Calcium in PDB 4n35: Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3

The structure of Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3, PDB code: 4n35 was solved by H.Feinberg, T.J.W.Rowntree, S.L.W.Tan, K.Drickamer, W.I.Weis, M.E.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.58 / 1.85
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.490, 79.490, 91.930, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.2

The binding sites of Calcium atom in the Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3 (pdb code 4n35). 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 Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3, PDB code: 4n35:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:24.2 occ:1.00 OE1 A:GLU293 2.4 27.7 1.0 OD1 A:ASP308 2.4 23.1 1.0 OD1 A:ASN307 2.4 20.1 1.0 O A:ASP308 2.5 18.7 1.0 OE1 A:GLU285 2.5 27.5 1.0 O4 A:NAG401 2.5 21.8 1.0 OD1 A:ASN287 2.5 24.3 1.0 O3 A:NAG401 2.6 24.4 1.0 C4 A:NAG401 3.2 25.5 1.0 CG A:ASP308 3.3 28.9 1.0 CD A:GLU285 3.4 20.8 1.0 C3 A:NAG401 3.4 27.4 1.0 CD A:GLU293 3.4 19.3 1.0 CG A:ASN287 3.4 28.8 1.0 CG A:ASN307 3.4 19.9 1.0 C A:ASP308 3.5 21.8 1.0 OE2 A:GLU285 3.7 25.0 1.0 OE2 A:GLU293 3.8 22.8 1.0 ND2 A:ASN307 3.8 19.7 1.0 N A:ASP308 3.8 17.4 1.0 ND2 A:ASN287 3.9 32.1 1.0 OD2 A:ASP308 3.9 24.5 1.0 CA A:ASP308 4.1 17.0 1.0 N A:ASN287 4.2 30.9 1.0 CB A:ASP308 4.3 19.3 1.0 CB A:ALA289 4.5 30.8 1.0 N A:ALA289 4.6 35.5 1.0 CB A:ASN287 4.6 27.3 1.0 CG A:GLU285 4.6 22.4 1.0 C5 A:NAG401 4.6 25.6 1.0 N A:ASN288 4.7 23.8 1.0 N A:ALA309 4.7 19.5 1.0 CG A:GLU293 4.7 26.1 1.0 C2 A:NAG401 4.7 27.9 1.0 C A:ASN307 4.7 18.3 1.0 CB A:ASN307 4.7 17.2 1.0 CA A:ASN287 4.8 32.3 1.0 CB A:GLU293 4.9 24.7 1.0 CA A:ASN307 5.0 18.1 1.0 C A:ASN287 5.0 30.5 1.0 CB A:GLU285 5.0 24.4 1.0

Calcium binding site 2 out of 4 in the Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:18.1 occ:1.00 OE1 B:GLU293 2.4 20.2 1.0 OD1 B:ASN287 2.4 21.4 1.0 OD1 B:ASP308 2.4 19.1 1.0 OD1 B:ASN307 2.5 18.4 1.0 OE1 B:GLU285 2.5 25.5 1.0 O B:ASP308 2.5 18.2 1.0 O3 B:NAG401 2.5 23.2 1.0 O4 B:NAG401 2.5 20.6 1.0 C4 B:NAG401 3.2 23.1 1.0 C3 B:NAG401 3.3 20.9 1.0 CD B:GLU285 3.4 21.2 1.0 CD B:GLU293 3.4 16.5 1.0 CG B:ASP308 3.4 19.6 1.0 CG B:ASN307 3.4 18.5 1.0 CG B:ASN287 3.4 24.6 1.0 C B:ASP308 3.6 15.6 1.0 OE2 B:GLU285 3.7 22.8 1.0 OE2 B:GLU293 3.7 18.8 1.0 ND2 B:ASN307 3.8 18.0 1.0 N B:ASP308 3.9 18.3 1.0 ND2 B:ASN287 4.0 23.2 1.0 OD2 B:ASP308 4.1 16.9 1.0 CA B:ASP308 4.1 15.2 1.0 N B:ASN287 4.2 20.4 1.0 CB B:ASP308 4.3 13.8 1.0 CB B:ASN287 4.6 26.4 1.0 N B:ASN288 4.6 20.7 1.0 CG B:GLU285 4.6 21.4 1.0 CG B:GLU293 4.7 16.1 1.0 C5 B:NAG401 4.7 24.8 1.0 C2 B:NAG401 4.7 22.2 1.0 N B:ALA309 4.7 12.1 1.0 C B:ASN307 4.7 17.6 1.0 CB B:ASN307 4.8 18.3 1.0 CA B:ASN287 4.8 22.0 1.0 N B:ALA289 4.8 23.5 1.0 CB B:GLU293 4.9 14.5 1.0 CB B:ALA289 4.9 22.1 1.0 C B:ASN287 5.0 26.2 1.0 CA B:ASN307 5.0 17.8 1.0

Calcium binding site 3 out of 4 in the Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:23.4 occ:1.00 OD1 C:ASP308 2.4 24.0 1.0 OE1 C:GLU293 2.4 24.1 1.0 OD1 C:ASN287 2.4 28.8 1.0 OD1 C:ASN307 2.4 22.2 1.0 OE1 C:GLU285 2.5 24.9 1.0 O C:ASP308 2.5 25.1 1.0 O4 C:NAG401 2.5 24.9 1.0 O3 C:NAG401 2.6 26.4 1.0 C4 C:NAG401 3.3 22.8 1.0 CD C:GLU285 3.3 24.6 1.0 CG C:ASP308 3.4 27.0 1.0 CD C:GLU293 3.4 22.6 1.0 CG C:ASN307 3.4 20.6 1.0 C3 C:NAG401 3.4 27.8 1.0 CG C:ASN287 3.4 29.4 1.0 C C:ASP308 3.6 18.9 1.0 OE2 C:GLU285 3.6 31.0 1.0 OE2 C:GLU293 3.7 26.8 1.0 ND2 C:ASN307 3.8 19.7 1.0 N C:ASP308 3.8 18.3 1.0 ND2 C:ASN287 4.1 29.3 1.0 OD2 C:ASP308 4.1 23.9 1.0 CA C:ASP308 4.1 18.5 1.0 N C:ASN287 4.2 22.8 1.0 CB C:ASP308 4.3 17.5 1.0 CB C:ASN287 4.5 28.3 1.0 CG C:GLU285 4.6 23.3 1.0 CG C:GLU293 4.7 22.7 1.0 N C:ASN288 4.7 22.7 1.0 C5 C:NAG401 4.7 29.3 1.0 N C:ALA309 4.7 15.4 1.0 CB C:ASN307 4.7 23.1 1.0 C C:ASN307 4.7 20.2 1.0 C2 C:NAG401 4.7 26.5 1.0 CA C:ASN287 4.8 27.8 1.0 N C:ALA289 4.8 29.6 1.0 CB C:GLU293 4.8 19.3 1.0 CB C:ALA289 4.9 31.4 1.0 CA C:ASN307 5.0 17.1 1.0

Calcium binding site 4 out of 4 in the Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Langerin Crd I313 Complexed with Glcnac-BETA1-3GAL-BETA1- 4GLC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca404 b:16.4 occ:1.00 OE1 D:GLU293 2.4 15.8 1.0 OD1 D:ASP308 2.4 15.4 1.0 OD1 D:ASN307 2.4 14.0 1.0 OD1 D:ASN287 2.4 18.9 1.0 O D:ASP308 2.5 14.5 1.0 OE1 D:GLU285 2.5 19.1 1.0 O4 D:NAG401 2.5 15.5 1.0 O3 D:NAG401 2.6 16.9 1.0 C4 D:NAG401 3.3 20.6 1.0 CG D:ASP308 3.4 15.1 1.0 CD D:GLU293 3.4 13.3 1.0 CG D:ASN307 3.4 13.8 1.0 CD D:GLU285 3.4 21.2 1.0 C3 D:NAG401 3.4 19.2 1.0 CG D:ASN287 3.5 19.8 1.0 C D:ASP308 3.6 13.3 1.0 ND2 D:ASN307 3.7 16.4 1.0 OE2 D:GLU285 3.7 20.9 1.0 OE2 D:GLU293 3.7 15.9 1.0 N D:ASP308 3.8 13.4 1.0 OD2 D:ASP308 4.0 16.1 1.0 CA D:ASP308 4.0 13.4 1.0 ND2 D:ASN287 4.1 20.2 1.0 N D:ASN287 4.2 17.6 1.0 CB D:ASP308 4.3 12.7 1.0 CB D:ASN287 4.6 21.5 1.0 CG D:GLU285 4.6 17.2 1.0 CG D:GLU293 4.6 17.3 1.0 N D:ASN288 4.6 16.4 1.0 C5 D:NAG401 4.7 21.2 1.0 N D:ALA309 4.7 10.7 1.0 CB D:ASN307 4.7 15.7 1.0 C D:ASN307 4.7 12.0 1.0 CA D:ASN287 4.7 17.4 1.0 C2 D:NAG401 4.8 20.0 1.0 CB D:GLU293 4.8 14.2 1.0 N D:ALA289 4.8 16.6 1.0 CB D:ALA289 4.9 21.2 1.0 CA D:ASN307 5.0 11.7 1.0 C D:ASN287 5.0 21.3 1.0

H.Feinberg, T.J.Rowntree, S.L.Tan, K.Drickamer, W.I.Weis, M.E.Taylor. Common Polymorphisms in Human Langerin Change Specificity For Glycan Ligands. J.Biol.Chem. V. 288 36762 2013.
ISSN: ISSN 0021-9258
PubMed: 24217250
DOI: 10.1074/JBC.M113.528000