Zinc in PDB 6j8r: Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01

The structure of Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01, PDB code: 6j8r was solved by G.-B.Li, S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 1.58
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.893, 60.984, 96.338, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.7

The binding sites of Zinc atom in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01 (pdb code 6j8r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01, PDB code: 6j8r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01


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 Dual Mbl/Sbl Inhibitor MS01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.7 occ:1.00 ND1 A:HIS116 2.0 13.3 1.0 NE2 A:HIS179 2.0 11.0 1.0 NE2 A:HIS114 2.1 11.2 1.0 S7 A:BHU303 2.3 19.6 1.0 CE1 A:HIS116 2.9 12.3 1.0 CE1 A:HIS114 3.0 8.9 1.0 CG A:HIS116 3.0 7.8 1.0 CE1 A:HIS179 3.0 16.5 1.0 CD2 A:HIS179 3.0 13.4 1.0 CD2 A:HIS114 3.0 9.1 1.0 C6 A:BHU303 3.1 18.0 1.0 CB A:HIS116 3.4 10.1 1.0 ZN A:ZN302 3.7 15.1 1.0 OD1 A:ASP118 4.0 12.0 1.0 NE2 A:HIS116 4.0 11.9 1.0 ND1 A:HIS114 4.1 9.3 1.0 CD2 A:HIS116 4.1 15.5 1.0 ND1 A:HIS179 4.1 14.4 1.0 CG A:HIS179 4.2 13.6 1.0 CG A:HIS114 4.2 7.9 1.0 CB A:CYS198 4.2 11.3 1.0 SG A:CYS198 4.3 11.9 1.0 C5 A:BHU303 4.6 23.0 1.0 OD2 A:ASP118 4.6 10.6 1.0 CG A:ASP118 4.7 12.2 1.0 CA A:HIS116 4.8 8.7 1.0

Zinc binding site 2 out of 2 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS01


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 Dual Mbl/Sbl Inhibitor MS01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.1 occ:1.00 OD2 A:ASP118 2.0 10.6 1.0 NE2 A:HIS240 2.1 10.3 1.0 S7 A:BHU303 2.2 19.6 1.0 SG A:CYS198 2.4 11.9 1.0 CE1 A:HIS240 3.0 12.4 1.0 CG A:ASP118 3.0 12.2 1.0 CD2 A:HIS240 3.1 10.4 1.0 C6 A:BHU303 3.4 18.0 1.0 OD1 A:ASP118 3.4 12.0 1.0 CB A:CYS198 3.5 11.3 1.0 ZN A:ZN301 3.7 11.7 1.0 NH2 A:ARG119 3.7 14.4 1.0 C5 A:BHU303 3.8 23.0 1.0 NE A:ARG119 4.1 7.2 1.0 ND1 A:HIS240 4.1 9.4 1.0 CG A:HIS240 4.2 9.2 1.0 CE1 A:HIS114 4.3 8.9 1.0 CZ A:ARG119 4.3 10.9 1.0 CB A:ASP118 4.3 9.1 1.0 C A:FMT304 4.3 33.5 1.0 C3 A:BHU303 4.4 34.2 1.0 NE2 A:HIS114 4.4 11.2 1.0 NE2 A:HIS179 4.5 11.0 1.0 CE1 A:HIS179 4.7 16.5 1.0 O A:HOH426 4.7 15.7 1.0 O1 A:FMT304 4.7 23.6 1.0 CA A:CYS198 4.7 10.5 1.0 N2 A:BHU303 4.8 22.9 1.0 O4 A:BHU303 5.0 31.2 1.0

Y.L.Wang, S.Liu, Z.J.Yu, Y.Lei, M.Y.Huang, Y.H.Yan, Q.Ma, Y.Zheng, H.Deng, Y.Sun, C.Wu, Y.Yu, Q.Chen, Z.Wang, Y.Wu, G.B.Li. Structure-Based Development of (1-(3'-Mercaptopropanamido)Methyl)Boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-Beta-Lactamases. J.Med.Chem. V. 62 7160 2019.
ISSN: ISSN 0022-2623
PubMed: 31269398
DOI: 10.1021/ACS.JMEDCHEM.9B00735