Sodium in PDB 6mz1: Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3

All present enzymatic activity of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3:
3.5.2.6;

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3, PDB code: 6mz1 was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.86 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.220, 106.720, 47.810, 90.00, 101.79, 90.00
R / Rfree (%)	14.1 / 16.1

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Sodium atom in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3 (pdb code 6mz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3, PDB code: 6mz1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:9.5 occ:1.00 O A:HOH665 2.4 14.3 1.0 O A:GLY238 2.5 5.7 1.0 O A:HOH561 2.5 14.0 1.0 O A:HOH531 2.6 8.4 1.0 O A:HOH630 2.6 12.9 1.0 O A:HOH443 2.8 8.6 1.0 C A:GLY238 3.4 5.1 1.0 O A:ALA272 4.0 7.8 1.0 N A:ASP240 4.3 5.2 1.0 N A:GLY238 4.3 4.4 1.0 CA A:GLY242 4.3 5.1 1.0 CA A:GLY238 4.3 4.9 1.0 CA A:ASP240 4.3 5.6 1.0 N A:GLY242 4.3 5.1 1.0 O A:HOH571 4.4 19.8 1.0 OG A:SER274 4.4 9.8 1.0 O B:HOH906 4.4 47.3 1.0 O B:HOH812 4.6 38.1 1.0 C A:ASP240 4.8 5.2 1.0 O A:HOH601 4.8 21.5 1.0 N A:THR243 4.8 4.2 1.0 O A:HOH455 4.8 26.4 1.0 C A:GLY242 4.8 4.5 1.0 O A:THR243 4.9 4.1 1.0 OD1 A:ASP240 4.9 11.3 1.0

Sodium binding site 2 out of 2 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:11.1 occ:1.00 O B:HOH702 2.4 15.7 1.0 O B:GLY238 2.5 6.5 1.0 O B:HOH615 2.5 15.0 1.0 O B:HOH654 2.6 13.7 1.0 O B:HOH558 2.6 9.5 1.0 O B:HOH440 2.8 10.5 1.0 C B:GLY238 3.5 5.8 1.0 O B:ALA272 3.9 9.6 1.0 O B:HOH724 4.2 39.5 1.0 O B:HOH655 4.2 19.2 1.0 N B:GLY238 4.3 5.0 1.0 CA B:GLY242 4.3 6.3 1.0 N B:ASP240 4.3 5.9 1.0 CA B:GLY238 4.3 5.5 1.0 N B:GLY242 4.3 6.2 1.0 CA B:ASP240 4.4 6.0 1.0 OG B:SER274 4.5 10.9 1.0 O A:HOH783 4.6 36.9 1.0 O B:HOH583 4.6 33.0 1.0 O B:HOH845 4.7 47.8 1.0 N B:THR243 4.8 5.6 1.0 O B:HOH593 4.8 15.9 1.0 C B:ASP240 4.8 6.0 1.0 C B:GLY242 4.8 5.7 1.0 O B:THR243 4.9 5.0 1.0

O.A.Pemberton, R.Sanishvili, M.T.Kemp, F.L.Kearns, H.L.Woodcock, Y.Chen. Mechanism of Proton Transfer in Class A Beta-Lactamase Catalysis and Inhibition By Avibactam To Be Published.