Sodium in PDB 5jxf: Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp

The structure of Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp, PDB code: 5jxf was solved by G.A.Bezerra, S.Fedosyuk, Y.Ohara-Nemoto, T.K.Nemoto, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	126.051, 70.689, 191.598, 90.00, 97.26, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp (pdb code 5jxf). 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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp, PDB code: 5jxf:

Sodium binding site 1 out of 1 in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp


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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp within 5.0Å range: probe atom residue distance (Å) B Occ D:Na803 b:57.8 occ:1.00 OH D:TYR584 2.4 62.5 1.0 N D:GLY576 2.9 51.8 1.0 OE2 D:GLU258 2.9 77.9 1.0 CD D:GLU258 3.0 80.1 1.0 OE1 D:GLU258 3.1 86.0 1.0 CZ D:TYR584 3.4 56.2 1.0 CA D:GLY576 3.4 53.9 1.0 CE2 D:TYR584 3.6 49.5 1.0 CG D:GLU258 3.8 70.3 1.0 CD D:PRO587 3.8 46.8 1.0 C D:LYS575 4.0 52.2 1.0 CG D:PRO587 4.0 53.3 1.0 CE D:LYS575 4.2 65.3 1.0 CD D:LYS575 4.2 57.4 1.0 C D:GLY576 4.2 57.3 1.0 CA D:LYS575 4.3 53.7 1.0 CG D:LYS575 4.4 54.0 1.0 O D:GLY576 4.5 48.1 1.0 CE1 D:TYR584 4.7 59.0 1.0 NZ D:LYS575 4.7 60.8 1.0 CB D:PRO587 4.7 49.7 1.0 N D:PRO587 4.8 46.8 1.0 CB D:GLU258 4.9 62.7 1.0 CB D:LYS575 5.0 50.7 1.0 CD2 D:TYR584 5.0 55.7 1.0

G.A.Bezerra, Y.Ohara-Nemoto, I.Cornaciu, S.Fedosyuk, G.Hoffmann, A.Round, J.A.Marquez, T.K.Nemoto, K.Djinovic-Carugo. Bacterial Protease Uses Distinct Thermodynamic Signatures For Substrate Recognition. Sci Rep V. 7 2848 2017.
ISSN: ESSN 2045-2322
PubMed: 28588213
DOI: 10.1038/S41598-017-03220-Y