Calcium in PDB 4n38: Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3

The structure of Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3, PDB code: 4n38 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)	39.56 / 2.00
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.030, 79.030, 91.390, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.3

The structure of Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 (pdb code 4n38). 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 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3, PDB code: 4n38:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-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 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:36.9 occ:1.00 OE1 A:GLU293 2.4 41.9 1.0 OE1 A:GLU285 2.4 35.4 1.0 OD1 A:ASN307 2.4 29.8 1.0 OD1 A:ASP308 2.5 30.3 1.0 O A:ASP308 2.5 27.1 1.0 OD1 A:ASN287 2.5 47.5 1.0 O4 A:NAG401 2.6 39.3 1.0 O3 A:NAG401 2.6 34.3 1.0 CG A:ASP308 3.3 32.7 1.0 CG A:ASN287 3.3 47.1 1.0 CD A:GLU285 3.3 33.6 1.0 C4 A:NAG401 3.4 34.4 1.0 CG A:ASN307 3.4 33.5 1.0 CD A:GLU293 3.4 36.1 1.0 C3 A:NAG401 3.5 34.8 1.0 C A:ASP308 3.5 28.4 1.0 ND2 A:ASN287 3.6 49.6 1.0 OE2 A:GLU285 3.6 34.4 1.0 ND2 A:ASN307 3.7 32.7 1.0 OE2 A:GLU293 3.7 38.9 1.0 N A:ASP308 3.8 27.3 1.0 OD2 A:ASP308 3.8 39.4 1.0 CA A:ASP308 4.0 29.5 1.0 N A:ASN287 4.2 44.8 1.0 CB A:ASP308 4.2 30.8 1.0 CG A:GLU285 4.5 30.3 1.0 CB A:ASN287 4.6 42.6 1.0 CB A:ALA289 4.6 49.5 1.0 N A:ALA309 4.7 27.8 1.0 CG A:GLU293 4.7 39.4 1.0 N A:ALA289 4.7 50.5 1.0 C A:ASN307 4.7 24.9 1.0 CB A:ASN307 4.7 25.3 1.0 N A:ASP288 4.8 43.2 1.0 C2 A:NAG401 4.8 35.6 1.0 C5 A:NAG401 4.8 36.5 1.0 CA A:ASN287 4.8 48.5 1.0 CB A:GLU293 4.9 37.3 1.0 CB A:GLU285 4.9 33.3 1.0 CA A:ASN307 5.0 27.6 1.0

Calcium binding site 2 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-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 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:26.6 occ:1.00 OE1 B:GLU293 2.4 26.3 1.0 OE1 B:GLU285 2.4 29.9 1.0 OD1 B:ASP308 2.4 24.3 1.0 OD1 B:ASN307 2.5 24.9 1.0 OD1 B:ASN287 2.5 31.1 1.0 O B:ASP308 2.5 24.4 1.0 O3 B:NAG401 2.5 33.6 1.0 O4 B:NAG401 2.6 27.7 1.0 C4 B:NAG401 3.3 30.5 1.0 CD B:GLU285 3.3 32.2 1.0 C3 B:NAG401 3.3 32.4 1.0 CG B:ASP308 3.3 28.5 1.0 CG B:ASN307 3.4 24.9 1.0 CG B:ASN287 3.4 34.8 1.0 CD B:GLU293 3.4 24.7 1.0 C B:ASP308 3.6 22.9 1.0 ND2 B:ASN307 3.7 25.1 1.0 OE2 B:GLU285 3.7 32.7 1.0 OE2 B:GLU293 3.8 24.0 1.0 N B:ASP308 3.8 24.9 1.0 ND2 B:ASN287 3.9 34.4 1.0 OD2 B:ASP308 4.0 24.7 1.0 CA B:ASP308 4.1 21.8 1.0 N B:ASN287 4.1 31.9 1.0 CB B:ASP308 4.3 23.5 1.0 CB B:ASN287 4.5 38.8 1.0 N B:ASP288 4.6 33.2 1.0 CG B:GLU285 4.6 27.1 1.0 CG B:GLU293 4.6 30.5 1.0 CA B:ASN287 4.7 35.9 1.0 C B:ASN307 4.7 28.1 1.0 CB B:ASN307 4.7 23.2 1.0 C2 B:NAG401 4.7 30.5 1.0 N B:ALA309 4.7 22.3 1.0 N B:ALA289 4.7 36.3 1.0 C5 B:NAG401 4.8 38.4 1.0 CB B:GLU293 4.8 24.9 1.0 CB B:ALA289 4.9 34.3 1.0 C B:ASN287 4.9 37.8 1.0 CA B:ASN307 4.9 22.3 1.0 CB B:GLU285 5.0 28.4 1.0

Calcium binding site 3 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-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 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:33.3 occ:1.00 OD1 C:ASN307 2.4 26.3 1.0 OD1 C:ASP308 2.4 29.7 1.0 O C:ASP308 2.4 27.9 1.0 OE1 C:GLU293 2.4 34.0 1.0 OD1 C:ASN287 2.4 39.6 1.0 OE1 C:GLU285 2.5 33.6 1.0 O3 C:NAG401 2.5 35.9 1.0 O4 C:NAG401 2.5 29.8 1.0 C4 C:NAG401 3.3 34.3 1.0 CG C:ASN307 3.3 23.9 1.0 C3 C:NAG401 3.4 36.4 1.0 CD C:GLU285 3.4 35.6 1.0 CD C:GLU293 3.4 32.8 1.0 CG C:ASN287 3.4 36.5 1.0 CG C:ASP308 3.4 32.0 1.0 C C:ASP308 3.5 30.9 1.0 ND2 C:ASN307 3.6 26.7 1.0 N C:ASP308 3.6 29.5 1.0 OE2 C:GLU293 3.8 34.5 1.0 OE2 C:GLU285 3.8 41.4 1.0 ND2 C:ASN287 4.0 38.2 1.0 CA C:ASP308 4.0 21.5 1.0 OD2 C:ASP308 4.2 34.3 1.0 N C:ASN287 4.3 33.2 1.0 CB C:ASP308 4.3 20.7 1.0 CB C:ASN287 4.5 34.0 1.0 C C:ASN307 4.5 22.6 1.0 CG C:GLU285 4.6 36.8 1.0 CB C:ASN307 4.6 29.3 1.0 CG C:GLU293 4.6 31.4 1.0 N C:ALA309 4.7 25.6 1.0 C2 C:NAG401 4.7 34.8 1.0 C5 C:NAG401 4.7 36.4 1.0 N C:ASP288 4.8 36.8 1.0 CB C:GLU293 4.8 25.7 1.0 CA C:ASN307 4.8 29.0 1.0 CA C:ASN287 4.9 39.1 1.0 N C:ALA289 5.0 34.8 1.0 CB C:ALA289 5.0 36.7 1.0

Calcium binding site 4 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-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 D288 Complexed with Glcnac-BETA1-3GAL- BETA1-4GLCNAC-Beta-CH2CH2N3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:29.1 occ:1.00 OD1 D:ASP308 2.4 30.5 1.0 OE1 D:GLU293 2.4 33.0 1.0 OE1 D:GLU285 2.4 32.3 1.0 O3 D:NAG401 2.5 31.4 1.0 OD1 D:ASN307 2.5 22.3 1.0 OD1 D:ASN287 2.5 33.5 1.0 O D:ASP308 2.6 27.9 1.0 O4 D:NAG401 2.6 32.2 1.0 CG D:ASP308 3.3 34.0 1.0 C4 D:NAG401 3.3 26.2 1.0 CD D:GLU285 3.3 37.5 1.0 C3 D:NAG401 3.4 28.8 1.0 CD D:GLU293 3.4 25.0 1.0 CG D:ASN307 3.4 22.5 1.0 CG D:ASN287 3.4 34.6 1.0 C D:ASP308 3.6 25.2 1.0 OE2 D:GLU285 3.7 33.9 1.0 ND2 D:ASN307 3.7 20.1 1.0 OE2 D:GLU293 3.7 30.1 1.0 N D:ASP308 3.8 21.7 1.0 ND2 D:ASN287 3.9 40.4 1.0 OD2 D:ASP308 4.0 33.8 1.0 N D:ASN287 4.1 30.4 1.0 CA D:ASP308 4.1 23.6 1.0 CB D:ASP308 4.3 26.4 1.0 CB D:ASN287 4.5 37.5 1.0 CG D:GLU285 4.6 31.0 1.0 CG D:GLU293 4.6 31.7 1.0 N D:ASP288 4.7 30.8 1.0 C2 D:NAG401 4.7 33.5 1.0 CA D:ASN287 4.7 38.7 1.0 CB D:ASN307 4.7 27.2 1.0 C D:ASN307 4.7 19.8 1.0 C5 D:NAG401 4.8 33.4 1.0 CB D:GLU293 4.8 28.1 1.0 N D:ALA309 4.8 24.9 1.0 N D:ALA289 4.8 37.7 1.0 CB D:ALA289 4.8 39.1 1.0 CA D:ASN307 5.0 24.2 1.0 CB D:GLU285 5.0 33.0 1.0 C D:ASN287 5.0 38.9 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