Zinc in PDB 6sp7: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133), PDB code: 6sp7 was solved by J.D.Docquier, C.Pozzi, F.De Luca, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.92 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.910, 79.040, 67.490, 90.00, 130.50, 90.00
R / Rfree (%)	18.9 / 24.4

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) (pdb code 6sp7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133), PDB code: 6sp7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.4 occ:1.00 O06 A:K9B306 1.9 16.1 1.0 ND1 A:HIS118 1.9 14.9 1.0 NE2 A:HIS116 2.1 13.7 1.0 NE2 A:HIS196 2.1 11.8 1.0 O07 A:K9B306 2.5 17.9 1.0 B05 A:K9B306 2.9 17.9 1.0 CE1 A:HIS118 2.9 16.0 1.0 CG A:HIS118 2.9 14.0 1.0 CE1 A:HIS116 2.9 14.1 1.0 CD2 A:HIS196 3.0 11.1 1.0 CE1 A:HIS196 3.1 12.8 1.0 CD2 A:HIS116 3.1 13.4 1.0 CB A:HIS118 3.3 13.1 1.0 O08 A:K9B306 3.8 14.7 1.0 NE2 A:HIS118 4.0 15.3 1.0 CD2 A:HIS118 4.0 15.2 1.0 C04 A:K9B306 4.0 19.7 1.0 ND1 A:HIS116 4.1 13.8 1.0 OD1 A:ASP120 4.1 15.5 1.0 CG A:HIS196 4.2 12.1 1.0 CG A:HIS116 4.2 12.9 1.0 ND1 A:HIS196 4.2 13.4 1.0 ZN A:ZN302 4.2 17.9 1.0 CB A:CYS221 4.4 12.1 1.0 SG A:CYS221 4.5 13.0 1.0 N03 A:K9B306 4.6 20.4 1.0 CA A:HIS118 4.7 13.2 1.0 O12 A:K9B306 4.8 16.2 1.0 O A:HOH469 4.8 18.8 1.0 C09 A:K9B306 4.9 17.4 1.0 N A:HIS118 5.0 11.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.9 occ:1.00 O08 A:K9B306 1.9 14.7 1.0 NE2 A:HIS263 2.2 14.5 1.0 O12 A:K9B306 2.2 16.2 1.0 OD2 A:ASP120 2.3 17.9 1.0 SG A:CYS221 2.3 13.0 1.0 C09 A:K9B306 2.9 17.4 1.0 B05 A:K9B306 3.0 17.9 1.0 O06 A:K9B306 3.0 16.1 1.0 CD2 A:HIS263 3.1 13.4 1.0 C11 A:K9B306 3.1 17.6 1.0 CE1 A:HIS263 3.2 13.1 1.0 CG A:ASP120 3.3 14.2 1.0 C10 A:K9B306 3.4 16.8 1.0 CB A:CYS221 3.4 12.1 1.0 OD1 A:ASP120 3.6 15.5 1.0 O07 A:K9B306 3.8 17.9 1.0 NH2 A:ARG121 3.9 23.6 1.0 C17 A:K9B306 4.0 18.6 1.0 O A:HOH416 4.2 16.3 1.0 ZN A:ZN301 4.2 14.4 1.0 ND1 A:HIS263 4.2 13.3 1.0 CG A:HIS263 4.2 12.6 1.0 C04 A:K9B306 4.3 19.7 1.0 C18 A:K9B306 4.3 20.3 1.0 O13 A:K9B306 4.3 19.3 1.0 NE A:ARG121 4.5 16.0 1.0 CE1 A:HIS196 4.5 12.8 1.0 NE2 A:HIS196 4.5 11.8 1.0 CA A:CYS221 4.6 12.7 1.0 CB A:ASP120 4.6 14.6 1.0 CZ A:ARG121 4.6 21.6 1.0 C14 A:K9B306 4.7 17.6 1.0 CE1 A:HIS116 4.8 14.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.8 occ:1.00 OXT A:ACT304 1.9 12.2 1.0 O A:ACT305 1.9 4.7 0.5 NE2 A:HIS170 2.2 19.1 1.0 C A:ACT305 2.7 5.1 0.5 OXT A:ACT305 2.8 5.0 0.5 C A:ACT304 2.9 14.1 1.0 CE1 A:HIS170 3.0 19.9 1.0 O A:ACT304 3.1 15.9 1.0 CD2 A:HIS170 3.2 17.7 1.0 CH3 A:ACT305 4.1 5.3 0.5 CB A:ALA135 4.1 14.3 1.0 ND1 A:HIS170 4.2 18.4 1.0 CH3 A:ACT304 4.3 13.4 1.0 CG A:HIS170 4.3 17.2 1.0 CA A:ALA135 4.6 14.1 1.0 O A:HOH424 4.7 23.6 1.0 CG2 A:THR169 5.0 18.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:15.6 occ:1.00 O06 E:K9B306 2.0 15.2 1.0 ND1 E:HIS118 2.1 17.9 1.0 NE2 E:HIS196 2.1 12.8 1.0 NE2 E:HIS116 2.2 13.1 1.0 O07 E:K9B306 2.5 20.1 1.0 B05 E:K9B306 2.9 19.0 1.0 CD2 E:HIS196 3.0 13.0 1.0 CG E:HIS118 3.0 16.4 1.0 CE1 E:HIS116 3.0 13.9 1.0 CE1 E:HIS118 3.1 18.0 1.0 CD2 E:HIS116 3.2 12.9 1.0 CE1 E:HIS196 3.2 13.4 1.0 CB E:HIS118 3.3 18.0 1.0 O08 E:K9B306 3.9 19.4 1.0 C04 E:K9B306 4.1 19.2 1.0 ND1 E:HIS116 4.2 13.1 1.0 CD2 E:HIS118 4.2 18.4 1.0 OD1 E:ASP120 4.2 17.2 1.0 NE2 E:HIS118 4.2 18.7 1.0 CG E:HIS196 4.2 12.3 1.0 ND1 E:HIS196 4.2 13.3 1.0 ZN E:ZN302 4.3 20.3 1.0 CG E:HIS116 4.3 12.6 1.0 CB E:CYS221 4.5 12.7 1.0 SG E:CYS221 4.5 14.9 1.0 O E:HOH420 4.7 17.3 1.0 N03 E:K9B306 4.7 25.4 1.0 CA E:HIS118 4.7 16.4 1.0 O12 E:K9B306 5.0 22.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:20.3 occ:1.00 O08 E:K9B306 2.0 19.4 1.0 SG E:CYS221 2.2 14.9 1.0 NE2 E:HIS263 2.3 16.6 1.0 OD2 E:ASP120 2.3 18.3 1.0 O12 E:K9B306 2.3 22.0 1.0 O06 E:K9B306 2.8 15.2 1.0 C09 E:K9B306 3.0 21.1 1.0 B05 E:K9B306 3.0 19.0 1.0 CE1 E:HIS263 3.2 16.0 1.0 CD2 E:HIS263 3.3 15.6 1.0 C11 E:K9B306 3.3 21.6 1.0 CB E:CYS221 3.3 12.7 1.0 CG E:ASP120 3.3 17.0 1.0 C10 E:K9B306 3.5 20.8 1.0 OD1 E:ASP120 3.7 17.2 1.0 NH2 E:ARG121 3.9 22.8 1.0 C17 E:K9B306 4.0 19.1 1.0 O07 E:K9B306 4.1 20.1 1.0 O E:HOH431 4.2 20.7 1.0 C04 E:K9B306 4.2 19.2 1.0 C18 E:K9B306 4.2 19.9 1.0 ZN E:ZN301 4.3 15.6 1.0 ND1 E:HIS263 4.3 16.0 1.0 NE E:ARG121 4.3 17.1 1.0 CG E:HIS263 4.4 15.2 1.0 O13 E:K9B306 4.4 23.4 1.0 NE2 E:HIS196 4.5 12.8 1.0 CA E:CYS221 4.5 14.1 1.0 CZ E:ARG121 4.6 19.5 1.0 CB E:ASP120 4.6 17.7 1.0 CE1 E:HIS196 4.7 13.4 1.0 CE1 E:HIS116 4.8 13.9 1.0 C14 E:K9B306 4.9 21.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Taniborbactam (Vnrx-5133) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn303 b:17.4 occ:1.00 OXT E:ACT304 2.0 10.7 1.0 NE2 E:HIS170 2.1 18.5 1.0 O E:ACT305 2.1 5.9 0.5 OXT E:ACT305 2.7 7.4 0.5 C E:ACT305 2.8 6.8 0.5 CE1 E:HIS170 2.9 19.6 1.0 C E:ACT304 3.0 13.9 1.0 CD2 E:HIS170 3.2 18.7 1.0 O E:ACT304 3.3 19.0 1.0 ND1 E:HIS170 4.1 17.9 1.0 CG E:HIS170 4.2 19.0 1.0 CB E:ALA135 4.3 14.9 1.0 CH3 E:ACT305 4.3 7.1 0.5 CH3 E:ACT304 4.4 13.8 1.0 CG2 E:THR169 4.8 16.7 1.0 CA E:ALA135 4.9 14.4 1.0

B.Liu, R.E.L.Trout, G.H.Chu, D.Mcgarry, R.W.Jackson, J.C.Hamrick, D.M.Daigle, S.M.Cusick, C.Pozzi, F.De Luca, M.Benvenuti, S.Mangani, J.D.Docquier, W.J.Weiss, D.C.Pevear, L.Xerri, C.J.Burns. Discovery of Taniborbactam (Vnrx-5133): A Broad-Spectrum Serine- and Metallo-Beta-Lactamase Inhibitor For Carbapenem-Resistant Bacterial Infections. J. Med. Chem. 2019.
ISSN: ISSN 1520-4804
PubMed: 31765155
DOI: 10.1021/ACS.JMEDCHEM.9B01518