Zinc in PDB 6hf5: Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor

The structure of Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor, PDB code: 6hf5 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)	51.32 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.292, 77.688, 79.327, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.4

The binding sites of Zinc atom in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor (pdb code 6hf5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor, PDB code: 6hf5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor


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 Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.4 occ:1.00 O A:HOH422 1.9 20.0 1.0 ND1 A:HIS116 2.0 24.0 1.0 NE2 A:HIS179 2.1 18.9 1.0 NE2 A:HIS114 2.1 19.9 1.0 CD2 A:HIS179 3.0 19.5 1.0 CG A:HIS116 3.0 23.3 1.0 CE1 A:HIS116 3.1 23.8 1.0 CD2 A:HIS114 3.1 21.2 1.0 CE1 A:HIS114 3.1 17.7 1.0 CE1 A:HIS179 3.2 20.7 1.0 CB A:HIS116 3.3 21.1 1.0 ZN A:ZN302 4.0 28.0 0.8 OD1 A:ASP118 4.0 28.5 1.0 NE2 A:HIS116 4.1 25.6 1.0 CD2 A:HIS116 4.1 23.6 1.0 CG A:HIS179 4.2 17.2 1.0 ND1 A:HIS114 4.2 21.0 1.0 ND1 A:HIS179 4.2 17.6 1.0 CG A:HIS114 4.2 19.7 1.0 O24 A:G1N306 4.2 26.9 0.8 SG A:CYS198 4.3 28.5 1.0 CB A:CYS198 4.3 23.1 1.0 ND2 A:ASN210 4.6 71.9 1.0 CA A:HIS116 4.7 24.5 1.0 OD2 A:ASP118 4.7 29.2 1.0 N3 A:G1N306 4.7 25.2 0.8 CG A:ASP118 4.8 28.8 1.0 C6 A:G1N306 4.8 30.8 0.8 O A:HOH449 5.0 32.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor


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 Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.0 occ:0.80 N3 A:G1N306 2.2 25.2 0.8 O24 A:G1N306 2.2 26.9 0.8 NE2 A:HIS240 2.3 26.0 1.0 OD2 A:ASP118 2.3 29.2 1.0 SG A:CYS198 2.4 28.5 1.0 O A:HOH422 2.5 20.0 1.0 C4 A:G1N306 2.9 30.1 0.8 C6 A:G1N306 2.9 30.8 0.8 CE1 A:HIS240 3.2 24.9 1.0 C2 A:G1N306 3.3 32.5 0.8 CD2 A:HIS240 3.4 23.7 1.0 CG A:ASP118 3.4 28.8 1.0 CB A:CYS198 3.6 23.1 1.0 OD1 A:ASP118 3.7 28.5 1.0 NH2 A:ARG119 4.0 34.5 1.0 ZN A:ZN301 4.0 25.4 1.0 O25 A:G1N306 4.1 28.5 0.8 C5 A:G1N306 4.2 37.7 0.8 ND1 A:HIS240 4.3 24.9 1.0 NE A:ARG119 4.4 24.4 1.0 O A:HOH453 4.4 32.6 1.0 CG A:HIS240 4.5 22.1 1.0 NE2 A:HIS179 4.6 18.9 1.0 CB A:ASP118 4.6 29.7 1.0 S1 A:G1N306 4.6 34.8 0.8 CE1 A:HIS179 4.6 20.7 1.0 CZ A:ARG119 4.7 29.3 1.0 CE1 A:HIS114 4.8 17.7 1.0 CA A:CYS198 4.8 20.5 1.0 NE2 A:HIS114 4.9 19.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor


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 Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-431 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:24.1 occ:1.00 OXT A:ACT304 1.8 23.3 1.0 O A:ACT305 2.0 24.6 1.0 NE2 A:HIS153 2.0 23.7 1.0 OXT A:ACT305 2.6 26.8 1.0 C A:ACT305 2.7 27.4 1.0 C A:ACT304 2.8 30.4 1.0 CE1 A:HIS153 2.9 26.8 1.0 O A:ACT304 3.1 24.2 1.0 CD2 A:HIS153 3.1 22.8 1.0 ND1 A:HIS153 4.1 24.0 1.0 CG A:HIS153 4.2 22.4 1.0 CH3 A:ACT305 4.2 28.3 1.0 CH3 A:ACT304 4.3 25.5 1.0 CB A:ALA132 4.3 22.7 1.0 CA A:ALA132 4.8 22.8 1.0 CG2 A:THR152 4.8 25.5 1.0

S.Leiris, A.Coelho, J.Castandet, M.Bayet, C.Lozano, J.Bougnon, J.Bousquet, M.Everett, M.Lemonnier, N.Sprynski, M.Zalacain, T.D.Pallin, M.C.Cramp, N.Jennings, G.Raphy, M.W.Jones, R.Pattipati, B.Shankar, R.Sivasubrahmanyam, A.K.Soodhagani, R.R.Juventhala, N.Pottabathini, S.Pothukanuri, M.Benvenuti, C.Pozzi, S.Mangani, F.De Luca, G.Cerboni, J.D.Docquier, D.T.Davies. Sar Studies Leading to the Identification of A Novel Series of Metallo-Beta-Lactamase Inhibitors For the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy in An Animal Infection Model. Acs Infect Dis. V. 5 131 2019.
ISSN: ESSN 2373-8227
PubMed: 30427656
DOI: 10.1021/ACSINFECDIS.8B00246