Sodium in PDB 6t46: Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide

The structure of Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide, PDB code: 6t46 was solved by I.Crespo, N.Bernardo, W.J.J.Meijer, D.R.Boer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.670, 93.282, 167.687, 90.00, 94.97, 90.00
R / Rfree (%)	20.2 / 26.2

The structure of Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide (pdb code 6t46). 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 Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide, PDB code: 6t46:

Sodium binding site 1 out of 1 in the Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Rap Conjugation Gene Regulator of the Plasmid PLS20 in Complex with the Phr* Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:38.9 occ:1.00 OD1 C:ASP192 3.1 74.7 1.0 OD1 C:ASP191 3.4 91.0 1.0 NH2 A:ARG362 3.7 61.5 1.0 CA C:ARG189 3.7 50.1 1.0 N C:ASP191 3.9 72.9 1.0 C C:ARG189 3.9 50.1 1.0 CB C:ASP191 4.0 74.2 1.0 N C:LEU190 4.0 41.9 1.0 CB C:ARG189 4.1 49.8 1.0 CG C:ASP191 4.2 88.9 1.0 NE A:ARG362 4.3 54.7 1.0 N C:ASP192 4.3 62.9 1.0 CG C:ASP192 4.3 63.7 1.0 CZ A:ARG362 4.5 56.4 1.0 CA C:ASP191 4.5 65.9 1.0 CG C:ARG189 4.5 49.0 1.0 O C:ARG189 4.5 54.1 1.0 O C:GLY188 4.8 41.0 1.0 C C:LEU190 4.9 52.2 1.0 C C:ASP191 4.9 70.7 1.0 N C:ARG189 5.0 40.6 1.0

I.Crespo, N.Bernardo, A.Miguel-Arribas, P.K.Singh, J.R.Luque-Ortega, C.Alfonso, M.Malfois, W.J.J.Meijer, D.R.Boer. Inactivation of the Dimeric RAPPLS20 Anti-Repressor of the Conjugation Operon Is Mediated By Signaling Peptide-Induced Tetramerization Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962