Sodium in PDB 8qzg: 1,3 L,D-Transpeptidase From Gluconobacter Oxydans

The structure of 1,3 L,D-Transpeptidase From Gluconobacter Oxydans, PDB code: 8qzg was solved by J.Ter Beek, R.P.Berntsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.41 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.778, 56.688, 93.019, 90, 90, 90
R / Rfree (%)	17 / 20.5

The structure of 1,3 L,D-Transpeptidase From Gluconobacter Oxydans also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the 1,3 L,D-Transpeptidase From Gluconobacter Oxydans (pdb code 8qzg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 1,3 L,D-Transpeptidase From Gluconobacter Oxydans, PDB code: 8qzg:

Sodium binding site 1 out of 1 in the 1,3 L,D-Transpeptidase From Gluconobacter Oxydans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1,3 L,D-Transpeptidase From Gluconobacter Oxydans within 5.0Å range: probe atom residue distance (Å) B Occ 1:Na402 b:22.7 occ:1.00 H 1:THR184 2.2 21.2 1.0 O 1:GLY174 2.7 19.4 1.0 O 1:HOH525 2.7 24.6 1.0 H 1:GLY174 2.8 22.4 1.0 HG23 1:ILE183 2.8 21.1 1.0 HG1 1:THR173 2.8 22.8 1.0 OG1 1:THR173 2.9 19.0 1.0 N 1:THR184 3.0 17.7 1.0 HB2 1:ARG145 3.1 24.1 1.0 HA 1:ILE183 3.1 21.8 1.0 HB 1:THR184 3.1 23.6 1.0 HD2 1:ARG145 3.2 27.7 1.0 N 1:GLY174 3.2 18.6 1.0 HB 1:THR173 3.2 23.2 1.0 C 1:GLY174 3.5 18.4 1.0 HA3 1:GLY174 3.6 21.6 1.0 CB 1:THR173 3.6 19.3 1.0 CA 1:GLY174 3.6 17.9 1.0 OG1 1:THR184 3.6 17.5 1.0 CB 1:THR184 3.7 19.6 1.0 CG2 1:ILE183 3.7 17.6 1.0 O 1:HOH545 3.7 23.1 1.0 CA 1:ILE183 3.8 18.1 1.0 C 1:ILE183 3.9 19.0 1.0 CA 1:THR184 3.9 18.4 1.0 C 1:THR173 3.9 17.7 1.0 HG22 1:ILE183 3.9 21.1 1.0 CB 1:ARG145 4.0 20.0 1.0 CD 1:ARG145 4.1 23.1 1.0 O 1:THR184 4.2 17.4 1.0 O 1:ARG145 4.2 21.0 1.0 CB 1:ILE183 4.3 16.2 1.0 HG1 1:THR184 4.3 21.1 1.0 HE22 1:GLN150 4.3 25.9 1.0 HG12 1:ILE183 4.3 23.8 1.0 HD3 1:ARG145 4.4 27.7 1.0 HG21 1:ILE183 4.4 21.1 1.0 CA 1:THR173 4.4 17.7 1.0 HB3 1:ARG145 4.5 24.1 1.0 HB3 1:PRO259 4.5 29.5 1.0 CG 1:ARG145 4.6 21.5 1.0 HG21 1:THR322 4.6 34.5 1.0 C 1:THR184 4.6 17.3 1.0 HA2 1:GLY174 4.6 21.6 1.0 HA 1:THR184 4.7 22.1 1.0 O 1:THR173 4.7 18.4 1.0 HG3 1:ARG145 4.8 25.8 1.0 HG22 1:THR173 4.8 26.5 1.0 N 1:THR175 4.8 20.5 1.0 O 1:TYR182 4.8 20.5 1.0 CG2 1:THR173 4.8 22.1 1.0 HA 1:ARG145 4.9 22.6 1.0 CG1 1:ILE183 4.9 19.8 1.0 CA 1:ARG145 4.9 18.8 1.0 HA 1:THR173 5.0 21.3 1.0

A.Espaillat, L.Alvarez, G.Torrens, J.T.Beek, V.Miguel-Ruano, O.Irazoki, F.Gago, J.A.Hermoso, R.P.A.Berntsson, F.Cava. A Distinctive Family of L,D-Transpeptidases Catalyzing L-Ala-Mdap Crosslinks in Alpha and Betaproteobacteria Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.10.31.564931