Sodium in PDB 6efd: Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide

The structure of Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide, PDB code: 6efd was solved by T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.645, 58.140, 75.959, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.8

The binding sites of Sodium atom in the Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide (pdb code 6efd). 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 and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide, PDB code: 6efd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:29.0 occ:1.00 O A:GLU247 2.2 39.2 1.0 OD2 A:ASP272 2.3 28.9 1.0 OD2 A:ASP346 2.4 35.5 1.0 OD1 A:ASP272 2.5 25.6 1.0 O A:HOH601 2.6 39.4 1.0 OD1 A:ASN273 2.6 33.6 0.5 CG A:ASP272 2.8 25.9 1.0 C A:GLU247 3.4 37.9 1.0 CG A:ASP346 3.4 33.9 1.0 OE1 A:GLU247 3.6 61.8 1.0 CG A:ASN273 3.7 31.9 0.5 CB A:ASP346 3.7 30.3 1.0 N A:ASN273 4.2 28.5 0.5 CA A:GLU247 4.2 44.3 1.0 ND2 A:ASN273 4.2 40.1 0.5 N A:ASN273 4.3 26.7 0.5 N A:SER274 4.3 28.2 1.0 CB A:ASN273 4.3 31.3 0.5 N A:ALA248 4.3 34.4 1.0 CB A:ASP272 4.3 23.2 1.0 OD1 A:ASN350 4.3 38.2 1.0 CA A:ALA248 4.4 34.7 1.0 CB A:SER274 4.4 33.4 1.0 OG A:SER274 4.4 28.0 1.0 CD A:GLU247 4.4 56.8 1.0 O A:HOH602 4.4 32.7 1.0 C A:ALA248 4.5 26.1 1.0 OD1 A:ASP346 4.6 28.8 1.0 O A:HOH653 4.6 33.9 1.0 CA A:ASN273 4.7 28.9 0.5 CB A:GLU247 4.7 40.6 1.0 N A:PRO249 4.8 24.9 1.0 O A:ALA248 4.8 25.4 1.0 CB A:ASN273 4.8 31.2 0.5 CD A:PRO249 4.8 23.6 1.0 CA A:ASN273 4.8 28.8 0.5 CA A:ASP272 4.9 21.6 1.0 CB A:ASN350 4.9 29.1 1.0 C A:ASP272 4.9 24.2 1.0 C A:ASN273 5.0 29.8 0.5

Sodium binding site 2 out of 2 in the Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hsa Siglec and Unique Domains in Complex with the Sialyl T Antigen Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:31.4 occ:1.00 O A:TYR377 2.4 32.5 1.0 OD1 A:ASP436 2.4 35.4 1.0 OD2 A:ASP436 2.4 29.3 1.0 O A:HOH763 2.4 40.5 1.0 O A:ASN374 2.5 28.4 1.0 CG A:ASP436 2.7 37.3 1.0 C A:ASN374 3.5 29.5 1.0 C A:TYR377 3.6 31.5 1.0 CD A:PRO379 4.1 32.9 1.0 CB A:ASP436 4.2 27.4 1.0 CA A:ASN374 4.3 28.0 1.0 OD1 A:ASP378 4.3 50.6 1.0 CB A:ASN374 4.3 23.9 1.0 ND2 A:ASN374 4.4 42.2 1.0 N A:GLU375 4.4 26.2 1.0 CA A:TYR377 4.5 24.9 1.0 N A:ASP378 4.5 31.0 1.0 N A:TYR377 4.5 26.3 1.0 OH A:TYR430 4.5 26.3 1.0 CA A:GLU375 4.5 28.0 1.0 CA A:ASP378 4.6 31.3 1.0 CG A:ASN374 4.7 35.4 1.0 CG A:PRO379 4.8 27.9 1.0 CB A:TYR377 4.8 27.6 1.0 C A:GLU375 4.8 26.8 1.0

T.M.Iverson, T.M.Iverson. N/A N/A.