Sodium in PDB 7kmj: Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C

The structure of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C, PDB code: 7kmj 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)	37.99 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.635, 58.173, 75.973, 90, 90, 90
R / Rfree (%)	19.1 / 21.6

The binding sites of Sodium atom in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C (pdb code 7kmj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C, PDB code: 7kmj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C


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 Sialyl Lewis C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.4 occ:1.00 O A:ASN374 2.3 23.9 1.0 OD2 A:ASP436 2.4 27.5 1.0 O A:HOH828 2.6 38.8 1.0 OD1 A:ASP436 2.8 29.0 1.0 CG A:ASP436 2.9 27.6 1.0 O A:TYR377 3.0 27.5 1.0 HD3 A:PRO379 3.3 35.7 1.0 C A:ASN374 3.4 23.0 1.0 HB2 A:ASN374 3.5 27.9 1.0 C A:TYR377 3.6 25.1 1.0 HA A:GLU375 3.6 28.5 1.0 H A:TYR377 3.7 26.3 1.0 HA A:ASP378 3.9 35.3 1.0 HD2 A:PRO379 3.9 35.7 1.0 HB2 A:TYR377 4.0 25.8 1.0 CD A:PRO379 4.0 29.8 1.0 HH A:TYR430 4.1 27.7 1.0 HA A:ASN374 4.1 26.4 1.0 CA A:ASN374 4.2 22.0 1.0 N A:GLU375 4.2 23.2 1.0 CB A:ASN374 4.3 23.2 1.0 CA A:GLU375 4.3 23.7 1.0 N A:TYR377 4.3 21.9 1.0 CA A:TYR377 4.3 22.6 1.0 CB A:ASP436 4.4 25.8 1.0 N A:ASP378 4.4 26.5 1.0 OH A:TYR430 4.5 23.1 1.0 HB3 A:ASP436 4.6 31.0 1.0 CA A:ASP378 4.6 29.4 1.0 C A:GLU375 4.6 22.6 1.0 CB A:TYR377 4.6 21.5 1.0 HB2 A:ASP436 4.7 31.0 1.0 HG2 A:PRO379 4.8 36.0 1.0 HE1 A:TYR430 4.9 25.6 1.0 CG A:PRO379 4.9 30.0 1.0 O A:GLU375 4.9 23.7 1.0 HG3 A:PRO379 5.0 36.0 1.0 CG A:ASN374 5.0 25.0 1.0 HB3 A:TYR377 5.0 25.8 1.0

Sodium binding site 2 out of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C


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 Sialyl Lewis C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:22.3 occ:1.00 O A:PRO317 2.7 17.1 1.0 OD1 A:ASN316 2.7 21.1 1.0 HD2 A:PRO317 2.9 19.6 1.0 HG3 A:ARG319 3.1 24.5 1.0 HA A:ASN316 3.4 19.9 1.0 N A:PRO317 3.4 15.8 1.0 CD A:PRO317 3.6 16.3 1.0 C A:PRO317 3.7 14.7 1.0 C A:ASN316 3.7 15.8 1.0 CG A:ASN316 3.8 20.7 1.0 CG A:ARG319 3.9 20.4 1.0 HG2 A:ARG319 3.9 24.5 1.0 HD3 A:ARG319 3.9 26.2 1.0 CA A:ASN316 4.0 16.5 1.0 HB2 A:PRO317 4.0 19.2 1.0 CA A:PRO317 4.0 14.8 1.0 O A:ASN316 4.3 16.8 1.0 HG2 A:PRO317 4.3 20.9 1.0 CB A:PRO317 4.3 16.0 1.0 CG A:PRO317 4.3 17.4 1.0 HD3 A:PRO317 4.4 19.6 1.0 CD A:ARG319 4.4 21.9 1.0 CB A:ASN316 4.5 18.6 1.0 HE A:ARG319 4.6 25.8 1.0 NE A:ARG319 4.8 21.5 1.0 HG3 A:GLU269 4.8 21.1 0.4 ND2 A:ASN316 4.8 23.7 1.0 HD21 A:ASN316 4.9 28.4 1.0 N A:LEU318 4.9 14.9 1.0 HA A:PRO317 4.9 17.7 1.0

Sodium binding site 3 out of 3 in the Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hsa Siglec and Unique Domains in Complex with Sialyl Lewis C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:30.0 occ:1.00 O A:GLU247 2.2 23.9 1.0 OD2 A:ASP346 2.3 23.0 1.0 OD2 A:ASP245 2.4 28.6 1.0 OD1 A:ASN273 2.4 23.5 1.0 OD2 A:ASP272 2.5 19.8 1.0 OD1 A:ASP272 2.5 21.2 1.0 OD1 A:ASP245 2.7 30.1 1.0 CG A:ASP272 2.9 19.7 1.0 CG A:ASP245 2.9 29.6 1.0 C A:GLU247 3.4 24.9 1.0 CG A:ASP346 3.4 23.5 1.0 HD22 A:ASN350 3.5 32.6 1.0 CG A:ASN273 3.5 23.6 1.0 HB3 A:ASP346 3.6 27.6 1.0 HB3 A:GLU247 3.6 34.2 1.0 HB2 A:ASP346 3.7 27.6 1.0 H A:SER274 3.7 23.1 1.0 H A:ASN273 3.8 21.1 1.0 H A:GLU247 3.8 35.0 1.0 CB A:ASP346 3.8 23.0 1.0 HB3 A:SER274 3.8 24.6 1.0 HD21 A:ASN273 3.9 31.5 1.0 HA A:ALA248 4.1 27.4 1.0 ND2 A:ASN273 4.1 26.3 1.0 HD3 A:PRO249 4.2 22.9 1.0 CA A:GLU247 4.2 27.7 1.0 HG A:SER274 4.2 26.1 1.0 HB2 A:ASN350 4.2 31.0 1.0 ND2 A:ASN350 4.3 27.1 1.0 N A:GLU247 4.3 29.2 1.0 N A:ASN273 4.3 17.6 1.0 N A:ALA248 4.4 24.2 1.0 CB A:GLU247 4.4 28.5 1.0 CB A:ASP272 4.4 17.7 1.0 N A:SER274 4.4 19.2 1.0 O A:HOH683 4.4 23.1 1.0 CB A:ASP245 4.4 30.6 1.0 OD1 A:ASP346 4.5 24.3 1.0 CA A:ALA248 4.5 22.8 1.0 C A:ALA248 4.5 20.7 1.0 O A:HOH642 4.6 19.9 1.0 CB A:SER274 4.6 20.5 1.0 HD21 A:ASN350 4.7 32.6 1.0 HB3 A:ASP245 4.7 36.8 1.0 OG A:SER274 4.7 21.7 1.0 CB A:ASN273 4.7 21.2 1.0 O A:ALA248 4.7 21.7 1.0 HB3 A:ASP272 4.8 21.3 1.0 HA A:ASP272 4.8 20.1 1.0 HG2 A:GLU247 4.8 35.9 1.0 HB2 A:ASP272 4.8 21.3 1.0 N A:PRO249 4.8 19.1 1.0 HB2 A:ASP245 4.8 36.8 1.0 HG3 A:PRO249 4.9 23.0 1.0 CA A:ASN273 4.9 18.7 1.0 CD A:PRO249 4.9 19.1 1.0 HD22 A:ASN273 5.0 31.5 1.0

B.A.Bensing, H.E.Stubbs, R.Agarwal, I.Yamakawa, K.Luong, K.Solakyildirim, H.Yu, A.Hadadianpour, M.A.Castro, K.P.Fialkowski, K.M.Morrison, Z.Wawrzak, X.Chen, C.B.Lebrilla, J.Baudry, J.C.Smith, P.M.Sullam, T.M.Iverson. Origins of Glycan Selectivity in Streptococcal Siglec-Like Adhesins Suggest Mechanisms of Receptor Adaptation. Nat Commun V. 13 2753 2022.
ISSN: ESSN 2041-1723
PubMed: 35585145
DOI: 10.1038/S41467-022-30509-Y