Zinc in PDB 6jn6: Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19

The structure of Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19, PDB code: 6jn6 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)	38.91 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.510, 79.236, 67.806, 90.00, 130.61, 90.00
R / Rfree (%)	15.6 / 18.7

The binding sites of Zinc atom in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19 (pdb code 6jn6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19, PDB code: 6jn6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


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 MS19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.1 occ:1.00 ND1 A:HIS116 2.0 8.7 1.0 NE2 A:HIS179 2.0 6.3 1.0 NE2 A:HIS114 2.1 6.9 1.0 S8 A:BY0304 2.3 11.2 1.0 CE1 A:HIS116 2.9 8.1 1.0 CE1 A:HIS114 3.0 5.6 1.0 CD2 A:HIS179 3.0 5.3 1.0 CG A:HIS116 3.0 5.5 1.0 CE1 A:HIS179 3.0 9.0 1.0 CD2 A:HIS114 3.1 5.6 1.0 C7 A:BY0304 3.2 10.9 1.0 CB A:HIS116 3.4 5.1 1.0 ZN A:ZN302 3.7 10.7 1.0 NE2 A:HIS116 4.0 11.9 1.0 OD1 A:ASP118 4.1 9.4 1.0 ND1 A:HIS114 4.1 6.2 1.0 CD2 A:HIS116 4.1 12.6 1.0 CB A:CYS198 4.1 6.7 1.0 ND1 A:HIS179 4.1 7.7 1.0 CG A:HIS179 4.1 5.8 1.0 CG A:HIS114 4.2 6.4 1.0 SG A:CYS198 4.4 8.5 1.0 C6 A:BY0304 4.7 19.8 1.0 OD2 A:ASP118 4.7 9.1 1.0 CA A:HIS116 4.8 6.0 1.0 CG A:ASP118 4.8 8.9 1.0

Zinc binding site 2 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


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 MS19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.7 occ:1.00 OD2 A:ASP118 2.0 9.1 1.0 NE2 A:HIS240 2.1 7.5 1.0 SG A:CYS198 2.3 8.5 1.0 S8 A:BY0304 2.3 11.2 1.0 CE1 A:HIS240 3.0 11.3 1.0 CG A:ASP118 3.0 8.9 1.0 CD2 A:HIS240 3.1 9.5 1.0 C7 A:BY0304 3.3 10.9 1.0 CB A:CYS198 3.4 6.7 1.0 OD1 A:ASP118 3.4 9.4 1.0 C6 A:BY0304 3.7 19.8 1.0 ZN A:ZN301 3.7 8.1 1.0 NH2 A:ARG119 3.8 14.5 1.0 ND1 A:HIS240 4.1 6.7 1.0 NE A:ARG119 4.1 10.5 1.0 CG A:HIS240 4.2 9.7 1.0 CE1 A:HIS114 4.2 5.6 1.0 CB A:ASP118 4.3 9.7 1.0 CZ A:ARG119 4.4 13.0 1.0 NE2 A:HIS114 4.5 6.9 1.0 C A:FMT305 4.5 19.0 1.0 C4 A:BY0304 4.5 23.2 1.0 NE2 A:HIS179 4.6 6.3 1.0 O A:HOH420 4.6 12.5 1.0 CA A:CYS198 4.7 6.7 1.0 N3 A:BY0304 4.8 30.6 1.0 O1 A:FMT305 4.9 20.4 1.0 CE1 A:HIS179 4.9 9.0 1.0 C9 A:BY0304 4.9 27.5 1.0

Zinc binding site 3 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


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 Dual Mbl/Sbl Inhibitor MS19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.2 occ:1.00 O1 A:FMT306 1.6 12.0 1.0 O2 A:FMT307 1.9 11.8 1.0 ND1 A:HIS251 2.1 8.3 1.0 C A:FMT307 2.7 13.4 1.0 C A:FMT306 2.7 13.3 1.0 O1 A:FMT307 2.9 16.7 1.0 CE1 A:HIS251 3.0 10.4 1.0 CG A:HIS251 3.1 10.6 1.0 O2 A:FMT306 3.2 22.0 1.0 CB A:HIS251 3.5 7.6 1.0 CA A:HIS251 3.7 6.4 1.0 NE2 A:HIS251 4.2 8.8 1.0 CD2 A:HIS251 4.2 7.2 1.0 ND2 A:ASN254 4.3 14.2 1.0 O A:HIS251 4.5 10.0 1.0 C A:HIS251 4.6 11.2 1.0 N A:HIS251 4.8 7.4 1.0 CD2 A:LEU203 4.8 13.1 1.0

Zinc binding site 4 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:8.6 occ:1.00 NE2 B:HIS114 2.0 6.4 1.0 ND1 B:HIS116 2.0 9.8 1.0 NE2 B:HIS179 2.0 8.1 1.0 S8 B:BY0304 2.3 13.7 1.0 CE1 B:HIS116 2.9 8.0 1.0 CE1 B:HIS114 3.0 8.0 1.0 CD2 B:HIS114 3.0 5.3 1.0 CE1 B:HIS179 3.0 11.0 1.0 CD2 B:HIS179 3.0 6.8 1.0 CG B:HIS116 3.0 6.9 1.0 C7 B:BY0304 3.1 13.1 1.0 CB B:HIS116 3.4 7.2 1.0 ZN B:ZN302 3.7 11.9 1.0 ND1 B:HIS114 4.0 6.9 1.0 CB B:CYS198 4.1 10.5 1.0 NE2 B:HIS116 4.1 13.4 1.0 OD1 B:ASP118 4.1 11.6 1.0 CG B:HIS114 4.1 6.4 1.0 ND1 B:HIS179 4.1 10.4 1.0 CD2 B:HIS116 4.1 11.9 1.0 CG B:HIS179 4.1 7.0 1.0 SG B:CYS198 4.3 9.6 1.0 C6 B:BY0304 4.6 17.3 1.0 OD2 B:ASP118 4.7 13.4 1.0 CG B:ASP118 4.8 8.0 1.0 CA B:HIS116 4.8 7.7 1.0

Zinc binding site 5 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:11.9 occ:1.00 OD2 B:ASP118 2.0 13.4 1.0 NE2 B:HIS240 2.1 8.5 1.0 SG B:CYS198 2.3 9.6 1.0 S8 B:BY0304 2.4 13.7 1.0 CG B:ASP118 3.0 8.0 1.0 CE1 B:HIS240 3.1 9.6 1.0 CD2 B:HIS240 3.1 7.4 1.0 CB B:CYS198 3.4 10.5 1.0 OD1 B:ASP118 3.4 11.6 1.0 C7 B:BY0304 3.5 13.1 1.0 ZN B:ZN301 3.7 8.6 1.0 NH2 B:ARG119 3.8 16.0 1.0 C6 B:BY0304 3.8 17.3 1.0 NE B:ARG119 4.1 12.7 1.0 ND1 B:HIS240 4.2 8.8 1.0 CG B:HIS240 4.2 8.4 1.0 CE1 B:HIS114 4.3 8.0 1.0 CB B:ASP118 4.3 11.9 1.0 CZ B:ARG119 4.4 13.2 1.0 NE2 B:HIS114 4.4 6.4 1.0 C B:FMT305 4.5 25.1 1.0 C4 B:BY0304 4.6 34.5 1.0 CA B:CYS198 4.6 6.6 1.0 NE2 B:HIS179 4.7 8.1 1.0 N3 B:BY0304 4.7 32.7 1.0 O B:HOH423 4.7 12.7 1.0 CE1 B:HIS179 4.8 11.0 1.0 O1 B:FMT305 4.9 22.7 1.0

Zinc binding site 6 out of 6 in the Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Metallo-Beta-Lactamase Vim-2 in Complex with Dual Mbl/Sbl Inhibitor MS19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:10.2 occ:1.00 O1 B:FMT307 1.8 11.2 1.0 O2 B:FMT306 1.9 9.4 1.0 ND1 B:HIS251 2.1 8.1 1.0 C B:FMT306 2.7 12.5 1.0 C B:FMT307 2.8 14.6 1.0 O1 B:FMT306 2.9 13.5 1.0 CE1 B:HIS251 3.1 8.7 1.0 CG B:HIS251 3.1 9.7 1.0 O2 B:FMT307 3.1 13.8 1.0 CB B:HIS251 3.4 7.4 1.0 CA B:HIS251 3.8 8.1 1.0 NE2 B:HIS251 4.2 7.3 1.0 CD2 B:HIS251 4.2 6.2 1.0 ND2 B:ASN254 4.4 12.5 1.0 CD2 B:LEU203 4.5 11.2 1.0 O B:HIS251 4.6 6.9 1.0 C B:HIS251 4.6 8.4 1.0 N B:HIS251 4.9 5.8 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