Sodium in PDB 8rov: Human Dectin-2 with Dimerization Domain

The structure of Human Dectin-2 with Dimerization Domain, PDB code: 8rov was solved by Y.Liu, J.W.Kim, H.Feinberg, N.Cull, W.I.Weis, M.E.Taylor, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.09 / 2.36
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.211, 65.03, 81.582, 90, 100.61, 90
R / Rfree (%)	22.2 / 28.4

The structure of Human Dectin-2 with Dimerization Domain also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Human Dectin-2 with Dimerization Domain (pdb code 8rov). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dectin-2 with Dimerization Domain, PDB code: 8rov:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:40.6 occ:1.00 O A:GLU174 2.2 39.7 1.0 O A:HOH502 2.3 40.5 1.0 O A:HIS171 2.4 41.2 1.0 OD2 A:ASP191 2.6 44.5 1.0 CZ2 A:TRP149 3.2 40.7 1.0 C A:GLU174 3.4 42.6 1.0 CG A:ASP191 3.5 43.1 1.0 C A:HIS171 3.6 43.4 1.0 CH2 A:TRP149 3.6 42.6 1.0 CB A:ASP191 3.7 43.4 1.0 CA A:GLU174 4.2 43.8 1.0 N A:HIS171 4.2 46.7 1.0 CB A:GLU174 4.2 42.2 1.0 N A:GLU174 4.2 44.5 1.0 CE2 A:TRP149 4.3 42.3 1.0 N A:GLN175 4.3 41.3 1.0 N A:SER172 4.4 43.1 1.0 CA A:GLN175 4.4 40.7 1.0 CA A:SER172 4.4 43.8 1.0 O A:SER172 4.4 47.1 1.0 CA A:HIS171 4.5 46.1 1.0 C A:SER172 4.5 44.5 1.0 CB A:PRO169 4.5 42.9 1.0 OD2 A:ASP142 4.6 42.3 1.0 OD1 A:ASP191 4.7 43.7 1.0 CZ3 A:TRP149 4.9 40.4 1.0 NE1 A:TRP149 4.9 43.6 1.0 N A:ASN170 5.0 44.0 1.0

Sodium binding site 2 out of 2 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:47.2 occ:1.00 O B:GLU174 2.3 42.7 1.0 O B:HIS171 2.3 55.2 1.0 O B:HOH505 2.3 44.1 1.0 OD2 B:ASP191 2.6 44.5 1.0 C B:GLU174 3.2 48.6 1.0 C B:HIS171 3.5 54.5 1.0 CG B:ASP191 3.6 47.2 1.0 CZ2 B:TRP149 3.6 42.6 1.0 CB B:ASP191 3.9 46.9 1.0 CA B:GLU174 4.0 49.8 1.0 CH2 B:TRP149 4.0 46.1 1.0 N B:GLU174 4.0 48.3 1.0 CB B:GLU174 4.1 48.4 1.0 O B:SER172 4.1 53.7 1.0 CA B:SER172 4.2 52.4 1.0 N B:GLN175 4.2 46.5 1.0 C B:SER172 4.2 50.7 1.0 N B:SER172 4.3 51.9 1.0 CA B:GLN175 4.3 46.5 1.0 N B:HIS171 4.4 53.4 1.0 CA B:HIS171 4.5 52.6 1.0 OD2 B:ASP142 4.6 45.4 1.0 CE2 B:TRP149 4.7 44.5 1.0 CB B:PRO169 4.7 46.4 1.0 OD1 B:ASP191 4.7 47.9 1.0 N B:ALA173 4.9 50.4 1.0 OD1 B:ASN147 5.0 46.1 1.0

Y.Liu, J.W.Kim, H.Feinberg, N.Cull, W.I.Weis, M.E.Taylor, K.Drickamer. Interactions That Define the Arrangement of Sugar-Binding Sites in Bdca-2 and Dectin-2 Dimers. Glycobiology 2024.
ISSN: ESSN 1460-2423
PubMed: 39361900
DOI: 10.1093/GLYCOB/CWAE082