Zinc in PDB 5evd: Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26:
3.5.2.6;

The structure of Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26, PDB code: 5evd was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.35 / 1.80
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.130, 105.130, 98.170, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 19.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26 (pdb code 5evd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26, PDB code: 5evd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26


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 Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.9 occ:1.00 ND1 A:HIS118 2.1 16.1 1.0 NE2 A:HIS196 2.1 17.7 1.0 NE2 A:HIS116 2.1 16.3 1.0 SAE A:VC2401 2.3 35.2 0.8 CD2 A:HIS196 2.9 16.6 1.0 CE1 A:HIS118 3.0 15.4 1.0 CD2 A:HIS116 3.0 17.2 1.0 CE1 A:HIS116 3.1 15.8 1.0 CG A:HIS118 3.1 16.4 1.0 CE1 A:HIS196 3.2 17.7 1.0 SAH A:VC2401 3.2 33.1 0.8 CAF A:VC2401 3.4 45.2 0.8 CB A:HIS118 3.5 16.8 1.0 O A:HOH538 3.7 46.9 1.0 ZN A:ZN403 3.8 25.0 1.0 CAK A:VC2401 3.9 44.0 0.8 CG A:HIS196 4.1 17.3 1.0 NE2 A:HIS118 4.1 14.8 1.0 CAG A:VC2401 4.1 44.5 0.8 ND1 A:HIS116 4.2 16.9 1.0 CG A:HIS116 4.2 17.9 1.0 CD2 A:HIS118 4.2 16.0 1.0 ND1 A:HIS196 4.2 17.6 1.0 OD1 A:ASP120 4.3 21.3 1.0 CD2 A:HIS121 4.3 18.9 1.0 NE2 A:HIS121 4.4 18.6 1.0 CA A:HIS118 4.9 18.1 1.0 OD2 A:ASP120 4.9 21.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26


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 Metallo-Beta-Lactamase L1 in Complex with the Bisthiazolidine Inhibitor D-VC26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:25.0 occ:1.00 SAE A:VC2401 2.0 35.2 0.8 OD2 A:ASP120 2.0 21.9 1.0 NE2 A:HIS121 2.0 18.6 1.0 NE2 A:HIS263 2.1 20.6 1.0 CG A:ASP120 2.9 22.4 1.0 CE1 A:HIS121 2.9 18.6 1.0 O A:HOH538 2.9 46.9 1.0 CAF A:VC2401 3.0 45.2 0.8 CD2 A:HIS121 3.0 18.9 1.0 CE1 A:HIS263 3.0 20.0 1.0 CD2 A:HIS263 3.1 20.8 1.0 OD1 A:ASP120 3.2 21.3 1.0 ZN A:ZN402 3.8 19.9 1.0 ND1 A:HIS121 4.0 18.6 1.0 CG A:HIS121 4.1 19.2 1.0 ND1 A:HIS263 4.1 19.5 1.0 CB A:ASP120 4.2 21.8 1.0 CG A:HIS263 4.2 19.7 1.0 CAK A:VC2401 4.3 44.0 0.8 NE2 A:HIS116 4.3 16.3 1.0 CE1 A:HIS116 4.3 15.8 1.0 O A:HOH561 4.5 36.7 1.0 OG A:SER221 4.8 19.7 1.0 O A:HOH633 4.8 53.9 1.0 CZ3 A:TRP39 5.0 24.3 1.0

P.Hinchliffe, M.M.Gonzalez, M.F.Mojica, J.M.Gonzalez, V.Castillo, C.Saiz, M.Kosmopoulou, C.L.Tooke, L.I.Llarrull, G.Mahler, R.A.Bonomo, A.J.Vila, J.Spencer. Cross-Class Metallo-Beta-Lactamase Inhibition By Bisthiazolidines Reveals Multiple Binding Modes. Proc.Natl.Acad.Sci.Usa V. 113 E3745 2016.
ISSN: ESSN 1091-6490
PubMed: 27303030
DOI: 10.1073/PNAS.1601368113