Zinc in PDB 5mxq: Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-90 Inhibitor

The structure of Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-90 Inhibitor, PDB code: 5mxq was solved by J.D.Docquier, F.De Luca, M.Benvenuti, F.Di Pisa, C.Pozzi, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.09 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.909, 77.900, 79.450, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.7

The structure of Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-90 Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Acquired Vim-2 Metallo-Beta-Lactamase in Complex with Ant-90 Inhibitor (pdb code 5mxq). 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-90 Inhibitor, PDB code: 5mxq:
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-90 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-90 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.8 occ:1.00 O A:ACT307 1.9 22.8 1.0 OXT A:ACT306 2.0 20.4 1.0 ND1 A:HIS251 2.2 16.2 1.0 O A:ACT306 2.6 17.9 1.0 C A:ACT306 2.7 19.1 1.0 C A:ACT307 2.9 23.8 1.0 CG A:HIS251 3.2 15.7 1.0 CE1 A:HIS251 3.2 15.5 1.0 OXT A:ACT307 3.2 21.3 1.0 CB A:HIS251 3.5 15.7 1.0 CA A:HIS251 3.8 15.9 1.0 CH3 A:ACT306 4.2 21.8 1.0 CH3 A:ACT307 4.3 20.9 1.0 ND2 A:ASN254 4.3 16.7 1.0 NE2 A:HIS251 4.3 14.0 1.0 CD2 A:HIS251 4.3 14.7 1.0 CD2 A:LEU203 4.4 19.2 1.0 O A:HIS251 4.6 17.9 1.0 C A:HIS251 4.6 16.9 1.0 N A:HIS251 4.9 14.8 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-90 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-90 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.6 occ:1.00 O A:HOH418 1.9 13.3 1.0 ND1 A:HIS116 2.0 17.1 1.0 NE2 A:HIS179 2.1 17.0 1.0 NE2 A:HIS114 2.2 17.4 1.0 CE1 A:HIS116 3.0 19.4 1.0 CG A:HIS116 3.0 17.5 1.0 CD2 A:HIS114 3.1 19.1 1.0 CD2 A:HIS179 3.1 15.2 1.0 CE1 A:HIS179 3.1 15.9 1.0 CE1 A:HIS114 3.2 16.2 1.0 CB A:HIS116 3.4 16.2 1.0 O A:HOH462 3.4 34.4 1.0 OD1 A:ASP118 3.9 23.0 1.0 ZN A:ZN303 4.0 25.7 1.0 NE2 A:HIS116 4.1 18.9 1.0 CD2 A:HIS116 4.1 19.0 1.0 ND1 A:HIS179 4.2 15.3 1.0 SG A:CYS198 4.2 21.6 1.0 CB A:CYS198 4.2 17.4 1.0 CG A:HIS179 4.2 14.3 1.0 CG A:HIS114 4.3 16.7 1.0 ND1 A:HIS114 4.3 15.8 1.0 O8 A:U8K304 4.3 12.2 0.6 ND2 A:ASN210 4.3 64.7 1.0 N6 A:U8K304 4.5 15.6 0.6 OD2 A:ASP118 4.8 23.9 1.0 CG A:ASP118 4.8 22.0 1.0 CA A:HIS116 4.8 16.5 1.0 C7 A:U8K304 5.0 14.3 0.6 O A:HOH432 5.0 26.0 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-90 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-90 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:25.7 occ:1.00 N6 A:U8K304 2.2 15.6 0.6 NE2 A:HIS240 2.3 18.4 1.0 OD2 A:ASP118 2.3 23.9 1.0 O8 A:U8K304 2.3 12.2 0.6 SG A:CYS198 2.4 21.6 1.0 O A:HOH418 2.5 13.3 1.0 C1 A:U8K304 3.0 15.9 0.6 C7 A:U8K304 3.0 14.3 0.6 C5 A:U8K304 3.1 17.6 0.6 CE1 A:HIS240 3.1 17.0 1.0 CD2 A:HIS240 3.3 18.8 1.0 CG A:ASP118 3.3 22.0 1.0 CB A:CYS198 3.6 17.4 1.0 OD1 A:ASP118 3.7 23.0 1.0 ZN A:ZN302 4.0 20.6 1.0 NH2 A:ARG119 4.0 29.3 1.0 O9 A:U8K304 4.2 13.1 0.6 ND1 A:HIS240 4.3 19.2 1.0 C2 A:U8K304 4.3 18.5 0.6 C4 A:U8K304 4.4 17.3 0.6 CG A:HIS240 4.4 17.6 1.0 O A:HOH439 4.4 21.2 1.0 O A:HOH462 4.4 34.4 1.0 NE A:ARG119 4.4 22.0 1.0 NE2 A:HIS179 4.5 17.0 1.0 CE1 A:HIS179 4.5 15.9 1.0 CB A:ASP118 4.6 22.7 1.0 CZ A:ARG119 4.7 24.7 1.0 CL A:CL305 4.7 19.5 0.4 CA A:CYS198 4.8 18.3 1.0 C3 A:U8K304 4.8 16.9 0.6 CE1 A:HIS114 4.9 16.2 1.0 NE2 A:HIS114 4.9 17.4 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