Calcium in PDB 3p5d: Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man

The structure of Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man, PDB code: 3p5d 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)	39.03 / 1.80
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.340, 79.340, 89.670, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man (pdb code 3p5d). 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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man, PDB code: 3p5d:
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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man


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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:23.0 occ:1.00 OD1 A:ASP308 2.4 17.9 1.0 OE1 A:GLU293 2.4 24.3 1.0 OD1 A:ASN307 2.4 22.5 1.0 O A:ASP308 2.5 18.5 1.0 OE1 A:GLU285 2.5 21.5 1.0 O4 A:MAN402 2.5 28.0 1.0 OD1 A:ASN287 2.5 26.0 1.0 O3 A:MAN402 2.5 27.7 1.0 CG A:ASP308 3.3 23.3 1.0 C4 A:MAN402 3.3 25.2 1.0 CD A:GLU285 3.3 28.0 1.0 C3 A:MAN402 3.4 26.6 1.0 CG A:ASN287 3.4 41.1 1.0 CG A:ASN307 3.4 19.6 1.0 CD A:GLU293 3.4 17.9 1.0 C A:ASP308 3.5 17.8 1.0 OE2 A:GLU285 3.7 24.5 1.0 N A:ASP308 3.7 16.1 1.0 ND2 A:ASN287 3.9 41.8 1.0 ND2 A:ASN307 3.9 20.0 1.0 OE2 A:GLU293 3.9 26.4 1.0 CA A:ASP308 4.0 16.5 1.0 OD2 A:ASP308 4.0 27.1 1.0 N A:ASN287 4.2 51.3 1.0 CB A:ASP308 4.2 17.7 1.0 CG A:GLU285 4.6 28.1 1.0 CB A:ASN287 4.6 31.4 1.0 N A:ASN288 4.6 24.3 1.0 N A:ALA309 4.7 15.9 1.0 C A:ASN307 4.7 18.6 1.0 CG A:GLU293 4.7 35.7 1.0 CB A:ASN307 4.7 16.4 1.0 C5 A:MAN402 4.7 28.1 1.0 N A:ALA289 4.8 49.2 1.0 CB A:ALA289 4.8 28.8 1.0 C2 A:MAN402 4.8 19.0 1.0 CA A:ASN287 4.8 60.2 1.0 CB A:GLU293 4.9 24.2 1.0 CB A:GLU285 4.9 28.3 1.0 CA A:ASN307 4.9 20.5 1.0

Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man


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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:24.3 occ:1.00 OE1 B:GLU293 2.4 21.7 1.0 OD1 B:ASP308 2.4 26.9 1.0 OD1 B:ASN287 2.4 28.6 1.0 OD1 B:ASN307 2.5 19.7 1.0 OE1 B:GLU285 2.5 24.0 1.0 O B:ASP308 2.5 23.2 1.0 O4 B:MAN402 2.5 23.1 1.0 O3 B:MAN402 2.5 24.2 1.0 C4 B:MAN402 3.3 27.9 1.0 CD B:GLU285 3.3 43.8 1.0 C3 B:MAN402 3.4 35.4 1.0 CD B:GLU293 3.4 21.9 1.0 CG B:ASN287 3.4 31.6 1.0 CG B:ASN307 3.4 22.4 1.0 CG B:ASP308 3.4 31.2 1.0 C B:ASP308 3.6 18.9 1.0 OE2 B:GLU285 3.6 26.4 1.0 OE2 B:GLU293 3.7 27.8 1.0 ND2 B:ASN307 3.7 18.4 1.0 N B:ASP308 3.8 23.9 1.0 ND2 B:ASN287 3.9 29.9 1.0 CA B:ASP308 4.1 19.4 1.0 OD2 B:ASP308 4.1 22.2 1.0 N B:ASN287 4.1 24.4 1.0 CB B:ASP308 4.3 16.8 1.0 CB B:ASN287 4.5 28.1 1.0 CG B:GLU285 4.6 26.5 1.0 CG B:GLU293 4.7 21.7 1.0 N B:ASN288 4.7 28.8 1.0 C B:ASN307 4.7 19.9 1.0 CA B:ASN287 4.7 30.0 1.0 N B:ALA309 4.7 19.3 1.0 CB B:ASN307 4.7 18.8 1.0 C2 B:MAN402 4.7 26.6 1.0 C5 B:MAN402 4.7 52.0 1.0 N B:ALA289 4.9 40.3 1.0 CB B:GLU293 4.9 29.3 1.0 CA B:ASN307 4.9 20.9 1.0 O2 B:MAN402 5.0 31.7 1.0 C B:ASN287 5.0 44.3 1.0 CB B:GLU285 5.0 15.5 1.0 CB B:ALA289 5.0 31.4 1.0

Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man


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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca500 b:26.2 occ:1.00 OD1 C:ASN307 2.4 19.4 1.0 OD1 C:ASP308 2.4 23.1 1.0 OE1 C:GLU293 2.4 26.6 1.0 O C:ASP308 2.4 26.6 1.0 OD1 C:ASN287 2.5 42.8 1.0 OE1 C:GLU285 2.5 25.0 1.0 O4 C:MAN402 2.5 24.6 1.0 O3 C:MAN402 2.6 23.6 1.0 C4 C:MAN402 3.3 24.4 1.0 C3 C:MAN402 3.4 32.5 1.0 CD C:GLU285 3.4 40.6 1.0 CD C:GLU293 3.4 22.1 1.0 CG C:ASN307 3.4 13.2 1.0 CG C:ASN287 3.4 27.1 1.0 CG C:ASP308 3.4 24.5 1.0 C C:ASP308 3.5 23.5 1.0 OE2 C:GLU285 3.7 29.9 1.0 OE2 C:GLU293 3.7 23.5 1.0 N C:ASP308 3.8 23.1 1.0 ND2 C:ASN307 3.8 22.8 1.0 ND2 C:ASN287 3.9 41.2 1.0 CA C:ASP308 4.0 18.5 1.0 OD2 C:ASP308 4.2 25.3 1.0 N C:ASN287 4.3 27.0 1.0 CB C:ASP308 4.3 15.8 1.0 CB C:ASN287 4.6 27.8 1.0 CG C:GLU285 4.6 22.4 1.0 N C:ASN288 4.7 32.0 1.0 N C:ALA309 4.7 16.1 1.0 CG C:GLU293 4.7 22.4 1.0 C C:ASN307 4.7 34.4 1.0 C5 C:MAN402 4.7 36.0 1.0 CB C:ASN307 4.7 19.8 1.0 C2 C:MAN402 4.7 29.3 1.0 N C:ALA289 4.8 22.9 1.0 CB C:GLU293 4.8 28.1 1.0 CA C:ASN287 4.9 30.2 1.0 CB C:ALA289 4.9 32.5 1.0 CA C:ASN307 4.9 27.1 1.0 O2 C:MAN402 5.0 34.8 1.0

Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man


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 MAN5 (Man ALPHA1-3(Man ALPHA1-6)Man ALPHA1-6)(Man- ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca500 b:29.4 occ:1.00 OD1 D:ASP308 2.4 25.0 1.0 OD1 D:ASN307 2.4 29.3 1.0 OD1 D:ASN287 2.5 30.9 1.0 OE1 D:GLU293 2.5 27.1 1.0 OE1 D:GLU285 2.5 29.0 1.0 O3 D:MAN402 2.5 34.0 1.0 O4 D:MAN402 2.5 31.8 1.0 O D:ASP308 2.6 27.1 1.0 C4 D:MAN402 3.2 34.2 1.0 CD D:GLU285 3.3 42.4 1.0 C3 D:MAN402 3.3 29.8 1.0 CG D:ASP308 3.4 43.0 1.0 CG D:ASN287 3.5 38.9 1.0 CG D:ASN307 3.5 16.1 1.0 CD D:GLU293 3.5 27.4 1.0 OE2 D:GLU285 3.6 31.9 1.0 C D:ASP308 3.6 25.9 1.0 N D:ASP308 3.8 18.8 1.0 OE2 D:GLU293 3.9 27.6 1.0 ND2 D:ASN307 3.9 22.2 1.0 ND2 D:ASN287 4.0 38.1 1.0 N D:ASN287 4.0 26.9 1.0 OD2 D:ASP308 4.1 27.9 1.0 CA D:ASP308 4.1 19.8 1.0 CB D:ASP308 4.4 29.9 1.0 CG D:GLU285 4.5 27.8 1.0 CB D:ASN287 4.6 31.6 1.0 N D:ASN288 4.7 30.5 1.0 CA D:ASN287 4.7 45.3 1.0 C2 D:MAN402 4.7 42.5 1.0 C5 D:MAN402 4.7 52.8 1.0 C D:ASN307 4.7 23.6 1.0 CB D:ASN307 4.8 25.5 1.0 CG D:GLU293 4.8 25.6 1.0 N D:ALA309 4.8 24.6 1.0 N D:ALA289 4.9 45.4 1.0 CA D:ASN307 4.9 30.5 1.0 O2 D:MAN402 4.9 45.5 1.0 C D:ASN287 4.9 47.3 1.0 CB D:GLU285 4.9 31.8 1.0 CB D:GLU293 5.0 28.6 1.0 CB D:ALA289 5.0 44.7 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