Sodium in PDB 5xnq: Crystal Structures of Human SALM5

The structure of Crystal Structures of Human SALM5, PDB code: 5xnq was solved by H.Liu, Z.Lin, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.88 / 2.80
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.601, 152.601, 93.822, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 26.9

The structure of Crystal Structures of Human SALM5 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Crystal Structures of Human SALM5 (pdb code 5xnq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structures of Human SALM5, PDB code: 5xnq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structures of Human SALM5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of Human SALM5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:78.0 occ:1.00 OE1 A:GLN208 2.5 99.0 1.0 OG A:SER265 2.8 70.7 1.0 O A:PRO241 2.9 73.7 1.0 CB A:ALA264 3.4 67.2 1.0 CD A:GLN208 3.5 94.0 1.0 N A:HIS243 3.5 81.3 1.0 CB A:HIS243 3.5 84.4 1.0 CA A:HIS243 3.7 82.9 1.0 CB A:SER265 3.7 72.0 1.0 C A:LEU242 3.7 76.5 1.0 N A:SER265 3.7 72.7 1.0 O A:LEU242 3.8 73.1 1.0 C A:PRO241 3.8 73.3 1.0 CG A:GLN208 4.0 86.7 1.0 C A:ALA264 4.2 70.7 1.0 CA A:ALA264 4.3 68.1 1.0 CB A:GLN208 4.3 73.1 1.0 CA A:SER265 4.3 71.8 1.0 CG A:HIS243 4.5 90.7 1.0 CB A:PRO241 4.5 71.0 1.0 ND1 A:HIS243 4.6 88.8 1.0 N A:LEU242 4.6 75.4 1.0 NE2 A:GLN208 4.6 97.8 1.0 CA A:LEU242 4.6 73.1 1.0 N A:ALA264 4.7 68.4 1.0 CA A:PRO241 4.7 72.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structures of Human SALM5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structures of Human SALM5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:68.4 occ:1.00 O A:ARG84 3.2 60.5 1.0 O A:HOH897 3.2 64.7 1.0 O A:ASN61 3.4 63.3 1.0 CE1 A:PHE62 3.6 49.1 1.0 O A:HOH928 3.7 73.8 1.0 CD1 A:PHE62 3.8 56.5 1.0 CZ A:PHE62 3.9 49.9 1.0 O A:HOH828 4.1 63.7 1.0 C A:ARG84 4.1 61.4 1.0 C A:ASN61 4.1 58.4 1.0 CG A:PHE62 4.5 61.5 1.0 CE2 A:PHE62 4.5 52.9 1.0 N A:ASN61 4.6 55.7 1.0 CA A:ASN85 4.6 60.8 1.0 C A:ASP60 4.6 53.0 1.0 CD2 A:PHE62 4.7 57.1 1.0 N A:ASN85 4.8 64.3 1.0 N A:PHE62 4.8 63.1 1.0 CA A:ASN61 4.8 53.4 1.0 CA A:ASP60 4.9 55.9 1.0 CG2 A:THR86 4.9 72.4 1.0 CA A:PHE62 4.9 61.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structures of Human SALM5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structures of Human SALM5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:80.5 occ:1.00 O A:HOH883 2.7 53.3 1.0 O A:HOH902 2.8 85.8 1.0 CL A:CL710 3.7 96.9 1.0 O A:ASN132 3.8 64.2 1.0 CA A:SER108 4.0 56.7 1.0 C A:SER108 4.0 59.6 1.0 O A:SER108 4.2 53.8 1.0 CB A:SER108 4.2 53.0 1.0 OG A:SER108 4.3 55.6 1.0 N A:ASN109 4.4 70.2 1.0 O A:HOH926 4.4 89.1 1.0 O A:ASN109 4.5 74.3 1.0 O A:HOH928 4.6 73.8 1.0 CL A:CL709 4.6 0.1 1.0 CB A:ASN132 4.8 57.0 1.0 C A:ASN132 4.9 66.8 1.0 C A:ASN109 5.0 65.7 1.0

Z.Lin, J.Liu, H.Ding, F.Xu, H.Liu. Structural Basis of SALM5-Induced Ptp Delta Dimerization For Synaptic Differentiation Nat Commun V. 9 268 2018.
ISSN: ESSN 2041-1723
PubMed: 29348579
DOI: 10.1038/S41467-017-02414-2