Sodium in PDB 8qd6: Anti SER245DHA (Pmsf)

The structure of Anti SER245DHA (Pmsf), PDB code: 8qd6 was solved by M.Schmalhofer, A.L.Vagstad, Q.Zhou, H.B.Bode, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.72, 154.97, 91.37, 90, 90, 90
R / Rfree (%)	16.7 / 18.8

The binding sites of Sodium atom in the Anti SER245DHA (Pmsf) (pdb code 8qd6). 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 Anti SER245DHA (Pmsf), PDB code: 8qd6:

Sodium binding site 1 out of 1 in the Anti SER245DHA (Pmsf)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Anti SER245DHA (Pmsf) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:41.2 occ:1.00 O A:ASP231 2.3 47.5 1.0 O A:ILE234 2.5 44.2 1.0 O A:LEU228 2.5 41.2 1.0 O A:GLU229 3.1 49.6 1.0 C A:ASP231 3.4 47.0 1.0 C A:GLU229 3.5 47.8 1.0 C A:ILE234 3.6 41.8 1.0 O A:HOH704 3.6 51.0 1.0 C A:LEU228 3.7 41.0 1.0 CA A:GLU229 3.8 45.2 1.0 N A:ASP231 4.0 47.3 1.0 OG A:SER236 4.1 48.2 1.0 N A:GLU229 4.2 42.5 1.0 N A:SER236 4.2 43.8 1.0 CA A:ASP231 4.3 46.7 1.0 CA A:ILE234 4.3 40.2 1.0 CB A:SER236 4.3 45.5 1.0 CB A:ILE234 4.3 38.4 1.0 N A:ALA232 4.3 48.3 1.0 N A:ASP230 4.3 48.5 1.0 N A:ILE234 4.3 40.7 1.0 CA A:ALA232 4.5 48.2 1.0 C A:ASP230 4.5 49.8 1.0 N A:ASN235 4.6 40.8 1.0 C A:ALA232 4.7 47.6 1.0 CA A:SER236 4.8 44.0 1.0 CB A:ASP231 4.8 44.7 1.0 CA A:ASN235 4.8 43.7 1.0 CG2 A:ILE234 4.9 36.6 1.0 CA A:LEU228 4.9 38.7 1.0 C A:ASN235 4.9 42.4 1.0 CA A:ASP230 5.0 50.9 1.0 O A:ALA232 5.0 50.5 1.0

M.Schmalhofer, A.L.Vagstad, Q.Zhou, H.B.Bode, M.Groll. Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments Adv Sci 2024.
ISSN: ESSN 2198-3844
DOI: 10.1002/ADVS.202400184