Sodium in PDB 4s2l: Crystal Structure of Oxa-163 Beta-Lactamase

All present enzymatic activity of Crystal Structure of Oxa-163 Beta-Lactamase:
3.5.2.6;

The structure of Crystal Structure of Oxa-163 Beta-Lactamase, PDB code: 4s2l was solved by V.Stojanoski, H.Liya, T.G.Palzkill, B.Prasad, B.Sankaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.17 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.870, 125.750, 49.710, 90.00, 116.78, 90.00
R / Rfree (%)	19.4 / 23.2

The binding sites of Sodium atom in the Crystal Structure of Oxa-163 Beta-Lactamase (pdb code 4s2l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Oxa-163 Beta-Lactamase, PDB code: 4s2l:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Oxa-163 Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Oxa-163 Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:16.9 occ:1.00 OE1 A:GLU256 2.5 24.4 1.0 OE2 A:GLU256 2.8 27.6 1.0 NE2 A:HIS38 2.9 31.9 1.0 CD A:GLU256 2.9 27.1 1.0 OE1 A:GLU37 3.0 40.1 1.0 CD2 A:HIS38 3.1 27.3 1.0 CG A:GLU37 3.3 34.0 1.0 CD A:GLU37 3.4 43.2 1.0 O A:HIS34 3.7 31.9 1.0 CB A:GLU37 3.9 32.6 1.0 CE1 A:HIS38 4.0 34.2 1.0 CA A:HIS34 4.0 20.0 1.0 ND1 A:HIS34 4.1 22.7 1.0 CG A:HIS38 4.3 28.3 1.0 CB A:HIS34 4.4 18.2 1.0 C A:HIS34 4.4 25.1 1.0 CG A:GLU256 4.4 22.8 1.0 OE2 A:GLU37 4.5 40.5 1.0 CG A:HIS34 4.7 23.1 1.0 ND1 A:HIS38 4.7 31.6 1.0 O A:ALA33 5.0 27.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Oxa-163 Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Oxa-163 Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:44.8 occ:1.00 OE2 B:GLU256 2.3 30.0 1.0 NE2 B:HIS38 2.6 30.4 1.0 CE1 B:HIS38 3.0 30.9 1.0 CD B:GLU256 3.1 28.8 1.0 O B:HOH599 3.1 35.1 1.0 OE1 B:GLU256 3.7 21.5 1.0 CD2 B:HIS38 3.9 25.4 1.0 CG B:GLU256 4.1 25.2 1.0 ND1 B:HIS38 4.2 25.0 1.0 CB B:ALA252 4.2 25.7 1.0 O B:HOH422 4.5 25.9 1.0 CG B:HIS38 4.7 23.9 1.0 C B:ALA252 4.9 20.6 1.0 O B:ALA252 4.9 21.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Oxa-163 Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Oxa-163 Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:37.7 occ:1.00 NH1 B:ARG174 2.3 32.5 1.0 OE2 B:GLU49 2.3 25.2 1.0 CZ B:ARG174 2.9 26.0 1.0 NE B:ARG174 3.0 19.7 1.0 O B:HOH651 3.1 35.2 1.0 CD B:GLU49 3.3 20.0 1.0 NE2 B:HIS178 3.3 19.9 1.0 OE1 B:GLU49 3.5 21.3 1.0 CD2 B:HIS178 3.6 16.9 1.0 NE2 B:GLN52 4.0 25.1 1.0 O B:HOH538 4.1 34.5 1.0 NZ B:LYS180 4.1 29.1 1.0 NH2 B:ARG174 4.2 29.3 1.0 O B:HOH716 4.3 40.9 1.0 CD B:ARG174 4.3 18.4 1.0 CB B:ARG174 4.4 19.5 1.0 O B:HOH566 4.4 42.8 1.0 O B:HOH648 4.4 35.1 1.0 CE1 B:HIS178 4.5 20.1 1.0 OE1 B:GLN52 4.5 28.6 1.0 CG B:GLU49 4.7 18.5 1.0 CG B:ARG174 4.7 17.2 1.0 CD B:GLN52 4.7 30.3 1.0 CG B:HIS178 4.8 17.8 1.0

V.Stojanoski, D.C.Chow, B.Fryszczyn, L.Hu, P.Nordmann, L.Poirel, B.Sankaran, B.V.Prasad, T.Palzkill. Structural Basis For Different Substrate Profiles of Two Closely Related Class D Beta-Lactamases and Their Inhibition By Halogens. Biochemistry V. 54 3370 2015.
ISSN: ISSN 0006-2960
PubMed: 25938261
DOI: 10.1021/ACS.BIOCHEM.5B00298