Sodium in PDB 9hfu: CAPRIN1 Peptide Bound to Spop Math Domain

The structure of CAPRIN1 Peptide Bound to Spop Math Domain, PDB code: 9hfu was solved by L.Makhlouf, E.Zeqiraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.66 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.808, 60.882, 57.117, 90, 90.05, 90
R / Rfree (%)	16.2 / 20.4

The binding sites of Sodium atom in the CAPRIN1 Peptide Bound to Spop Math Domain (pdb code 9hfu). 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 CAPRIN1 Peptide Bound to Spop Math Domain, PDB code: 9hfu:

Sodium binding site 1 out of 1 in the CAPRIN1 Peptide Bound to Spop Math Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CAPRIN1 Peptide Bound to Spop Math Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:23.6 occ:1.00 O B:HOH348 2.2 28.5 1.0 O B:ALA61 2.3 25.7 1.0 OG B:SER58 2.4 23.3 1.0 O B:SER59 2.4 20.9 1.0 OD1 B:ASP63 2.5 19.2 1.0 OG B:SER59 2.7 20.4 1.0 H B:ASP63 3.1 23.3 1.0 H B:SER59 3.2 19.3 1.0 C B:SER59 3.2 17.5 1.0 HG B:SER59 3.2 24.5 1.0 CG B:ASP63 3.3 22.1 1.0 N B:SER59 3.3 16.1 1.0 HB3 B:SER58 3.4 22.7 1.0 C B:ALA61 3.4 30.3 1.0 CB B:SER58 3.5 18.9 1.0 CA B:SER59 3.5 15.5 1.0 OD2 B:ASP63 3.6 20.6 1.0 CB B:SER59 3.7 17.2 1.0 H B:ALA61 3.7 25.5 1.0 N B:ALA61 3.8 21.2 1.0 C B:SER58 3.9 16.1 1.0 N B:ASP63 3.9 19.4 1.0 O B:HOH313 4.0 22.1 1.0 HB3 B:ALA61 4.0 30.9 1.0 CA B:ALA61 4.1 26.7 1.0 HB2 B:SER58 4.2 22.7 1.0 H B:LEU65 4.2 15.5 1.0 HB3 B:SER59 4.2 20.7 1.0 HA B:ASN62 4.2 29.3 1.0 H B:LYS64 4.2 20.3 1.0 CA B:SER58 4.2 16.8 1.0 C B:GLY60 4.3 28.7 1.0 N B:GLY60 4.3 23.9 1.0 HB2 B:SER59 4.3 20.7 1.0 O B:HOH341 4.4 27.0 1.0 O B:HOH346 4.4 34.5 1.0 N B:ASN62 4.5 24.6 1.0 O B:LEU65 4.5 16.1 1.0 CB B:ASP63 4.5 15.7 1.0 HA B:SER58 4.5 20.2 1.0 HA B:SER59 4.5 18.7 1.0 CB B:ALA61 4.6 25.7 1.0 HA2 B:GLY60 4.7 35.2 1.0 CA B:GLY60 4.7 29.3 1.0 CA B:ASP63 4.7 14.3 1.0 CA B:ASN62 4.7 24.4 1.0 HB3 B:ASP63 4.7 18.9 1.0 N B:LYS64 4.7 16.9 1.0 O B:SER58 4.7 21.2 1.0 HB2 B:LEU65 4.9 16.0 1.0 C B:ASN62 4.9 18.9 1.0 O B:GLY60 4.9 33.0 1.0 N B:LEU65 5.0 12.9 1.0 HA B:ALA61 5.0 32.1 1.0

L.Makhlouf, M.Mishra, H.Makhlouf, I.Manfield, L.Busino, E.Zeqiraj. Sequence Rules For A Long Spop-Binding Degron Required For Protein Ubiquitylation. Biochem.J. 2025.
ISSN: ESSN 1470-8728
PubMed: 40178506
DOI: 10.1042/BCJ20253041