Zinc in PDB 7chv: Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid

The structure of Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid, PDB code: 7chv 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)	34.33 / 2.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.655, 78.891, 79.808, 90, 90, 90
R / Rfree (%)	24.5 / 36.4

The binding sites of Zinc atom in the Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid (pdb code 7chv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid, PDB code: 7chv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-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 Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:38.5 occ:1.00 ND1 A:HIS116 1.9 33.7 1.0 NE2 A:HIS179 2.0 28.8 1.0 O A:HOH411 2.0 23.4 1.0 NE2 A:HIS114 2.1 38.6 1.0 CE1 A:HIS114 2.7 33.3 1.0 CE1 A:HIS116 2.9 41.0 1.0 CG A:HIS116 2.9 39.5 1.0 CD2 A:HIS179 3.0 29.0 1.0 CE1 A:HIS179 3.0 38.7 1.0 CD2 A:HIS114 3.2 36.6 1.0 CB A:HIS116 3.3 41.1 1.0 ZN A:ZN302 3.8 35.9 1.0 OD1 A:ASP118 3.9 41.2 1.0 ND1 A:HIS114 3.9 40.7 1.0 NE2 A:HIS116 4.0 45.8 1.0 CD2 A:HIS116 4.0 41.2 1.0 ND1 A:HIS179 4.1 30.2 1.0 CG A:HIS179 4.1 20.0 1.0 CB A:CYS198 4.2 36.8 1.0 CG A:HIS114 4.2 37.2 1.0 SG A:CYS198 4.2 38.0 1.0 O08 A:FZX304 4.4 44.4 1.0 OD2 A:ASP118 4.5 37.0 1.0 CG A:ASP118 4.6 37.0 1.0 N05 A:FZX304 4.7 37.8 1.0 CA A:HIS116 4.8 42.1 1.0

Zinc binding site 2 out of 3 in the Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-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 Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:35.9 occ:1.00 OD2 A:ASP118 2.2 37.0 1.0 NE2 A:HIS240 2.2 44.6 1.0 O08 A:FZX304 2.2 44.4 1.0 N05 A:FZX304 2.3 37.8 1.0 SG A:CYS198 2.4 38.0 1.0 O A:HOH411 2.4 23.4 1.0 C04 A:FZX304 2.9 44.6 1.0 C06 A:FZX304 3.0 39.7 1.0 CE1 A:HIS240 3.1 45.3 1.0 CD2 A:HIS240 3.2 42.8 1.0 CG A:ASP118 3.3 37.0 1.0 CB A:CYS198 3.3 36.8 1.0 C01 A:FZX304 3.5 33.4 1.0 OD1 A:ASP118 3.7 41.2 1.0 ZN A:ZN301 3.8 38.5 1.0 NH2 A:ARG119 3.9 49.7 1.0 N03 A:FZX304 4.2 39.6 1.0 ND1 A:HIS240 4.2 41.9 1.0 O07 A:FZX304 4.2 52.8 1.0 CG A:HIS240 4.3 40.1 1.0 NE2 A:HIS179 4.3 28.8 1.0 C02 A:FZX304 4.4 45.0 1.0 NE A:ARG119 4.5 35.9 1.0 CA A:CYS198 4.5 34.3 1.0 CE1 A:HIS179 4.6 38.7 1.0 CB A:ASP118 4.6 43.7 1.0 CE1 A:HIS114 4.6 33.3 1.0 CZ A:ARG119 4.6 33.2 1.0 NE2 A:HIS114 4.9 38.6 1.0

Zinc binding site 3 out of 3 in the Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-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 Metallo-Beta-Lactamase Vim-2 in Complex with 1-Benzyl-1H-Imidazole-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:39.3 occ:1.00 O2 A:FMT306 1.8 38.3 1.0 ND1 A:HIS251 2.1 34.0 1.0 O1 A:FMT305 2.5 27.9 1.0 C A:FMT305 2.7 34.5 1.0 C A:FMT306 2.8 45.9 1.0 CE1 A:HIS251 3.0 32.7 1.0 CG A:HIS251 3.2 39.1 1.0 O1 A:FMT306 3.2 52.6 1.0 CB A:HIS251 3.5 35.1 1.0 CA A:HIS251 3.8 34.6 1.0 O2 A:FMT305 3.9 55.6 1.0 NE2 A:HIS251 4.1 41.8 1.0 CD2 A:HIS251 4.2 35.1 1.0 CD2 A:LEU203 4.3 36.4 1.0 O A:HIS251 4.6 39.7 1.0 ND2 A:ASN254 4.6 41.4 1.0 C A:HIS251 4.6 45.5 1.0 N A:HIS251 4.8 38.3 1.0

Q.-Q.Dai, Y.-H.Yan, X.-L.Ning, G.Li, L.Guo, G.-B.Li. Ancphore: A Versatile Tool For Anchor Pharmacophore Steered Drug Discovery and Its Applications in Discovery of New Inhibitors Targeting Metallo Beta-Lactamases and Indoleamine/Tryptophan 2,3-Dioxygenases To Be Published.