Calcium in PDB 3p5g: Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal)

The structure of Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal), PDB code: 3p5g was solved by H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 1.60
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.860, 79.860, 90.170, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.9

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal) (pdb code 3p5g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal), PDB code: 3p5g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal)


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 Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:19.6 occ:1.00 OD1 A:ASP308 2.4 18.8 1.0 OE1 A:GLU293 2.4 20.4 1.0 OD1 A:ASN307 2.4 17.9 1.0 OD1 A:ASN287 2.5 23.8 1.0 O A:ASP308 2.5 16.7 1.0 OE1 A:GLU285 2.5 19.4 1.0 O3 A:FUC402 2.5 20.8 1.0 O2 A:FUC402 2.6 24.9 1.0 CG A:ASP308 3.3 21.8 1.0 C3 A:FUC402 3.3 15.9 1.0 CD A:GLU285 3.3 21.3 1.0 CD A:GLU293 3.4 14.7 1.0 C2 A:FUC402 3.4 19.1 1.0 CG A:ASN287 3.4 34.6 1.0 CG A:ASN307 3.4 14.9 1.0 C A:ASP308 3.5 13.9 1.0 OE2 A:GLU285 3.7 21.1 1.0 OE2 A:GLU293 3.7 21.2 1.0 N A:ASP308 3.7 16.2 1.0 ND2 A:ASN307 3.9 15.6 1.0 ND2 A:ASN287 3.9 22.5 1.0 CA A:ASP308 4.0 11.4 1.0 OD2 A:ASP308 4.0 22.9 1.0 N A:ASN287 4.2 23.5 1.0 CB A:ASP308 4.2 16.4 1.0 N A:ASN288 4.5 24.7 1.0 CB A:ASN287 4.5 30.5 1.0 N A:ALA289 4.5 33.6 1.0 CB A:ALA289 4.6 28.4 1.0 CG A:GLU285 4.6 22.7 1.0 C A:ASN307 4.6 22.6 1.0 CG A:GLU293 4.7 21.1 1.0 N A:ALA309 4.7 12.7 1.0 CB A:ASN307 4.7 13.4 1.0 C4 A:FUC402 4.8 22.3 1.0 CA A:ASN287 4.8 30.7 1.0 C1 A:FUC402 4.8 22.6 1.0 CB A:GLU293 4.9 17.4 1.0 CA A:ASN307 4.9 15.9 1.0 O2 A:GAL401 4.9 30.5 1.0 CB A:GLU285 4.9 17.4 1.0 C A:ASN287 4.9 26.1 1.0

Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal)


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 Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:18.6 occ:1.00 OD1 B:ASN287 2.4 19.1 1.0 OD1 B:ASP308 2.4 18.3 1.0 OE1 B:GLU293 2.4 18.4 1.0 OD1 B:ASN307 2.5 18.2 1.0 O B:ASP308 2.5 18.4 1.0 OE1 B:GLU285 2.5 18.4 1.0 O3 B:FUC402 2.5 18.0 1.0 O2 B:FUC402 2.5 20.1 1.0 CG B:ASP308 3.3 28.8 1.0 CD B:GLU285 3.3 17.4 1.0 C3 B:FUC402 3.3 22.4 1.0 C2 B:FUC402 3.4 21.4 1.0 CG B:ASN287 3.4 26.6 1.0 CD B:GLU293 3.4 16.1 1.0 CG B:ASN307 3.4 17.8 1.0 C B:ASP308 3.5 15.8 1.0 OE2 B:GLU285 3.6 25.6 1.0 OE2 B:GLU293 3.7 21.0 1.0 N B:ASP308 3.7 16.1 1.0 ND2 B:ASN307 3.8 17.0 1.0 OD2 B:ASP308 4.0 18.7 1.0 CA B:ASP308 4.0 14.6 1.0 ND2 B:ASN287 4.0 22.5 1.0 N B:ASN287 4.1 17.0 1.0 CB B:ASP308 4.2 16.3 1.0 CB B:ASN287 4.5 26.1 1.0 CG B:GLU285 4.6 16.8 1.0 N B:ASN288 4.6 21.8 1.0 C B:ASN307 4.7 22.8 1.0 CA B:ASN287 4.7 22.3 1.0 N B:ALA309 4.7 14.9 1.0 CG B:GLU293 4.7 18.4 1.0 CB B:ASN307 4.7 16.7 1.0 C4 B:FUC402 4.7 21.5 1.0 C1 B:FUC402 4.8 27.6 1.0 N B:ALA289 4.8 23.5 1.0 CB B:GLU293 4.9 14.7 1.0 CA B:ASN307 4.9 19.3 1.0 C B:ASN287 4.9 34.4 1.0 CB B:ALA289 5.0 20.8 1.0 O2 B:GLA401 5.0 26.9 1.0

Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca500 b:20.0 occ:1.00 OD1 C:ASP308 2.4 18.8 1.0 OD1 C:ASN307 2.4 17.4 1.0 OE1 C:GLU293 2.4 19.9 1.0 OD1 C:ASN287 2.4 22.4 1.0 O C:ASP308 2.5 18.3 1.0 O3 C:FUC402 2.5 20.3 1.0 O2 C:FUC402 2.5 21.6 1.0 OE1 C:GLU285 2.5 22.8 1.0 C3 C:FUC402 3.3 36.1 1.0 C2 C:FUC402 3.3 23.2 1.0 CG C:ASP308 3.4 20.8 1.0 CG C:ASN307 3.4 13.2 1.0 CD C:GLU285 3.4 24.4 1.0 CD C:GLU293 3.4 16.8 1.0 CG C:ASN287 3.4 38.0 1.0 C C:ASP308 3.5 15.2 1.0 OE2 C:GLU285 3.7 23.0 1.0 ND2 C:ASN307 3.7 21.3 1.0 N C:ASP308 3.7 18.5 1.0 OE2 C:GLU293 3.8 19.2 1.0 ND2 C:ASN287 4.0 24.4 1.0 CA C:ASP308 4.0 14.1 1.0 OD2 C:ASP308 4.1 20.4 1.0 N C:ASN287 4.1 18.8 1.0 CB C:ASP308 4.3 17.1 1.0 CB C:ASN287 4.6 21.0 1.0 N C:ASN288 4.6 23.4 1.0 CG C:GLU285 4.6 16.6 1.0 C4 C:FUC402 4.7 46.5 1.0 CG C:GLU293 4.7 19.9 1.0 C C:ASN307 4.7 21.6 1.0 C1 C:FUC402 4.7 33.2 1.0 N C:ALA309 4.7 15.0 1.0 CB C:ASN307 4.7 16.2 1.0 CA C:ASN287 4.7 24.1 1.0 N C:ALA289 4.8 21.5 1.0 CB C:GLU293 4.8 17.9 1.0 CB C:ALA289 4.9 22.6 1.0 CA C:ASN307 4.9 17.1 1.0 O C:HOH112 4.9 28.0 1.0 C C:ASN287 5.0 30.7 1.0 O4 C:FUC402 5.0 44.5 1.0

Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Carbohydrate-Recognition Domain of Human Langerin with Blood Group B Trisaccharide (Gal ALPHA1-3(Fuc ALPHA1-2)Gal) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca500 b:23.8 occ:1.00 OD1 D:ASP308 2.4 18.5 1.0 OD1 D:ASN307 2.4 21.4 1.0 OD1 D:ASN287 2.4 24.6 1.0 OE1 D:GLU293 2.4 24.7 1.0 O3 D:FUC402 2.5 26.9 1.0 OE1 D:GLU285 2.5 24.1 1.0 O2 D:FUC402 2.5 28.1 1.0 O D:ASP308 2.6 21.9 1.0 C3 D:FUC402 3.2 31.9 1.0 C2 D:FUC402 3.3 23.6 1.0 CG D:ASN287 3.3 32.1 1.0 CG D:ASP308 3.4 19.6 1.0 CD D:GLU293 3.4 17.7 1.0 CG D:ASN307 3.4 17.6 1.0 CD D:GLU285 3.4 32.9 1.0 C D:ASP308 3.6 17.8 1.0 OE2 D:GLU293 3.7 26.9 1.0 N D:ASP308 3.8 18.4 1.0 ND2 D:ASN287 3.8 32.9 1.0 ND2 D:ASN307 3.8 21.9 1.0 OE2 D:GLU285 3.8 28.1 1.0 OD2 D:ASP308 4.0 20.8 1.0 CA D:ASP308 4.1 15.3 1.0 N D:ASN287 4.1 20.0 1.0 CB D:ASP308 4.3 18.9 1.0 CB D:ASN287 4.5 28.8 1.0 N D:ASN288 4.6 25.5 1.0 C4 D:FUC402 4.6 75.3 1.0 CG D:GLU285 4.7 19.9 1.0 CA D:ASN287 4.7 24.6 1.0 C D:ASN307 4.7 20.2 1.0 C1 D:FUC402 4.7 70.5 1.0 CG D:GLU293 4.7 25.4 1.0 CB D:ASN307 4.7 16.4 1.0 N D:ALA309 4.8 16.5 1.0 N D:ALA289 4.9 32.8 1.0 C D:ASN287 4.9 39.5 1.0 CA D:ASN307 4.9 20.5 1.0 CB D:GLU293 5.0 18.6 1.0 CB D:ALA289 5.0 29.9 1.0 CB D:GLU285 5.0 18.0 1.0

H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis. Structural Basis For Langerin Recognition of Diverse Pathogen and Mammalian Glycans Through A Single Binding Site. J.Mol.Biol. V. 405 1027 2011.
ISSN: ISSN 0022-2836
PubMed: 21112338
DOI: 10.1016/J.JMB.2010.11.039