Sodium in PDB 7b3s: Oxa-10 Beta-Lactamase with S67DHA Modification

All present enzymatic activity of Oxa-10 Beta-Lactamase with S67DHA Modification:
3.5.2.6;

The structure of Oxa-10 Beta-Lactamase with S67DHA Modification, PDB code: 7b3s was solved by P.A.Lang, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.896, 97.205, 125.898, 90, 90, 90
R / Rfree (%)	16.5 / 20.3

The binding sites of Sodium atom in the Oxa-10 Beta-Lactamase with S67DHA Modification (pdb code 7b3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Oxa-10 Beta-Lactamase with S67DHA Modification, PDB code: 7b3s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Oxa-10 Beta-Lactamase with S67DHA Modification


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oxa-10 Beta-Lactamase with S67DHA Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:16.6 occ:1.00 O A:HOH617 2.8 27.4 1.0 O A:HOH584 2.8 15.5 1.0 N A:ALA98 3.0 14.1 1.0 CA A:ARG97 3.5 12.3 1.0 CG A:PRO118 3.6 13.3 1.0 CB A:ARG97 3.7 11.4 1.0 CZ3 A:TRP102 3.8 10.6 1.0 C A:ARG97 3.8 12.8 1.0 CE3 A:TRP102 3.8 13.1 1.0 CD A:PRO118 3.8 11.6 1.0 CB A:ALA98 3.8 22.2 1.0 CG A:ARG97 4.0 11.2 1.0 CB A:PRO118 4.0 12.9 1.0 CA A:ALA98 4.0 18.9 1.0 O A:PRO96 4.8 17.5 1.0 CD A:ARG97 4.8 10.3 1.0 N A:ARG97 4.9 15.4 1.0 N A:PRO118 4.9 12.6 1.0 O A:ARG97 5.0 13.5 1.0

Sodium binding site 2 out of 3 in the Oxa-10 Beta-Lactamase with S67DHA Modification


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oxa-10 Beta-Lactamase with S67DHA Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:27.3 occ:1.00 O A:HOH622 2.9 50.2 1.0 NE A:ARG250 3.1 18.1 1.0 O A:HOH664 3.3 37.1 1.0 NH1 A:ARG250 3.3 22.2 1.0 CZ A:ARG250 3.6 21.1 1.0 CE A:LYS251 3.9 57.0 1.0 O A:LEU247 4.0 20.3 1.0 CA A:PRO248 4.0 22.4 1.0 CG A:ARG250 4.1 22.1 1.0 CD A:ARG250 4.2 20.3 1.0 CG A:LYS251 4.3 31.9 1.0 C A:LEU247 4.4 26.0 1.0 N A:PRO248 4.4 18.3 1.0 CD A:LYS251 4.6 40.6 1.0 CG A:LEU247 4.7 26.2 1.0 CB A:LYS251 4.8 25.1 1.0 C A:PRO248 4.8 18.2 1.0 CG2 A:THR206 4.9 19.6 1.0 O A:PRO248 4.9 19.0 1.0 CB A:PRO248 4.9 33.5 1.0 NH2 A:ARG250 4.9 22.9 1.0

Sodium binding site 3 out of 3 in the Oxa-10 Beta-Lactamase with S67DHA Modification


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Oxa-10 Beta-Lactamase with S67DHA Modification within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:65.0 occ:1.00 CB B:MET19 2.9 43.0 0.7 N B:MET19 3.0 29.3 0.7 CA B:MET19 3.3 36.8 0.7 OE1 B:GLU171 3.4 41.5 1.0 CD B:GLU171 4.1 30.2 1.0 CG B:GLU168 4.2 33.7 1.0 O B:VAL167 4.3 14.5 1.0 CA B:GLU168 4.3 13.3 1.0 CG2 B:VAL167 4.3 13.0 1.0 N B:GLU168 4.4 10.0 1.0 C B:VAL167 4.5 12.0 1.0 SG B:CYS51 4.5 29.7 1.0 SG B:CYS44 4.5 27.7 1.0 CB B:GLU171 4.6 13.7 1.0 O B:HOH545 4.6 51.6 1.0 OE2 B:GLU171 4.6 33.0 1.0 CB B:CYS44 4.7 18.9 1.0 C B:MET19 4.8 24.7 0.7 O B:HOH487 4.9 20.8 1.0 CB B:GLU168 4.9 16.8 1.0 CB B:VAL167 4.9 12.4 1.0 O B:HOH462 4.9 53.8 1.0 CG B:GLU171 5.0 15.6 1.0 O B:HOH402 5.0 49.5 1.0

P.A.Lang, R.Raj, A.Tumber, C.T.Lohans, P.Rabe, C.V.Robinson, J.Brem, C.J.Schofield. Studies on Enmetazobactam Clarify Mechanisms of Widely Used Beta-Lactamase Inhibitors. Proc.Natl.Acad.Sci.Usa V. 119 10119 2022.
ISSN: ESSN 1091-6490
PubMed: 35486701
DOI: 10.1073/PNAS.2117310119