Sodium in PDB 2xdj: Crystal Structure of the N-Terminal Domain of E.Coli Ybgf

The structure of Crystal Structure of the N-Terminal Domain of E.Coli Ybgf, PDB code: 2xdj was solved by A.M.Krachler, A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.41 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.409, 40.870, 237.867, 90.00, 90.00, 90.00
R / Rfree (%)	22.524 / 27.447

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf (pdb code 2xdj). 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 the N-Terminal Domain of E.Coli Ybgf, PDB code: 2xdj:

Sodium binding site 1 out of 1 in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf


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 the N-Terminal Domain of E.Coli Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1069 b:26.2 occ:1.00 NE2 C:GLN57 3.2 29.9 1.0 OE1 E:GLN57 3.3 34.9 1.0 OE1 D:GLN57 3.3 27.1 1.0 CG E:GLN57 3.3 28.4 1.0 CG C:GLN57 3.4 28.6 1.0 CG D:GLN57 3.7 27.1 1.0 CD E:GLN57 3.8 33.8 1.0 CD C:GLN57 3.8 33.8 1.0 CD D:GLN57 4.0 26.9 1.0 CD1 D:ILE60 4.0 35.8 1.0 CB D:GLN57 4.0 26.9 1.0 CD1 E:ILE60 4.0 25.8 1.0 CD1 C:ILE60 4.0 26.7 1.0 CA D:GLN57 4.2 28.3 1.0 CB E:GLN57 4.4 26.6 1.0 CB C:GLN57 4.4 22.6 1.0 CA E:GLN57 4.7 25.9 1.0 CA C:GLN57 4.7 23.1 1.0 CG2 D:ILE60 4.7 28.0 1.0 CB D:ILE60 4.8 28.1 1.0 N D:GLN57 4.9 28.1 1.0

A.M.Krachler, A.Sharma, A.Cauldwell, G.Papadakos, C.Kleanthous. Tola Modulates the Oligomeric Status of Ybgf in the Bacterial Periplasm. J.Mol.Biol. V. 403 270 2010.
ISSN: ISSN 0022-2836
PubMed: 20816983
DOI: 10.1016/J.JMB.2010.08.050