Sodium in PDB 5edf: Crystal Structure of the Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis

The structure of Crystal Structure of the Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis, PDB code: 5edf was solved by E.Sviridova, L.Bumba, P.Rezacova, P.Sebo, I.Kuta Smatanova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.20 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.293, 38.829, 165.670, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.3

The binding sites of Sodium atom in the Crystal Structure of the Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis (pdb code 5edf). 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 Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis, PDB code: 5edf:

Sodium binding site 1 out of 1 in the Crystal Structure of the Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis


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 Selenomethionine-Substituted Iron-Regulated Protein Frpd From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:39.6 occ:1.00 OH2 A:1PE302 2.7 43.0 1.0 C13 A:1PE302 3.1 40.3 1.0 OH7 A:1PE302 3.2 54.1 1.0 OH6 A:1PE302 3.4 48.5 1.0 C14 A:1PE302 3.4 50.0 1.0 C12 A:1PE302 3.6 42.8 1.0 C25 A:1PE302 3.6 47.8 1.0 OH4 A:1PE302 3.7 38.4 1.0 C16 A:1PE302 3.8 50.9 1.0 C15 A:1PE302 3.8 47.0 1.0 C26 A:1PE302 3.8 50.9 1.0 OH5 A:1PE302 3.9 49.4 1.0 C24 A:1PE302 3.9 42.6 1.0 CE1 A:TYR80 3.9 17.0 1.0 C22 A:1PE302 4.2 45.1 1.0 C23 A:1PE302 4.4 45.0 1.0 CD1 A:TYR80 4.4 16.7 1.0 O A:HOH422 4.5 22.9 1.0 OH3 A:1PE302 4.6 43.5 1.0 CZ A:TYR80 4.8 16.3 1.0 OH A:TYR80 4.9 18.0 1.0

E.Sviridova, P.Rezacova, A.Bondar, V.Veverka, P.Novak, G.Schenk, D.I.Svergun, I.Kuta Smatanova, L.Bumba. Structural Basis of the Interaction Between the Putative Adhesion-Involved and Iron-Regulated Frpd and Frpc Proteins of Neisseria Meningitidis. Sci Rep V. 7 40408 2017.
ISSN: ESSN 2045-2322
PubMed: 28084396
DOI: 10.1038/SREP40408