Sodium in PDB 6x3q: Hsa Siglec and Unique Domains in Complex with 3'Sialyl-N- Acetyllactosamine Trisaccharide

The structure of Hsa Siglec and Unique Domains in Complex with 3'Sialyl-N- Acetyllactosamine Trisaccharide, PDB code: 6x3q 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)	32.42 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.743, 57.738, 75.86, 90, 90, 90
R / Rfree (%)	20.6 / 23.3

The binding sites of Sodium atom in the Hsa Siglec and Unique Domains in Complex with 3'Sialyl-N- Acetyllactosamine Trisaccharide (pdb code 6x3q). 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 3'Sialyl-N- Acetyllactosamine Trisaccharide, PDB code: 6x3q:
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 3'Sialyl-N- Acetyllactosamine 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 3'Sialyl-N- Acetyllactosamine Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:29.5 occ:1.00 OD2 A:ASP346 2.2 39.4 1.0 O A:GLU247 2.2 47.9 1.0 OD1 A:ASP272 2.4 37.1 1.0 OD2 A:ASP272 2.6 38.7 1.0 OD2 A:ASP245 2.6 47.9 1.0 OD1 A:ASP245 2.6 90.0 1.0 OD1 A:ASN273 2.8 53.0 1.0 CG A:ASP245 2.8 83.8 1.0 CG A:ASP272 2.8 46.5 1.0 CG A:ASP346 3.3 44.7 1.0 C A:GLU247 3.4 59.0 1.0 HD22 A:ASN350 3.5 89.8 1.0 HB3 A:ASP346 3.6 42.3 1.0 H A:SER274 3.7 48.0 1.0 HB3 A:GLU247 3.7 88.6 1.0 HA A:ALA248 3.8 46.8 1.0 HB3 A:SER274 3.8 42.1 1.0 H A:ASN273 3.8 51.1 1.0 HB2 A:ASP346 3.8 42.3 1.0 CB A:ASP346 3.9 35.2 1.0 CG A:ASN273 3.9 53.3 1.0 HD21 A:ASN273 4.0 75.3 1.0 O A:HOH613 4.1 44.9 1.0 H A:GLU247 4.1 171.8 1.0 CB A:ASP245 4.2 114.1 1.0 HB2 A:ASN350 4.2 54.4 1.0 HB3 A:ASP245 4.2 137.0 1.0 N A:ALA248 4.2 43.3 1.0 CA A:ALA248 4.3 38.9 1.0 C A:ALA248 4.3 38.8 1.0 HG A:SER274 4.3 47.8 1.0 OD1 A:ASP346 4.3 35.1 1.0 CB A:ASP272 4.3 41.2 1.0 CA A:GLU247 4.4 88.0 1.0 ND2 A:ASN273 4.4 62.7 1.0 HD3 A:PRO249 4.4 42.9 1.0 N A:ASN273 4.4 42.5 1.0 ND2 A:ASN350 4.4 74.8 1.0 O A:HOH624 4.5 42.9 1.0 CB A:GLU247 4.5 73.8 1.0 N A:SER274 4.5 40.0 1.0 N A:GLU247 4.5 143.1 1.0 N A:PRO249 4.6 32.4 1.0 O A:ALA248 4.6 34.0 1.0 CB A:SER274 4.7 35.0 1.0 HG2 A:GLU247 4.7 86.7 1.0 HA A:ASP272 4.7 41.8 1.0 HB2 A:ASP245 4.7 137.0 1.0 HB3 A:ASP272 4.8 49.6 1.0 HB2 A:ASP272 4.8 49.6 1.0 HA A:PRO249 4.8 38.2 1.0 OG A:SER274 4.9 39.7 1.0 HD21 A:ASN350 4.9 89.8 1.0 CA A:ASP272 4.9 34.8 1.0 HG3 A:PRO249 4.9 38.8 1.0 CB A:ASN350 5.0 45.3 1.0 CD A:PRO249 5.0 35.7 1.0 HB3 A:ASN350 5.0 54.4 1.0

Sodium binding site 2 out of 2 in the Hsa Siglec and Unique Domains in Complex with 3'Sialyl-N- Acetyllactosamine 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 3'Sialyl-N- Acetyllactosamine Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:45.4 occ:1.00 O A:HOH662 2.2 42.3 1.0 O A:TYR377 2.4 46.8 1.0 O A:ASN374 2.4 35.7 1.0 OD1 A:ASP436 2.7 49.0 1.0 OD2 A:ASP436 2.7 35.3 1.0 CG A:ASP436 3.0 54.0 1.0 C A:ASN374 3.4 43.4 1.0 HA A:GLU375 3.4 54.7 1.0 C A:TYR377 3.6 43.9 1.0 HB2 A:ASN374 3.7 34.2 1.0 H A:TYR377 3.9 50.5 1.0 HD3 A:PRO379 4.0 54.3 1.0 HD2 A:PRO379 4.1 54.3 1.0 N A:GLU375 4.1 38.6 1.0 CA A:GLU375 4.2 45.5 1.0 CA A:ASN374 4.3 42.9 1.0 HA A:ASN374 4.3 51.6 1.0 HB2 A:TYR377 4.4 42.4 1.0 CB A:ASN374 4.4 28.5 1.0 N A:TYR377 4.4 42.0 1.0 CB A:ASP436 4.5 41.2 1.0 N A:ASP378 4.5 45.3 1.0 CA A:TYR377 4.5 40.8 1.0 CD A:PRO379 4.5 45.2 1.0 C A:GLU375 4.6 35.8 1.0 CA A:ASP378 4.6 44.0 1.0 HB3 A:ASP436 4.6 49.6 1.0 HD22 A:ASN374 4.7 60.3 1.0 HH A:TYR430 4.7 38.5 1.0 O A:GLU375 4.8 44.5 1.0 CG A:ASN374 4.9 43.2 1.0 HB2 A:ASP436 4.9 49.6 1.0 H A:GLU375 5.0 46.4 1.0 OH A:TYR430 5.0 32.0 1.0 CB A:TYR377 5.0 35.2 1.0

T.M.Iverson, H.E.Stubbs, T.M.Iverson. N/A N/A.