Zinc in PDB 5jmx: Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305

All present enzymatic activity of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305:
3.5.2.6;

The structure of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305, PDB code: 5jmx was solved by D.Stepanovs, M.A.Mcdonough, C.J.Schofield, D.Zhang, J.Brem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.95 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.250, 61.240, 69.050, 90.00, 93.09, 90.00
R / Rfree (%)	14.6 / 18.6

The structure of Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305 (pdb code 5jmx). 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- 305, PDB code: 5jmx:
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- 305


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- 305 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.3 occ:1.00 NE2 A:HIS240 2.1 22.2 1.0 OD2 A:ASP120 2.1 27.8 1.0 O01 A:DZ5304 2.2 35.3 1.0 SG A:CYS198 2.3 22.4 1.0 S13 A:DZ5304 2.4 35.1 1.0 C02 A:DZ5304 2.9 35.4 1.0 CE1 A:HIS240 3.0 23.0 1.0 C04 A:DZ5304 3.1 35.3 1.0 CD2 A:HIS240 3.1 26.8 1.0 CG A:ASP120 3.2 29.4 1.0 CB A:CYS198 3.4 19.8 1.0 OD1 A:ASP120 3.5 26.1 1.0 ZN A:ZN302 3.8 20.1 1.0 NH2 A:ARG121 4.1 28.8 1.0 O03 A:DZ5304 4.1 35.4 1.0 ND1 A:HIS240 4.2 24.0 1.0 CG A:HIS240 4.2 22.5 1.0 NE A:ARG121 4.3 22.5 1.0 CE1 A:HIS116 4.3 18.6 1.0 CB A:ASP120 4.4 28.3 1.0 NE2 A:HIS179 4.4 15.9 1.0 C05 A:DZ5304 4.5 35.6 1.0 O A:HOH448 4.5 24.6 1.0 NE2 A:HIS116 4.5 18.1 1.0 CZ A:ARG121 4.5 26.7 1.0 CA A:CYS198 4.6 17.4 1.0 O A:HOH578 4.7 52.2 1.0 CE1 A:HIS179 4.8 21.4 1.0 O A:HOH466 4.9 52.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bcii Metallo-Beta-Lactamase in Complex with Dz- 305


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- 305 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.1 occ:1.00 NE2 A:HIS179 2.0 15.9 1.0 NE2 A:HIS116 2.0 18.1 1.0 ND1 A:HIS118 2.0 20.2 1.0 S13 A:DZ5304 2.3 35.1 1.0 CE1 A:HIS179 3.0 21.4 1.0 CD2 A:HIS179 3.0 15.2 1.0 CE1 A:HIS116 3.0 18.6 1.0 CD2 A:HIS116 3.0 17.3 1.0 CG A:HIS118 3.0 20.2 1.0 CE1 A:HIS118 3.0 21.7 1.0 C04 A:DZ5304 3.1 35.3 1.0 CB A:HIS118 3.3 21.8 1.0 C05 A:DZ5304 3.7 35.6 1.0 ZN A:ZN301 3.8 26.3 1.0 C06 A:DZ5304 3.8 35.8 1.0 OD1 A:ASP120 4.0 26.1 1.0 C02 A:DZ5304 4.1 35.4 1.0 O01 A:DZ5304 4.1 35.3 1.0 ND1 A:HIS116 4.1 17.5 1.0 ND1 A:HIS179 4.1 17.7 1.0 C07 A:DZ5304 4.1 36.0 1.0 CG A:HIS179 4.1 16.2 1.0 NE2 A:HIS118 4.2 23.2 1.0 CG A:HIS116 4.2 16.4 1.0 CD2 A:HIS118 4.2 20.3 1.0 CB A:CYS198 4.2 19.8 1.0 SG A:CYS198 4.4 22.4 1.0 CG2 A:THR180 4.4 17.4 1.0 C12 A:DZ5304 4.4 35.9 1.0 OD2 A:ASP120 4.7 27.8 1.0 O A:HOH466 4.8 52.6 1.0 CG A:ASP120 4.8 29.4 1.0 CA A:HIS118 4.8 21.2 1.0 C08 A:DZ5304 4.9 36.1 1.0

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