Sodium in PDB 7si0: Ige-Fc in Complex with 813

The structure of Ige-Fc in Complex with 813, PDB code: 7si0 was solved by L.F.Pennington, T.J.Jardetzky, S.Kleinboelting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.59 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.958, 132.005, 177.434, 90, 90, 90
R / Rfree (%)	21 / 26.1

The binding sites of Sodium atom in the Ige-Fc in Complex with 813 (pdb code 7si0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ige-Fc in Complex with 813, PDB code: 7si0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ige-Fc in Complex with 813


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ige-Fc in Complex with 813 within 5.0Å range: probe atom residue distance (Å) B Occ I:Na201 b:28.2 occ:1.00 OG I:SER51 3.6 38.4 1.0 CD1 I:TRP106 3.9 51.3 1.0 ND2 I:ASN59 4.1 46.2 1.0 OD1 I:ASN36 4.2 37.0 1.0 CB I:SER51 4.3 36.8 1.0 CZ2 I:TRP48 4.3 41.8 1.0 CG I:TRP106 4.3 49.4 1.0 NE1 I:TRP106 4.4 51.8 1.0 CE2 J:TYR100 4.5 50.8 1.0 CZ J:TYR100 4.6 52.1 1.0 CB I:TRP106 4.7 48.8 1.0 OH J:TYR100 4.7 53.6 1.0 CE2 I:TRP48 4.8 41.5 1.0 NE1 I:TRP48 4.8 39.8 1.0 OG I:SER34 4.8 36.9 1.0 CD2 J:TYR100 5.0 49.7 1.0 OD1 J:ASP98 5.0 54.0 1.0

Sodium binding site 2 out of 3 in the Ige-Fc in Complex with 813


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ige-Fc in Complex with 813 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na201 b:38.5 occ:1.00 OG E:SER51 3.9 62.0 1.0 CD1 E:TRP106 3.9 56.9 1.0 CG E:TRP106 4.0 55.1 1.0 OD1 E:ASN36 4.1 55.7 1.0 CB E:TRP106 4.2 54.1 1.0 CB E:SER51 4.3 60.3 1.0 CE2 F:TYR100 4.3 61.5 1.0 NE1 E:TRP106 4.5 57.7 1.0 OH F:TYR100 4.5 63.5 1.0 CZ2 E:TRP48 4.5 61.9 1.0 CZ F:TYR100 4.5 62.7 1.0 OG E:SER34 4.6 54.7 1.0 CD2 E:TRP106 4.7 54.9 1.0 CB E:SER34 4.8 56.2 1.0 CE2 E:TRP106 5.0 56.5 1.0 CE2 E:TRP48 5.0 60.3 1.0 CD2 F:TYR100 5.0 60.8 1.0 NE1 E:TRP48 5.0 58.3 1.0

Sodium binding site 3 out of 3 in the Ige-Fc in Complex with 813


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ige-Fc in Complex with 813 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na201 b:28.4 occ:1.00 OG K:SER51 3.7 41.8 1.0 OD1 K:ASN36 3.9 41.0 1.0 CD1 K:TRP106 4.0 49.1 1.0 ND2 K:ASN59 4.2 43.4 1.0 CE2 L:TYR100 4.3 54.5 1.0 CB K:SER51 4.3 40.5 1.0 CG K:TRP106 4.3 48.3 1.0 NE1 K:TRP106 4.5 49.5 1.0 OG K:SER34 4.6 41.0 1.0 CZ L:TYR100 4.6 55.2 1.0 CB K:TRP106 4.7 48.0 1.0 CZ2 K:TRP48 4.7 45.0 1.0 CD2 L:TYR100 4.7 54.0 1.0 OH L:TYR100 4.8 55.9 1.0 NE1 K:TRP48 4.9 43.4 1.0 CD2 K:TRP106 5.0 48.2 1.0

L.F.Pennington, P.Gasser, S.Kleinboelting, C.Zhang, G.Skiniotis, A.Eggel, T.S.Jardetzky. Directed Evolution of and Structural Insights Into Antibody-Mediated Disruption of A Stable Receptor-Ligand Complex. Nat Commun V. 12 7069 2021.
ISSN: ESSN 2041-1723
PubMed: 34862384
DOI: 10.1038/S41467-021-27397-Z