Zinc in PDB 6eum: Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307

All present enzymatic activity of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307:
3.5.2.6;

The structure of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307, PDB code: 6eum was solved by D.Stepanovs, M.A.Mcdonough, C.J.Schofield, D.Zhang, A.El-Husseiny, J.Brem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.53 / 1.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.180, 61.440, 70.180, 90.00, 93.20, 90.00
R / Rfree (%)	12.8 / 15.1

The structure of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307 (pdb code 6eum). 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 Bcii Metallo-Beta-Lactamase in Complex with Dz- 307, PDB code: 6eum:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307


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 Bcii Metallo-Beta-Lactamase in Complex with Dz- 307 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.2 occ:0.75 OD A:CSO198 1.1 25.5 0.2 SG A:CSO198 1.8 15.8 0.2 NE2 A:HIS240 2.0 18.8 1.0 OD2 A:ASP120 2.1 20.2 1.0 SG A:CSO198 2.3 14.4 0.8 S A:BY5304 2.3 17.8 0.8 O A:BY5304 2.3 17.6 0.8 CE1 A:HIS240 3.0 18.5 1.0 CD2 A:HIS240 3.0 17.8 1.0 CG A:ASP120 3.1 17.7 1.0 C A:BY5304 3.1 18.3 0.8 C1 A:BY5304 3.1 18.4 0.8 CB A:CSO198 3.3 14.6 0.8 CB A:CSO198 3.4 17.5 0.2 OD1 A:ASP120 3.5 19.7 1.0 ZN A:ZN302 3.8 15.7 1.0 NH2 A:ARG121 4.0 21.0 1.0 ND1 A:HIS240 4.1 19.3 1.0 NE A:ARG121 4.2 16.8 1.0 CG A:HIS240 4.2 18.7 1.0 O1 A:BY5304 4.2 23.8 0.8 CE1 A:HIS116 4.3 13.8 1.0 CB A:ASP120 4.3 17.5 1.0 C2 A:BY5304 4.4 21.1 0.8 NE2 A:HIS179 4.5 14.6 1.0 NE2 A:HIS116 4.5 14.5 1.0 CZ A:ARG121 4.5 17.2 1.0 O A:HOH452 4.5 19.6 1.0 CA A:CSO198 4.5 14.3 0.8 CA A:CSO198 4.5 15.2 0.2 F1 A:BY5304 4.7 26.5 0.8 CE1 A:HIS179 4.8 14.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 307


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 Bcii Metallo-Beta-Lactamase in Complex with Dz- 307 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.7 occ:1.00 ND1 A:HIS118 2.0 15.9 1.0 NE2 A:HIS179 2.0 14.6 1.0 NE2 A:HIS116 2.0 14.5 1.0 S A:BY5304 2.3 17.8 0.8 OD A:CSO198 2.9 25.5 0.2 CE1 A:HIS118 3.0 15.2 1.0 CE1 A:HIS116 3.0 13.8 1.0 CG A:HIS118 3.0 15.4 1.0 CD2 A:HIS116 3.0 13.9 1.0 CD2 A:HIS179 3.0 13.5 1.0 CE1 A:HIS179 3.0 14.5 1.0 C1 A:BY5304 3.2 18.4 0.8 CB A:HIS118 3.3 18.1 1.0 ZN A:ZN301 3.8 17.2 0.8 C2 A:BY5304 3.9 21.1 0.8 O A:BY5304 4.0 17.6 0.8 OD1 A:ASP120 4.0 19.7 1.0 C A:BY5304 4.0 18.3 0.8 C3 A:BY5304 4.0 21.5 0.8 NE2 A:HIS118 4.1 17.1 1.0 ND1 A:HIS116 4.1 13.0 1.0 CD2 A:HIS118 4.1 16.5 1.0 CG A:HIS116 4.2 12.1 1.0 ND1 A:HIS179 4.2 14.2 1.0 CB A:CSO198 4.2 17.5 0.2 SG A:CSO198 4.2 15.8 0.2 CG A:HIS179 4.2 12.6 1.0 CB A:CSO198 4.3 14.6 0.8 C4 A:BY5304 4.3 20.7 0.8 CG2 A:THR180 4.4 14.2 1.0 F A:BY5304 4.4 25.3 0.8 SG A:CSO198 4.5 14.4 0.8 C8 A:BY5304 4.5 24.9 0.8 OD2 A:ASP120 4.7 20.2 1.0 CA A:HIS118 4.8 16.9 1.0 CG A:ASP120 4.8 17.7 1.0 O1 A:BY5304 5.0 23.8 0.8

D.Zhang, M.S.Markoulides, D.Stepanovs, A.M.Rydzik, A.El-Hussein, C.Bon, J.J.A.G.Kamps, K.D.Umland, P.M.Collins, S.T.Cahill, D.Y.Wang, F.Von Delft, J.Brem, M.A.Mcdonough, C.J.Schofield. Structure Activity Relationship Studies on Rhodanines and Derived Enethiol Inhibitors of Metallo-Beta-Lactamases. Bioorg. Med. Chem. V. 26 2928 2018.
ISSN: ESSN 1464-3391
PubMed: 29655609
DOI: 10.1016/J.BMC.2018.02.043