Zinc in PDB 7yhb: Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid, PDB code: 7yhb was solved by G.-B.Li, Y.-H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.09 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.517, 79.293, 67.395, 90, 130.16, 90
R / Rfree (%)	26.3 / 30.8

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid (pdb code 7yhb). 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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid, PDB code: 7yhb:
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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic 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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.0 occ:1.00 O22 A:ITV303 1.7 22.2 1.0 OD2 A:ASP118 2.0 16.0 1.0 NE2 A:HIS240 2.1 16.8 1.0 SG A:CYS198 2.5 13.6 1.0 CE1 A:HIS240 2.9 17.6 1.0 O A:HOH425 3.0 17.5 1.0 P02 A:ITV303 3.1 20.2 1.0 CG A:ASP118 3.1 17.1 1.0 CD2 A:HIS240 3.2 13.7 1.0 CB A:CYS198 3.3 19.0 1.0 OD1 A:ASP118 3.6 17.6 1.0 O01 A:ITV303 3.7 16.0 1.0 C03 A:ITV303 3.8 17.1 1.0 NH2 A:ARG119 3.9 22.8 1.0 ND1 A:HIS240 4.1 19.8 1.0 NE A:ARG119 4.2 20.5 1.0 O21 A:ITV303 4.2 20.5 1.0 CG A:HIS240 4.2 14.6 1.0 O A:HOH463 4.3 12.8 1.0 C20 A:ITV303 4.3 22.1 1.0 ZN A:ZN302 4.3 18.1 1.0 CB A:ASP118 4.4 19.6 1.0 CZ A:ARG119 4.5 19.1 1.0 CE1 A:HIS114 4.5 22.0 1.0 CA A:CYS198 4.5 17.8 1.0 C04 A:ITV303 4.6 21.3 1.0 NE2 A:HIS179 4.6 16.0 1.0 CE1 A:HIS179 4.6 18.3 1.0 NE2 A:HIS114 4.9 18.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic 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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.1 occ:1.00 O A:HOH425 1.9 17.5 1.0 NE2 A:HIS179 2.0 16.0 1.0 ND1 A:HIS116 2.0 17.8 1.0 NE2 A:HIS114 2.0 18.1 1.0 O A:HOH402 2.6 12.4 1.0 CE1 A:HIS114 2.9 22.0 1.0 CD2 A:HIS179 2.9 14.4 1.0 CG A:HIS116 2.9 15.9 1.0 CE1 A:HIS116 3.0 17.2 1.0 CE1 A:HIS179 3.0 18.3 1.0 CD2 A:HIS114 3.1 19.4 1.0 CB A:HIS116 3.3 18.4 1.0 O22 A:ITV303 3.7 22.2 1.0 ND1 A:HIS114 4.0 16.6 1.0 OD1 A:ASP118 4.0 17.6 1.0 CG A:HIS179 4.1 14.5 1.0 ND1 A:HIS179 4.1 15.0 1.0 NE2 A:HIS116 4.1 21.0 1.0 CD2 A:HIS116 4.1 24.5 1.0 CG A:HIS114 4.1 15.1 1.0 O21 A:ITV303 4.3 20.5 1.0 ZN A:ZN301 4.3 17.0 1.0 CA A:HIS116 4.7 14.9 1.0 CB A:CYS198 4.7 19.0 1.0 P02 A:ITV303 4.7 20.2 1.0 OD2 A:ASP118 4.9 16.0 1.0 CG A:ASP118 4.9 17.1 1.0 N A:HIS116 4.9 14.2 1.0 O A:HOH428 4.9 23.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic 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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:13.7 occ:1.00 O22 B:ITV303 1.7 14.7 1.0 OD2 B:ASP118 2.0 15.3 1.0 NE2 B:HIS240 2.1 15.8 1.0 SG B:CYS198 2.5 9.9 1.0 P02 B:ITV303 3.0 21.5 1.0 CE1 B:HIS240 3.0 15.7 1.0 CG B:ASP118 3.1 20.4 1.0 CD2 B:HIS240 3.1 12.2 1.0 O B:HOH410 3.1 12.0 0.1 O B:HOH410 3.3 10.0 0.3 CB B:CYS198 3.4 14.2 1.0 OD1 B:ASP118 3.5 17.5 1.0 C03 B:ITV303 3.7 21.7 1.0 O21 B:ITV303 3.7 22.6 1.0 NH2 B:ARG119 3.9 22.8 1.0 C20 B:ITV303 4.1 29.5 1.0 ND1 B:HIS240 4.2 16.6 1.0 CG B:HIS240 4.2 14.5 1.0 O B:HOH429 4.2 17.2 1.0 O01 B:ITV303 4.2 22.4 1.0 NE B:ARG119 4.2 16.1 1.0 CB B:ASP118 4.3 17.1 1.0 C04 B:ITV303 4.4 25.0 1.0 ZN B:ZN302 4.5 17.4 1.0 CA B:CYS198 4.5 13.3 1.0 CZ B:ARG119 4.5 19.1 1.0 CE1 B:HIS114 4.6 14.6 1.0 NE2 B:HIS179 4.7 10.6 1.0 CE1 B:HIS179 4.8 15.9 1.0 NE2 B:HIS114 4.9 17.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vim-2 Mbl in Complex with (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic 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 (2-(4-Phenyl-1H-1,2,3- Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.4 occ:1.00 O B:HOH410 1.6 12.0 0.1 O B:HOH410 1.8 10.0 0.3 NE2 B:HIS179 2.0 10.6 1.0 ND1 B:HIS116 2.0 19.1 1.0 NE2 B:HIS114 2.2 17.0 1.0 O B:HOH419 2.7 21.5 1.0 O B:HOH410 2.7 12.6 0.6 CG B:HIS116 3.0 16.5 1.0 CE1 B:HIS179 3.0 15.9 1.0 CD2 B:HIS179 3.0 13.6 1.0 CE1 B:HIS116 3.0 16.4 1.0 CD2 B:HIS114 3.0 16.6 1.0 CE1 B:HIS114 3.1 14.6 1.0 CB B:HIS116 3.3 13.3 1.0 O22 B:ITV303 3.7 14.7 1.0 OD1 B:ASP118 4.1 17.5 1.0 ND1 B:HIS179 4.1 13.5 1.0 CD2 B:HIS116 4.1 18.7 1.0 NE2 B:HIS116 4.1 20.7 1.0 CG B:HIS179 4.2 15.7 1.0 CG B:HIS114 4.2 14.5 1.0 ND1 B:HIS114 4.2 13.4 1.0 O01 B:ITV303 4.4 22.4 1.0 ZN B:ZN301 4.5 13.7 1.0 CB B:CYS198 4.5 14.2 1.0 P02 B:ITV303 4.7 21.5 1.0 CA B:HIS116 4.7 14.4 1.0 O B:HOH452 4.8 18.3 1.0 OD2 B:ASP118 4.9 15.3 1.0 CG B:ASP118 4.9 20.4 1.0 O B:HOH505 4.9 20.4 1.0 N B:HIS116 4.9 13.5 1.0

Y.H.Yan, H.S.Ding, K.R.Zhu, B.S.Mu, Y.Zheng, M.Y.Huang, C.Zhou, W.F.Li, Z.Wang, Y.Wu, G.B.Li. Metal Binding Pharmacophore Click-Derived Discovery of New Broad-Spectrum Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 257 15473 2023.
ISSN: ISSN 0223-5234
PubMed: 37209449
DOI: 10.1016/J.EJMECH.2023.115473