Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Carbohydrate Recognition Domain of Dectin-2 Complexed with A Mammalian-Type High Mannose MAN9GLCNAC2 Oligosaccharide, PDB code: 5vyb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca308 b:38.2 occ:1.00 OD1 A:ASP191 2.4 27.2 1.0 O4 A:MAN302 2.4 39.3 0.5 OD1 A:ASN190 2.4 41.3 1.0 OE1 A:GLU174 2.4 46.6 1.0 OD1 A:ASN170 2.4 44.6 1.0 O3 A:MAN302 2.5 39.1 0.5 OE1 A:GLU168 2.5 42.4 1.0 O A:ASP191 2.5 38.2 1.0 C3 A:MAN302 3.2 44.6 0.5 C4 A:MAN302 3.3 41.2 0.5 CD A:GLU174 3.4 47.1 1.0 CG A:ASN170 3.4 37.4 1.0 CD A:GLU168 3.4 38.4 1.0 CG A:ASP191 3.5 39.0 1.0 CG A:ASN190 3.5 48.0 1.0 OE2 A:GLU168 3.6 39.0 1.0 C A:ASP191 3.7 33.6 1.0 OE2 A:GLU174 3.7 44.1 1.0 ND2 A:ASN170 3.7 41.6 1.0 N A:ASP191 4.0 37.0 1.0 ND2 A:ASN190 4.0 44.8 1.0 OD2 A:ASP191 4.2 35.2 1.0 CA A:ASP191 4.2 26.1 1.0 CB A:ASP191 4.5 33.7 1.0 N A:ASN170 4.6 36.9 1.0 C5 A:MAN302 4.6 40.4 0.5 C2 A:MAN302 4.7 41.7 0.5 CG A:GLU168 4.7 25.8 1.0 CG A:GLU174 4.7 43.8 1.0 CB A:ASN170 4.7 29.7 1.0 C A:ASN190 4.7 40.8 1.0 N A:VAL192 4.8 33.4 1.0 CB A:ASN190 4.8 38.5 1.0 CB A:GLU174 4.9 37.8 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca309 b:47.0 occ:1.00 O A:VAL116 2.4 41.6 1.0 OE2 A:GLU122 2.4 43.4 1.0 O A:HOH414 2.4 44.8 1.0 O A:HOH408 2.4 48.8 1.0 OE1 A:GLU203 2.4 49.1 1.0 OD1 A:ASN118 2.4 57.2 1.0 OE1 A:GLU122 2.9 54.9 1.0 CD A:GLU122 3.0 48.5 1.0 OE2 A:GLU203 3.0 51.1 1.0 CD A:GLU203 3.1 50.6 1.0 CG A:ASN118 3.6 61.1 1.0 C A:VAL116 3.6 42.4 1.0 OH A:TYR91 4.1 38.3 1.0 N A:ASN118 4.2 42.0 1.0 CB A:ASN118 4.3 43.2 1.0 CA A:VAL116 4.4 36.5 1.0 O A:HOH409 4.5 61.9 1.0 CG A:GLU122 4.5 47.4 1.0 CB A:VAL116 4.5 35.5 1.0 N A:VAL116 4.5 45.9 1.0 N A:PHE117 4.6 44.0 1.0 CG A:GLU203 4.6 41.8 1.0 ND2 A:ASN118 4.6 38.6 1.0 OG A:SER89 4.6 63.5 1.0 CA A:PHE117 4.6 46.5 1.0 C A:PHE117 4.8 33.7 1.0 CG1 A:VAL116 4.9 38.5 1.0 CA A:ASN118 4.9 40.4 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