Sodium in PDB 7b3u: Oxa-10 Beta-Lactamase with Covalent Modification

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

The structure of Oxa-10 Beta-Lactamase with Covalent Modification, PDB code: 7b3u 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)	52.87 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.935, 97.222, 125.988, 90, 90, 90
R / Rfree (%)	15.5 / 17.7

The binding sites of Sodium atom in the Oxa-10 Beta-Lactamase with Covalent Modification (pdb code 7b3u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Oxa-10 Beta-Lactamase with Covalent Modification, PDB code: 7b3u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Oxa-10 Beta-Lactamase with Covalent 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 Covalent Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:15.3 occ:1.00 H A:ALA98 2.3 18.9 1.0 HA A:ARG97 2.9 17.4 1.0 O A:HOH646 2.9 24.9 1.0 O A:HOH584 2.9 17.2 1.0 HG3 A:PRO118 2.9 15.9 1.0 N A:ALA98 3.1 15.8 1.0 HZ3 A:TRP102 3.2 19.2 1.0 HB3 A:ARG97 3.2 16.0 1.0 HD3 A:PRO118 3.2 14.9 1.0 HE3 A:TRP102 3.2 17.6 1.0 HG2 A:ARG97 3.3 16.8 1.0 HB2 A:ALA98 3.4 25.0 1.0 HB3 A:PRO118 3.4 17.0 1.0 CA A:ARG97 3.5 14.5 1.0 CG A:PRO118 3.6 13.3 1.0 CB A:ARG97 3.7 13.3 1.0 HB3 A:ALA98 3.7 25.0 1.0 CZ3 A:TRP102 3.8 16.0 1.0 C A:ARG97 3.8 15.5 1.0 CE3 A:TRP102 3.9 14.6 1.0 CD A:PRO118 3.9 12.4 1.0 CB A:ALA98 3.9 20.8 1.0 CG A:ARG97 3.9 14.0 1.0 CB A:PRO118 4.0 14.2 1.0 CA A:ALA98 4.1 17.9 1.0 HD2 A:PRO118 4.4 14.9 1.0 HG2 A:PRO118 4.5 15.9 1.0 HA A:ALA98 4.6 21.6 1.0 HB2 A:ARG97 4.6 16.0 1.0 HG3 A:ARG97 4.6 16.8 1.0 HB2 A:PRO118 4.6 17.0 1.0 HD3 A:ARG97 4.6 15.9 1.0 O A:PRO96 4.8 21.1 1.0 H A:MET99 4.8 23.9 1.0 HB1 A:ALA98 4.8 25.0 1.0 N A:ARG97 4.8 15.7 1.0 CD A:ARG97 4.9 13.2 1.0 N A:PRO118 4.9 12.1 1.0 O A:HOH415 4.9 40.1 1.0 O A:HOH704 5.0 29.8 1.0

Sodium binding site 2 out of 2 in the Oxa-10 Beta-Lactamase with Covalent 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 Covalent Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:25.9 occ:1.00 HE A:ARG250 2.3 21.4 1.0 HH11 A:ARG250 2.6 25.2 1.0 O A:HOH683 2.9 41.6 1.0 HA A:PRO248 2.9 26.9 1.0 NE A:ARG250 3.1 17.8 1.0 O A:HOH701 3.3 36.5 1.0 NH1 A:ARG250 3.4 21.0 1.0 HG2 A:ARG250 3.5 23.0 1.0 HG3 A:LYS251 3.5 30.8 1.0 CZ A:ARG250 3.7 19.5 1.0 HG A:LEU247 3.8 30.2 1.0 CA A:PRO248 3.9 22.4 1.0 HD2 A:LYS251 4.0 46.7 1.0 O A:LEU247 4.0 19.3 1.0 HG21 A:THR206 4.0 20.5 1.0 CE A:LYS251 4.1 51.4 1.0 CG A:ARG250 4.1 19.2 1.0 HH12 A:ARG250 4.1 25.2 1.0 HG3 A:ARG250 4.2 23.0 1.0 CD A:ARG250 4.2 18.2 1.0 HB2 A:LYS251 4.2 25.9 1.0 CG A:LYS251 4.3 25.6 1.0 CD A:LYS251 4.3 38.9 1.0 N A:PRO248 4.4 19.4 1.0 C A:LEU247 4.4 19.3 1.0 HB3 A:PRO248 4.4 32.8 1.0 HG3 A:PRO248 4.5 36.8 1.0 H A:LYS251 4.6 22.8 1.0 HD23 A:LEU247 4.6 31.7 1.0 CG A:LEU247 4.7 25.2 1.0 CB A:PRO248 4.7 27.3 1.0 HD3 A:ARG250 4.7 21.8 1.0 HB3 A:LEU247 4.7 27.7 1.0 C A:PRO248 4.7 23.4 1.0 O A:PRO248 4.8 22.6 1.0 CB A:LYS251 4.8 21.6 1.0 HG22 A:THR206 4.9 20.5 1.0 CG2 A:THR206 4.9 17.1 1.0 HD2 A:ARG250 4.9 21.8 1.0 O A:HOH526 5.0 28.0 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