Calcium in PDB 5k8y: Structure of the Mus Musclus Langerin Carbohydrate Recognition Domain

The structure of Structure of the Mus Musclus Langerin Carbohydrate Recognition Domain, PDB code: 5k8y was solved by B.Loll, J.Aretz, C.Rademacher, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.32 / 2.40
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	143.310, 143.310, 143.310, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The binding sites of Calcium atom in the Structure of the Mus Musclus Langerin Carbohydrate Recognition Domain (pdb code 5k8y). 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 Mus Musclus Langerin Carbohydrate Recognition Domain, PDB code: 5k8y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Mus Musclus Langerin Carbohydrate Recognition Domain


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 Mus Musclus Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:58.7 occ:1.00 O A:HOH512 2.3 32.7 1.0 OD1 A:ASN290 2.3 60.3 1.0 OD1 A:ASP311 2.3 56.9 1.0 OD1 A:ASN310 2.3 59.7 1.0 O A:ASP311 2.3 58.1 1.0 OE1 A:GLU296 2.3 52.2 1.0 OE2 A:GLU288 2.3 60.1 1.0 O A:HOH504 2.5 42.3 1.0 OE1 A:GLU288 2.9 64.0 1.0 CD A:GLU288 3.0 60.4 1.0 CG A:ASN290 3.2 62.3 1.0 CG A:ASN310 3.4 57.6 1.0 ND2 A:ASN290 3.5 60.5 1.0 CD A:GLU296 3.5 49.4 1.0 C A:ASP311 3.5 55.5 1.0 CG A:ASP311 3.6 56.5 1.0 OE2 A:GLU296 4.0 47.8 1.0 ND2 A:ASN310 4.0 57.4 1.0 N A:ASP311 4.0 56.4 1.0 CA A:ASP311 4.2 54.5 1.0 OD2 A:ASP311 4.4 54.1 1.0 CG A:GLU288 4.5 56.3 1.0 CB A:ASP311 4.5 56.1 1.0 N A:GLY312 4.6 54.0 1.0 CB A:ASN310 4.6 56.2 1.0 N A:ASN290 4.7 60.4 1.0 CB A:ASN290 4.7 61.9 1.0 CG A:GLU296 4.7 47.3 1.0 C A:ASN310 4.7 56.2 1.0 CB A:ALA292 4.8 52.3 1.0 CA A:GLY312 4.9 54.0 1.0 N A:ASN291 4.9 59.5 1.0 N A:ALA292 4.9 59.1 1.0 CA A:ASN310 5.0 55.1 1.0

Calcium binding site 2 out of 2 in the Structure of the Mus Musclus Langerin Carbohydrate Recognition Domain


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 Mus Musclus Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:47.3 occ:1.00 OD1 B:ASP311 2.3 47.4 1.0 OE1 B:GLU296 2.3 50.9 1.0 OD1 B:ASN310 2.3 44.9 1.0 OE1 B:GLU288 2.3 46.5 1.0 OD1 B:ASN290 2.3 47.5 1.0 O B:ASP311 2.3 47.9 1.0 CD B:GLU288 3.0 45.1 1.0 O B:HOH514 3.1 28.8 1.0 CD B:GLU296 3.1 51.1 1.0 OE2 B:GLU288 3.1 43.0 1.0 CG B:ASN290 3.3 47.0 1.0 CG B:ASN310 3.3 45.4 1.0 CG B:ASP311 3.4 47.0 1.0 OE2 B:GLU296 3.4 48.4 1.0 C B:ASP311 3.5 46.6 1.0 O B:HOH508 3.6 35.2 1.0 ND2 B:ASN290 3.7 46.1 1.0 ND2 B:ASN310 3.7 44.3 1.0 N B:ASP311 3.8 48.6 1.0 CA B:ASP311 4.0 46.2 1.0 OD2 B:ASP311 4.1 46.7 1.0 CG B:GLU288 4.3 44.2 1.0 CB B:ASP311 4.3 46.6 1.0 N B:ASN290 4.4 47.0 1.0 CG B:GLU296 4.5 49.9 1.0 CB B:ASN290 4.5 47.7 1.0 N B:GLY312 4.6 47.0 1.0 CB B:ASN310 4.7 46.2 1.0 CB B:GLU296 4.7 52.2 1.0 C B:ASN310 4.7 48.2 1.0 N B:ASN291 4.8 50.9 1.0 CB B:GLU288 4.9 45.8 1.0 CA B:ASN310 4.9 47.5 1.0 CA B:ASN290 4.9 47.9 1.0

J.Hanske, J.Schulze, J.Aretz, R.Mcbride, B.Loll, H.Schmidt, Y.Knirel, W.Rabsch, M.C.Wahl, J.C.Paulson, C.Rademacher. Bacterial Polysaccharide Specificity of the Pattern Recognition Receptor Langerin Is Highly Species-Dependent. J. Biol. Chem. V. 292 862 2017.
ISSN: ESSN 1083-351X
PubMed: 27903635
DOI: 10.1074/JBC.M116.751750