Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Human Dectin-2 with Dimerization Domain (pdb code 8rov). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Dectin-2 with Dimerization Domain, PDB code: 8rov:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:45.5 occ:1.00 OD1 A:ASP191 2.3 43.7 1.0 O3 A:MMA403 2.4 52.5 1.0 OD1 A:ASN190 2.4 47.7 1.0 O4 A:MMA403 2.4 53.0 1.0 O A:ASP191 2.5 44.5 1.0 OE1 A:GLU174 2.6 45.8 1.0 OE1 A:GLU168 2.6 45.7 1.0 OD1 A:ASN170 2.6 47.9 1.0 C3 A:MMA403 3.1 54.1 1.0 C4 A:MMA403 3.2 55.1 1.0 CG A:ASP191 3.3 43.1 1.0 CD A:GLU168 3.4 47.5 1.0 CG A:ASN190 3.5 48.2 1.0 OE2 A:GLU168 3.6 47.0 1.0 C A:ASP191 3.6 43.8 1.0 CG A:ASN170 3.6 47.0 1.0 CD A:GLU174 3.7 48.2 1.0 N A:ASP191 3.8 43.1 1.0 ND2 A:ASN190 3.9 50.6 1.0 OD2 A:ASP191 4.0 44.5 1.0 ND2 A:ASN170 4.0 47.3 1.0 CA A:ASP191 4.1 42.8 1.0 OE2 A:GLU174 4.2 49.6 1.0 CB A:ASP191 4.3 43.4 1.0 N A:ASN170 4.5 44.0 1.0 C2 A:MMA403 4.6 55.8 1.0 C5 A:MMA403 4.6 58.7 1.0 C A:ASN190 4.6 44.1 1.0 CG A:GLU168 4.7 48.1 1.0 CB A:ASN190 4.7 43.9 1.0 N A:VAL192 4.8 42.6 1.0 CG A:GLU174 4.9 45.4 1.0 CB A:GLU174 4.9 42.2 1.0 CA A:ASN190 4.9 44.3 1.0 CB A:ASN170 4.9 45.8 1.0 CD2 A:HIS171 5.0 48.6 1.0 O2 A:MMA403 5.0 58.8 1.0

Calcium binding site 2 out of 4 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:49.5 occ:1.00 O A:HOH507 2.1 49.3 1.0 O A:HOH509 2.3 49.0 1.0 O A:VAL116 2.4 46.9 1.0 OD1 A:ASN118 2.4 51.9 1.0 OE2 A:GLU122 2.5 45.3 1.0 OE1 A:GLU203 2.6 46.2 1.0 OE2 A:GLU203 2.6 48.4 1.0 CD A:GLU203 3.0 49.4 1.0 CD A:GLU122 3.2 49.5 1.0 OE1 A:GLU122 3.3 52.8 1.0 C A:VAL116 3.5 47.5 1.0 CG A:ASN118 3.6 49.6 1.0 CB A:VAL116 4.3 46.7 1.0 CA A:VAL116 4.3 46.8 1.0 OH A:TYR91 4.3 50.7 1.0 N A:ASN118 4.4 49.7 1.0 N A:VAL116 4.5 46.0 1.0 N A:PHE117 4.5 48.2 1.0 ND2 A:ASN118 4.5 48.2 1.0 CB A:ASN118 4.5 49.4 1.0 CG A:GLU203 4.5 45.7 1.0 CA A:PHE117 4.6 49.0 1.0 CG A:GLU122 4.7 49.7 1.0 CG1 A:VAL116 4.8 45.7 1.0 C A:PHE117 4.8 49.9 1.0 OG A:SER89 4.9 49.6 1.0

Calcium binding site 3 out of 4 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:47.2 occ:1.00 OD1 B:ASP191 2.2 47.9 1.0 O3 B:MMA403 2.3 53.8 1.0 OE1 B:GLU174 2.3 51.1 1.0 OD1 B:ASN190 2.5 51.7 1.0 O B:ASP191 2.6 47.5 1.0 OD1 B:ASN170 2.7 51.2 1.0 OE1 B:GLU168 2.7 49.9 1.0 O4 B:MMA403 2.8 54.2 1.0 CG B:ASP191 3.3 47.2 1.0 C3 B:MMA403 3.4 56.1 1.0 CD B:GLU174 3.5 49.6 1.0 C4 B:MMA403 3.5 57.8 1.0 C B:ASP191 3.6 46.3 1.0 CG B:ASN190 3.6 52.0 1.0 CD B:GLU168 3.6 53.2 1.0 CG B:ASN170 3.8 50.0 1.0 N B:ASP191 3.8 49.0 1.0 OE2 B:GLU168 3.9 55.0 1.0 OE2 B:GLU174 4.0 51.6 1.0 OD2 B:ASP191 4.0 44.5 1.0 ND2 B:ASN190 4.0 51.8 1.0 CA B:ASP191 4.1 45.2 1.0 CB B:ASP191 4.3 46.9 1.0 ND2 B:ASN170 4.3 50.4 1.0 N B:ASN170 4.4 48.0 1.0 O2 B:MMA403 4.6 61.1 1.0 C2 B:MMA403 4.6 61.2 1.0 CG B:GLU174 4.7 50.5 1.0 N B:VAL192 4.7 45.2 1.0 C B:ASN190 4.8 48.1 1.0 CB B:GLU174 4.8 48.4 1.0 CG B:GLU168 4.9 51.0 1.0 CB B:ASN170 4.9 49.9 1.0 CB B:ASN190 4.9 50.2 1.0 N B:HIS171 4.9 53.4 1.0 C5 B:MMA403 5.0 61.8 1.0

Calcium binding site 4 out of 4 in the Human Dectin-2 with Dimerization Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Dectin-2 with Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:50.1 occ:1.00 O B:HOH509 2.2 49.1 1.0 O B:VAL116 2.4 51.1 1.0 OD1 B:ASN118 2.4 52.5 1.0 OE2 B:GLU122 2.4 49.9 1.0 OE2 B:GLU203 2.6 51.1 1.0 OE1 B:GLU203 2.7 49.9 1.0 CD B:GLU203 3.0 51.6 1.0 OE1 B:GLU122 3.1 51.8 1.0 CD B:GLU122 3.1 52.1 1.0 C B:VAL116 3.6 49.0 1.0 CG B:ASN118 3.6 52.5 1.0 OH B:TYR91 4.2 52.0 1.0 CA B:VAL116 4.4 48.2 1.0 CB B:VAL116 4.4 48.9 1.0 ND2 B:ASN118 4.5 53.0 1.0 N B:ASN118 4.5 50.5 1.0 CG B:GLU203 4.5 48.6 1.0 N B:PHE117 4.5 50.4 1.0 N B:VAL116 4.5 47.4 1.0 CB B:ASN118 4.6 52.3 1.0 CG B:GLU122 4.6 53.0 1.0 CA B:PHE117 4.6 50.5 1.0 CG1 B:VAL116 4.8 47.8 1.0 C B:PHE117 4.9 51.8 1.0 OG B:SER89 4.9 49.5 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