3 1.0 ND1 B:HIS116 1.9 24.4 1.0 NE2 B:HIS114 2.0 14.8 1.0 NE2 B:HIS179 2.0 23.6 1.0 CE1 B:HIS116 2.6 26.2 1.0 CG B:HIS116 2.7 15.6 1.0 CD2 B:HIS114 2.7 20.1 1.0 CE1 B:HIS179 3.0 35.1 1.0 CD2 B:HIS179 3.1 21.9 1.0 CE1 B:HIS114 3.1 19.2 1.0 CB B:HIS116 3.3 16.1 1.0 NE2 B:HIS116 3.4 24.2 1.0 CD2 B:HIS116 3.5 31.4 1.0 CG B:HIS114 3.9 27.7 1.0 ZN B:ZN302 4.0 28.2 1.0 ND1 B:HIS114 4.1 23.9 1.0 ND1 B:HIS179 4.1 27.7 1.0 CG B:HIS179 4.2 20.9 1.0 C2 B:PEG304 4.4 35.1 1.0 O19 B:HQF303 4.4 23.3 1.0 O1 B:PEG304 4.4 35.3 1.0 OD1 B:ASP118 4.4 33.6 1.0 SG B:CYS198 4.5 26.4 1.0 CB B:CYS198 4.5 29.4 1.0 CA B:HIS116 4.6 24.6 1.0 C1 B:PEG304 4.8 41.7 1.0 OD2 B:ASP118 4.8 12.6 1.0 N B:HIS116 4.8 26.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with 1-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-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-((2- Aminobenzo[D]Thiazol-6-Yl)Methyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:28.2 occ:1.00 O19 B:HQF303 2.1 23.3 1.0 OD2 B:ASP118 2.1 12.6 1.0 NE2 B:HIS240 2.2 20.9 1.0 O B:HOH429 2.3 10.3 1.0 SG B:CYS198 2.6 26.4 1.0 N01 B:HQF303 2.6 37.0 1.0 C17 B:HQF303 3.0 34.6 1.0 CE1 B:HIS240 3.0 22.5 1.0 C02 B:HQF303 3.2 34.2 1.0 CG B:ASP118 3.2 21.7 1.0 CD2 B:HIS240 3.3 20.8 1.0 OD1 B:ASP118 3.5 33.6 1.0 CB B:CYS198 3.7 29.4 1.0 O1 B:PEG304 3.8 35.3 1.0 C05 B:HQF303 3.8 32.7 1.0 ZN B:ZN301 4.0 28.7 1.0 NH2 B:ARG119 4.1 23.4 1.0 O18 B:HQF303 4.2 41.0 1.0 ND1 B:HIS240 4.2 15.8 1.0 CG B:HIS240 4.4 18.7 1.0 N03 B:HQF303 4.4 28.9 1.0 CB B:ASP118 4.5 23.2 1.0 NE2 B:HIS179 4.6 23.6 1.0 O B:HOH410 4.6 18.6 1.0 NE2 B:HIS114 4.6 14.8 1.0 NE B:ARG119 4.6 37.2 1.0 C2 B:PEG304 4.6 35.1 1.0 C04 B:HQF303 4.8 32.0 1.0 CE1 B:HIS179 4.8 35.1 1.0 CE1 B:HIS114 4.8 19.2 1.0 C1 B:PEG304 4.9 41.7 1.0 CZ B:ARG119 4.9 18.3 1.0 CA B:CYS198 4.9 26.6 1.0 ND1 B:HIS116 4.9 24.4 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