Sodium in PDB 5oxo: Peptst Apo Structure

The structure of Peptst Apo Structure, PDB code: 5oxo was solved by M.Martinez Molledo, E.M.Quistgaard, C.Loew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.100, 110.300, 110.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.7

The binding sites of Sodium atom in the Peptst Apo Structure (pdb code 5oxo). 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 Peptst Apo Structure, PDB code: 5oxo:

Sodium binding site 1 out of 1 in the Peptst Apo Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peptst Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:34.4 occ:1.00 O A:SER316 2.3 39.6 1.0 O A:HOH610 2.4 27.3 1.0 O A:PHE319 2.4 31.1 1.0 O A:HOH751 2.4 45.7 1.0 OG A:SER316 2.9 45.0 1.0 C A:SER316 3.4 36.7 1.0 C A:PHE319 3.4 31.6 1.0 N A:VAL321 3.8 24.2 1.0 CB A:SER316 3.9 43.6 1.0 O A:HOH762 3.9 44.5 1.0 CA A:PRO320 4.1 24.2 1.0 N A:PRO320 4.1 26.6 1.0 N A:PHE319 4.2 29.4 1.0 C A:PRO320 4.3 23.9 1.0 CA A:SER316 4.3 40.2 1.0 N A:SER317 4.3 32.9 1.0 C A:SER317 4.3 31.1 1.0 CA A:SER317 4.3 33.6 1.0 CA A:PHE319 4.4 33.0 1.0 OE2 A:GLU171 4.5 40.9 1.0 CB A:VAL321 4.5 28.5 1.0 O A:SER317 4.5 31.9 1.0 O A:HOH732 4.6 53.6 1.0 OE1 A:GLU171 4.6 42.4 1.0 CA A:VAL321 4.6 23.0 1.0 N A:TRP318 4.8 32.5 1.0 CD A:GLU171 5.0 40.5 1.0 O A:HOH630 5.0 38.6 1.0

M.Martinez Molledo, E.M.Quistgaard, A.Flayhan, J.Pieprzyk, C.Low. Multispecific Substrate Recognition in A Proton-Dependent Oligopeptide Transporter. Structure V. 26 467 2018.
ISSN: ISSN 1878-4186
PubMed: 29429879
DOI: 10.1016/J.STR.2018.01.005