Sodium in PDB 8st6: Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome

The structure of Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome, PDB code: 8st6 was solved by H.E.Stubbs, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.39 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.067, 57.695, 75.952, 90, 90, 90
R / Rfree (%)	17.1 / 20.8

The binding sites of Sodium atom in the Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome (pdb code 8st6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome, PDB code: 8st6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:19.5 occ:1.00 O A:GLU247 2.2 28.2 1.0 OD1 A:ASN273 2.4 32.2 1.0 OD2 A:ASP346 2.5 30.4 1.0 OD1 A:ASP272 2.6 22.0 1.0 OD2 A:ASP272 2.6 23.3 1.0 CG A:ASP272 3.0 21.7 1.0 C A:GLU247 3.3 29.1 1.0 HD21 A:ASN350 3.4 44.0 1.0 CG A:ASN273 3.5 31.3 1.0 CG A:ASP346 3.5 29.7 1.0 H A:SER274 3.6 25.5 1.0 HB3 A:ASP346 3.6 33.6 1.0 H A:ASN273 3.6 25.3 1.0 HB3 A:SER274 3.7 27.6 1.0 HD22 A:ASN273 3.8 41.7 1.0 HB2 A:ASP346 3.8 33.6 1.0 CB A:ASP346 3.9 28.0 1.0 ND2 A:ASN273 4.0 34.8 1.0 N A:ASN273 4.2 21.1 1.0 N A:ALA248 4.2 26.9 1.0 HG A:SER274 4.2 30.2 1.0 CA A:GLU247 4.3 32.8 1.0 ND2 A:ASN350 4.3 36.7 1.0 HB2 A:ASN350 4.3 40.6 1.0 O A:HOH712 4.3 29.9 1.0 CA A:ALA248 4.3 25.0 1.0 N A:SER274 4.3 21.2 1.0 N A:GLU247 4.4 32.4 1.0 C A:ALA248 4.4 21.4 1.0 O A:HOH621 4.4 28.4 1.0 CB A:ASP272 4.4 20.1 1.0 CB A:SER274 4.6 23.0 1.0 CB A:ASN273 4.6 26.6 1.0 HD22 A:ASN350 4.6 44.0 1.0 CB A:GLU247 4.6 37.5 1.0 OD1 A:ASP346 4.7 30.0 1.0 HA A:ASP272 4.7 22.1 1.0 O A:ALA248 4.7 22.3 1.0 OG A:SER274 4.8 25.1 1.0 CA A:ASN273 4.8 22.4 1.0 N A:PRO249 4.8 19.9 1.0 HB3 A:ASP272 4.9 24.1 1.0 HD21 A:ASN273 4.9 41.7 1.0 HB3 A:ASN273 4.9 31.9 1.0 HB2 A:ASP272 4.9 24.1 1.0 C A:ASN273 4.9 21.7 1.0 CD A:PRO249 4.9 20.4 1.0 C A:ASP272 5.0 19.2 1.0 CA A:ASP272 5.0 18.4 1.0

Sodium binding site 2 out of 2 in the Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:23.8 occ:1.00 O A:TYR377 2.2 23.2 1.0 O A:ASN374 2.4 20.0 1.0 OD2 A:ASP436 2.4 25.0 1.0 O A:HOH817 2.4 28.9 1.0 O A:HOH808 2.5 38.7 1.0 OD1 A:ASP436 2.7 27.5 1.0 CG A:ASP436 2.9 23.3 1.0 HD3 A:PRO379 3.2 28.6 1.0 C A:ASN374 3.4 20.1 1.0 C A:TYR377 3.4 18.4 1.0 HB2 A:ASN374 3.6 19.9 1.0 HA A:GLU375 3.6 20.6 1.0 H A:TYR377 3.6 20.9 1.0 HD21 A:ASN374 3.7 55.0 1.0 HA A:ASP378 3.8 28.5 0.8 O A:HOH732 3.9 34.8 1.0 HD2 A:PRO379 3.9 28.6 1.0 HB2 A:TYR377 4.0 20.7 1.0 CD A:PRO379 4.0 23.8 1.0 HA A:ASN374 4.2 23.0 1.0 CA A:ASN374 4.2 19.2 1.0 CB A:ASN374 4.2 16.6 1.0 HH A:TYR430 4.2 25.3 1.0 N A:GLU375 4.2 19.1 1.0 N A:TYR377 4.2 17.4 1.0 ND2 A:ASN374 4.2 45.9 1.0 CA A:TYR377 4.2 18.0 1.0 CA A:GLU375 4.3 17.2 1.0 N A:ASP378 4.3 20.8 1.0 CB A:ASP436 4.3 19.9 1.0 OH A:TYR430 4.5 21.1 1.0 CA A:ASP378 4.5 23.7 0.8 HB3 A:ASP436 4.6 23.9 1.0 CB A:TYR377 4.6 17.2 1.0 CG A:ASN374 4.6 27.6 1.0 C A:GLU375 4.7 18.9 1.0 HB2 A:ASP436 4.7 23.9 1.0 O A:HOH868 4.7 43.0 1.0 HD22 A:ASN374 4.8 55.0 1.0 HG2 A:PRO379 4.8 33.7 1.0 CG A:PRO379 4.8 28.0 1.0 HE1 A:TYR430 4.8 21.9 1.0 HG3 A:PRO379 4.9 33.7 1.0 HB3 A:TYR377 5.0 20.7 1.0 O A:HOH775 5.0 29.5 1.0 O A:GLU375 5.0 20.4 1.0

H.E.Stubbs, T.M.Iverson. Hsa Siglec + Unique Domains Bound to NEU5GC ALPHA2,3 Gal Beta Ome To Be Published.