Sodium in PDB 6mz2: Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9

All present enzymatic activity of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9:
3.5.2.6;

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9, PDB code: 6mz2 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)	34.17 / 0.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.161, 106.842, 47.913, 90.00, 101.82, 90.00
R / Rfree (%)	11.6 / 12.7

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 also contains other interesting chemical elements:

Potassium

(K)

13 atoms

The binding sites of Sodium atom in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 (pdb code 6mz2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9, PDB code: 6mz2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


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 7.9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:9.8 occ:1.00 O A:HOH646 2.5 14.9 1.0 O A:HOH605 2.6 12.8 1.0 O A:GLY238 2.6 6.0 1.0 O A:HOH712 2.7 13.2 1.0 O A:HOH509 2.7 9.8 1.0 O A:HOH445 2.8 8.5 1.0 HA2 A:GLY242 3.6 6.3 1.0 C A:GLY238 3.6 5.1 1.0 HA A:ASP240 3.6 6.4 1.0 H A:GLY242 3.7 6.4 1.0 O A:HOH624 3.9 30.3 1.0 O A:ALA272 4.0 8.0 1.0 H A:GLY238 4.1 6.0 1.0 N A:ASP240 4.3 5.3 1.0 CA A:ASP240 4.3 5.3 1.0 CA A:GLY242 4.3 5.3 1.0 HB2 A:SER237 4.3 10.4 1.0 N A:GLY242 4.3 5.3 1.0 OG A:SER274 4.4 12.5 1.0 H A:THR243 4.4 5.7 1.0 N A:GLY238 4.5 5.0 1.0 CA A:GLY238 4.5 5.5 1.0 HA2 A:GLY238 4.6 6.5 1.0 C A:ASP240 4.8 5.1 1.0 O A:HOH592 4.8 24.4 1.0 O A:HOH514 4.8 26.9 1.0 N A:THR243 4.9 4.7 1.0 H A:SER274 4.9 9.7 1.0 OD1 A:ASP240 4.9 11.7 1.0 C A:GLY242 4.9 4.8 1.0 O A:HOH706 4.9 33.4 1.0

Sodium binding site 2 out of 4 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


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 7.9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:17.2 occ:0.61 O B:HOH533 2.5 18.8 1.0 O A:HOH467 2.5 18.7 1.0 O B:TRP229 2.6 14.3 1.0 O B:THR227 2.6 17.1 1.0 OH A:TYR105 2.8 9.0 0.7 O A:HOH688 3.1 19.8 1.0 O B:HOH630 3.2 16.8 1.0 OH A:TYR105 3.3 10.0 0.3 HE1 A:TYR105 3.4 10.2 0.7 HA B:THR230 3.6 11.1 1.0 C B:TRP229 3.7 11.4 1.0 C B:THR227 3.8 17.0 1.0 CZ A:TYR105 3.8 8.3 0.7 CE1 A:TYR105 3.9 8.5 0.7 HE2 A:TYR105 4.1 11.2 0.3 HA B:THR227 4.1 21.3 1.0 CZ A:TYR105 4.2 9.5 0.3 O A:HOH411 4.2 12.9 1.0 O B:HOH755 4.2 15.7 1.0 O B:HOH659 4.2 12.9 1.0 N B:TRP229 4.3 12.2 1.0 H B:TRP229 4.4 14.6 1.0 C B:SER228 4.4 14.2 1.0 CA B:THR230 4.4 9.3 1.0 CE2 A:TYR105 4.5 9.3 0.3 N B:THR230 4.5 9.5 1.0 HA B:SER228 4.5 18.3 1.0 CA B:THR227 4.5 17.8 1.0 CA B:TRP229 4.6 11.5 1.0 H B:VAL231 4.7 8.3 1.0 N B:SER228 4.7 16.0 1.0 O B:SER228 4.8 16.0 1.0 CA B:SER228 4.8 15.2 1.0 HB B:THR227 4.8 24.6 1.0 K A:K310 4.8 11.7 0.3 OAD A:NXL301 4.8 8.5 0.2 HG23 B:VAL231 4.9 10.2 1.0 O B:HOH593 4.9 19.3 1.0

Sodium binding site 3 out of 4 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:18.7 occ:0.34 O A:HOH831 2.2 18.9 1.0 O B:HOH755 2.4 15.7 1.0 O A:HOH688 2.7 19.8 1.0 O B:HOH519 2.8 16.6 1.0 HD2 A:TYR129 2.8 7.8 1.0 HG23 B:THR230 2.9 13.0 1.0 HE2 A:TYR129 3.3 8.7 1.0 CD2 A:TYR129 3.4 6.5 1.0 HB2 A:PRO107 3.4 10.4 1.0 CE2 A:TYR129 3.7 7.3 1.0 CG2 B:THR230 3.7 10.8 1.0 O B:HOH630 3.8 16.8 1.0 HG21 B:THR230 3.8 13.0 1.0 HD11 A:ILE108 3.9 8.8 1.0 HG3 A:PRO107 4.0 10.1 1.0 HD13 A:ILE108 4.1 8.8 1.0 CB A:PRO107 4.2 8.7 1.0 OG1 B:THR230 4.2 14.6 1.0 HA B:THR230 4.2 11.1 1.0 HG2 A:PRO107 4.3 10.1 1.0 HB3 A:PRO107 4.3 10.4 1.0 O A:HOH563 4.3 15.2 1.0 CG A:PRO107 4.4 8.4 1.0 HB3 A:TYR129 4.4 6.0 1.0 HG22 B:THR230 4.4 13.0 1.0 O A:HOH411 4.4 12.9 1.0 HB3 B:LYS212 4.5 6.6 1.0 H B:VAL231 4.5 8.3 1.0 CG A:TYR129 4.5 5.3 1.0 CB B:THR230 4.5 11.3 1.0 CD1 A:ILE108 4.5 7.3 1.0 O A:HOH665 4.6 15.4 1.0 K A:K310 4.6 11.7 0.3 HD3 B:LYS212 4.7 9.2 1.0 CZ A:TYR129 4.9 7.4 1.0 CA B:THR230 4.9 9.3 1.0 O B:HOH556 5.0 14.3 1.0 CB A:TYR129 5.0 5.0 1.0

Sodium binding site 4 out of 4 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:13.8 occ:1.00 O B:HOH714 2.5 17.5 1.0 O B:HOH626 2.5 17.1 1.0 O B:GLY238 2.7 8.4 1.0 O B:HOH634 2.7 17.4 1.0 O B:HOH563 2.7 14.2 1.0 O B:HOH449 2.8 13.8 1.0 HA2 B:GLY242 3.5 8.5 1.0 C B:GLY238 3.6 6.7 1.0 HA B:ASP240 3.7 8.7 1.0 H B:GLY242 3.7 8.6 1.0 O B:HOH675 3.7 22.7 1.0 O B:ALA272 4.0 11.5 1.0 H B:GLY238 4.1 6.9 1.0 CA B:GLY242 4.3 7.1 1.0 HB2 B:SER237 4.3 10.7 1.0 N B:GLY242 4.3 7.2 1.0 N B:ASP240 4.4 7.0 1.0 CA B:ASP240 4.4 7.2 1.0 OG B:SER274 4.4 13.8 1.0 H B:THR243 4.5 7.1 1.0 N B:GLY238 4.5 5.8 1.0 CA B:GLY238 4.5 6.4 1.0 HA2 B:GLY238 4.6 7.7 1.0 O B:HOH590 4.7 32.0 1.0 O B:HOH663 4.8 22.7 1.0 C B:ASP240 4.8 7.0 1.0 N B:THR243 4.9 6.0 1.0 C B:GLY242 4.9 6.5 1.0 O B:HOH645 4.9 24.4 1.0 OD1 B:ASP240 5.0 12.2 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.