Sodium in PDB 5vyb: Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide

The structure of Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide, PDB code: 5vyb was solved by H.Feinberg, S.A.F.Jegouzo, M.J.Rex, K.Drickamer, M.E.Taylor, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.23 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.055, 78.834, 76.459, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24

The structure of Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide (pdb code 5vyb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide, PDB code: 5vyb:

Sodium binding site 1 out of 1 in the Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:43.2 occ:1.00 O A:HIS171 2.4 46.9 1.0 O A:HOH402 2.4 27.7 1.0 O A:GLU174 2.4 37.8 1.0 OD2 A:ASP191 2.5 35.2 1.0 CZ2 A:TRP149 3.2 39.1 1.0 C A:HIS171 3.4 31.9 1.0 CG A:ASP191 3.4 39.0 1.0 C A:GLU174 3.5 38.4 1.0 CH2 A:TRP149 3.6 34.6 1.0 CB A:ASP191 3.7 33.7 1.0 CA A:SER172 4.0 51.5 1.0 N A:SER172 4.1 35.4 1.0 CB A:PRO169 4.1 34.0 1.0 N A:HIS171 4.1 38.4 1.0 CB A:GLU174 4.2 37.8 1.0 CA A:GLU174 4.2 43.2 1.0 N A:GLU174 4.3 43.3 1.0 CE2 A:TRP149 4.3 36.0 1.0 C A:SER172 4.3 48.1 1.0 CA A:HIS171 4.4 43.5 1.0 O A:SER172 4.4 41.9 1.0 N A:GLN175 4.5 34.7 1.0 OD1 A:ASP191 4.6 27.2 1.0 OD2 A:ASP142 4.7 44.5 1.0 CA A:GLN175 4.7 43.0 1.0 N A:ASN170 4.8 36.9 1.0 CZ3 A:TRP149 4.9 35.0 1.0 NE1 A:TRP149 4.9 33.0 1.0

H.Feinberg, S.A.F.Jegouzo, M.J.Rex, K.Drickamer, W.I.Weis, M.E.Taylor. Mechanism of Pathogen Recognition By Human Dectin-2. J. Biol. Chem. V. 292 13402 2017.
ISSN: ESSN 1083-351X
PubMed: 28652405
DOI: 10.1074/JBC.M117.799080