Sodium in PDB 6ged: Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna

The structure of Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna, PDB code: 6ged was solved by A.Schmitt, R.P.A.Berntsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.73 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.017, 93.026, 99.097, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.2

The binding sites of Sodium atom in the Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna (pdb code 6ged). 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 Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna, PDB code: 6ged:

Sodium binding site 1 out of 1 in the Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Adhesin Domain of Prgb From Enterococcus Faecalis Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:27.1 occ:1.00 O A:HOH794 2.3 34.2 1.0 O A:SER442 2.3 23.5 1.0 OD1 A:ASN444 2.5 24.3 1.0 O A:HOH776 2.6 33.9 1.0 OE1 A:GLU455 2.6 28.2 1.0 OG A:SER442 2.9 25.7 1.0 CD A:GLU455 3.2 31.2 1.0 C A:SER442 3.4 20.3 1.0 OE2 A:GLU455 3.6 30.0 1.0 O A:HOH726 3.6 25.4 1.0 CG A:ASN444 3.6 26.0 1.0 CB A:SER442 3.6 22.8 1.0 O A:HOH710 3.7 40.9 1.0 CA A:SER442 4.1 18.7 1.0 N A:ASN444 4.1 17.0 1.0 O A:HOH712 4.2 29.6 1.0 OD2 A:ASP503 4.2 24.3 1.0 CB A:ASN444 4.3 17.5 1.0 CG A:GLU455 4.3 27.5 1.0 N A:LEU443 4.4 16.3 1.0 O A:TRP544 4.6 20.1 1.0 ND2 A:ASN444 4.6 21.7 1.0 CB A:GLU455 4.7 18.9 1.0 O A:HOH778 4.7 30.0 1.0 CA A:LEU443 4.7 18.4 1.0 CA A:ASN444 4.9 16.4 1.0 C A:LEU443 5.0 16.9 1.0

A.Schmitt, K.Jiang, M.I.Camacho, V.R.Jonna, A.Hofer, F.Westerlund, P.J.Christie, R.P.Berntsson. Prgb Promotes Aggregation, Biofilm Formation, and Conjugation Through Dna Binding and Compaction. Mol. Microbiol. V. 109 291 2018.
ISSN: ESSN 1365-2958
PubMed: 29723434
DOI: 10.1111/MMI.13980