Sodium in PDB 6chk: Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris

The structure of Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris, PDB code: 6chk was solved by Y.Patskovsky, R.Toro, I.G.Shabalin, M.Kowiel, P.J.Porebski, W.Minor, M.Jaskolski, R.Bhosle, N.Al Obaidi, S.Chamala, J.D.Attonito, A.Scottglenn, S.Chowdhury, J.Lafleur, R.D.Siedel, B.Hillerich, J.Love, K.L.Whalen, J.A.Gerlt, S.C.Almo, E.F.I.Enzyme Function Initiative, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	108.715, 108.715, 125.395, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 19

The structure of Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris (pdb code 6chk). 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 Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris, PDB code: 6chk:

Sodium binding site 1 out of 1 in the Crystal Structure of Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris


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 Laci Family Transcriptional Regulator From Lactobacillus Casei, Target Efi-512911, with Bound Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:38.4 occ:1.00 O A:HOH601 2.3 29.1 1.0 O A:HOH662 2.4 40.6 1.0 O A:HOH722 2.4 51.6 1.0 O A:HOH744 2.5 39.5 1.0 O A:ASP269 2.7 31.1 1.0 O A:HOH614 2.9 31.1 1.0 C A:ASP269 3.8 30.7 1.0 O A:HOH667 3.9 37.8 1.0 O A:ASP270 4.1 23.7 1.0 CE1 A:HIS176 4.1 25.8 1.0 ND1 A:HIS176 4.3 25.4 1.0 O A:PRO268 4.3 26.3 1.0 O A:HOH674 4.3 53.1 1.0 C A:ASP270 4.4 28.0 1.0 CA A:ASP270 4.6 27.4 1.0 N A:ASP270 4.6 26.0 1.0 CA A:ASP269 4.6 34.6 1.0 OD1 A:ASP243 4.9 35.9 1.0 O A:ASP243 4.9 21.0 1.0 O A:HOH708 5.0 54.6 1.0

M.Kowiel, D.Brzezinski, P.J.Porebski, I.G.Shabalin, M.Jaskolski, W.Minor. Automatic Recognition of Ligands in Electron Density By Machine Learning. Bioinformatics V. 35 452 2019.
ISSN: ESSN 1367-4811
PubMed: 30016407
DOI: 10.1093/BIOINFORMATICS/BTY626