Calcium in PDB 7ytq: Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand

The structure of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand, PDB code: 7ytq was solved by K.Wangkanont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 1.60
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	80.03, 80.03, 90.07, 90, 90, 90
R / Rfree (%)	18.3 / 21.3

The structure of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand (pdb code 7ytq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand, PDB code: 7ytq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:23.7 occ:1.00 OD1 A:ASP308 2.3 22.6 1.0 OD1 A:ASN307 2.3 24.5 1.0 OE1 A:GLU285 2.3 29.3 1.0 O3 A:JMI402 2.4 25.6 0.9 OD1 A:ASN287 2.5 27.8 1.0 OE1 A:GLU293 2.5 25.2 1.0 O4 A:JMI402 2.5 25.8 0.9 O A:ASP308 2.6 25.2 1.0 CD A:GLU285 3.3 30.2 1.0 C3 A:JMI402 3.3 26.9 0.9 CG A:ASP308 3.3 30.4 1.0 C4 A:JMI402 3.3 26.5 0.9 CG A:ASN307 3.4 22.2 1.0 CG A:ASN287 3.4 26.5 1.0 CD A:GLU293 3.5 22.6 1.0 OE2 A:GLU285 3.6 32.4 1.0 C A:ASP308 3.6 20.0 1.0 N A:ASP308 3.7 22.0 1.0 ND2 A:ASN307 3.8 19.6 1.0 OE2 A:GLU293 3.8 30.6 1.0 ND2 A:ASN287 3.9 30.3 1.0 OD2 A:ASP308 4.0 26.6 1.0 CA A:ASP308 4.0 19.6 1.0 N A:ASN287 4.1 27.9 1.0 CB A:ASP308 4.3 21.1 1.0 CG A:GLU285 4.5 25.6 1.0 CB A:ASN287 4.6 25.4 1.0 N A:ASN288 4.6 28.1 1.0 C2 A:JMI402 4.7 28.0 0.9 CB A:ASN307 4.7 22.7 1.0 C A:ASN307 4.7 25.1 1.0 C5 A:JMI402 4.7 30.8 0.9 CA A:ASN287 4.8 29.4 1.0 CG A:GLU293 4.8 26.6 1.0 N A:ALA289 4.8 31.3 1.0 N A:ALA309 4.8 18.0 1.0 CB A:ALA289 4.8 34.8 1.0 CA A:ASN307 4.9 23.9 1.0 O2 A:JMI402 4.9 37.6 0.9 CB A:GLU285 4.9 25.9 1.0 CB A:GLU293 4.9 25.0 1.0 C A:ASN287 5.0 35.0 1.0

Calcium binding site 2 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:24.7 occ:1.00 OD1 B:ASP308 2.3 22.4 1.0 O3 B:JMI402 2.4 28.5 0.8 OE1 B:GLU293 2.4 29.8 1.0 OD1 B:ASN287 2.4 29.5 1.0 OD1 B:ASN307 2.5 24.5 1.0 OE1 B:GLU285 2.5 25.9 1.0 O B:ASP308 2.6 25.3 1.0 O4 B:JMI402 2.7 24.3 0.8 CG B:ASN287 3.2 27.7 1.0 C3 B:JMI402 3.3 29.9 0.8 CG B:ASP308 3.3 24.7 1.0 CD B:GLU293 3.3 27.8 1.0 C4 B:JMI402 3.4 24.1 0.8 CD B:GLU285 3.4 27.9 1.0 CG B:ASN307 3.5 19.9 1.0 ND2 B:ASN287 3.6 38.6 1.0 OE2 B:GLU293 3.6 26.5 1.0 C B:ASP308 3.6 21.1 1.0 OE2 B:GLU285 3.8 30.3 1.0 N B:ASP308 3.8 19.4 1.0 ND2 B:ASN307 3.8 20.3 1.0 OD2 B:ASP308 3.9 29.6 1.0 CA B:ASP308 4.1 17.0 1.0 N B:ASN287 4.1 27.5 1.0 CB B:ASP308 4.3 22.2 1.0 CB B:ASN287 4.5 29.5 1.0 N B:ASN288 4.6 29.6 1.0 CG B:GLU293 4.6 24.8 1.0 CB B:ALA289 4.6 36.7 1.0 N B:ALA289 4.6 32.4 1.0 C2 B:JMI402 4.7 31.7 0.8 CG B:GLU285 4.7 24.9 1.0 CA B:ASN287 4.7 32.2 1.0 C B:ASN307 4.7 22.1 1.0 N B:ALA309 4.8 22.4 1.0 CB B:ASN307 4.8 22.8 1.0 CB B:GLU293 4.8 25.1 1.0 C5 B:JMI402 4.8 31.7 0.8 C B:ASN287 4.9 35.0 1.0 CA B:ASN307 5.0 22.8 1.0 CB B:GLU285 5.0 27.3 1.0

Calcium binding site 3 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:21.0 occ:1.00 OD1 C:ASP308 2.3 18.0 1.0 OD1 C:ASN307 2.4 19.8 1.0 OE1 C:GLU293 2.4 22.5 1.0 OD1 C:ASN287 2.5 26.2 1.0 OE1 C:GLU285 2.5 24.9 1.0 O3 C:JMI403 2.5 26.0 0.9 O C:ASP308 2.5 20.9 1.0 O4 C:JMI403 2.6 21.2 0.9 CG C:ASP308 3.3 21.5 1.0 CD C:GLU293 3.3 18.3 1.0 C4 C:JMI403 3.4 20.2 0.9 C3 C:JMI403 3.4 26.3 0.9 CG C:ASN307 3.4 13.0 1.0 CD C:GLU285 3.4 25.1 1.0 CG C:ASN287 3.5 29.0 1.0 C C:ASP308 3.6 18.2 1.0 OE2 C:GLU293 3.6 23.5 1.0 ND2 C:ASN307 3.7 17.7 1.0 OE2 C:GLU285 3.8 26.9 1.0 N C:ASP308 3.8 16.6 1.0 ND2 C:ASN287 4.0 29.2 1.0 OD2 C:ASP308 4.0 21.5 1.0 CA C:ASP308 4.1 15.2 1.0 N C:ASN287 4.2 20.8 1.0 CB C:ASP308 4.3 18.6 1.0 CG C:GLU285 4.6 20.7 1.0 N C:ASN288 4.6 26.9 1.0 CB C:ASN287 4.7 25.8 1.0 CG C:GLU293 4.7 19.8 1.0 CB C:ASN307 4.7 21.8 1.0 C C:ASN307 4.7 17.9 1.0 C2 C:JMI403 4.8 26.0 0.9 N C:ALA309 4.8 17.1 1.0 N C:ALA289 4.8 24.5 1.0 C5 C:JMI403 4.8 28.1 0.9 CB C:ALA289 4.8 27.6 1.0 CA C:ASN287 4.8 24.9 1.0 CB C:GLU293 4.9 19.9 1.0 CA C:ASN307 4.9 16.0 1.0

Calcium binding site 4 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:17.6 occ:1.00 OD1 D:ASP308 2.3 15.3 1.0 OD1 D:ASN307 2.4 16.3 1.0 OD1 D:ASN287 2.4 21.5 1.0 O4 D:JMI403 2.5 17.9 0.8 OE1 D:GLU285 2.5 20.8 1.0 O3 D:JMI403 2.5 18.2 0.8 O D:ASP308 2.5 18.3 1.0 OE1 D:GLU293 2.5 18.2 1.0 C4 D:JMI403 3.3 22.1 0.8 C3 D:JMI403 3.3 24.1 0.8 CG D:ASP308 3.3 18.0 1.0 CD D:GLU285 3.4 21.0 1.0 CG D:ASN307 3.4 14.0 1.0 CD D:GLU293 3.4 16.4 1.0 CG D:ASN287 3.4 22.1 1.0 C D:ASP308 3.6 13.3 1.0 ND2 D:ASN307 3.7 17.8 1.0 OE2 D:GLU293 3.7 19.6 1.0 OE2 D:GLU285 3.8 20.4 1.0 N D:ASP308 3.8 16.3 1.0 ND2 D:ASN287 4.0 25.3 1.0 CA D:ASP308 4.0 14.5 1.0 OD2 D:ASP308 4.1 19.2 1.0 N D:ASN287 4.2 21.6 1.0 CB D:ASP308 4.3 16.1 1.0 CG D:GLU285 4.6 15.4 1.0 CB D:ASN287 4.6 19.6 1.0 C2 D:JMI403 4.7 23.5 0.8 C5 D:JMI403 4.7 26.3 0.8 N D:ASN288 4.7 24.1 1.0 N D:ALA309 4.7 13.5 1.0 CB D:ASN307 4.7 15.3 1.0 C D:ASN307 4.7 16.1 1.0 CG D:GLU293 4.8 17.7 1.0 CA D:ASN287 4.8 18.9 1.0 N D:ALA289 4.8 23.8 1.0 CB D:ALA289 4.9 26.9 1.0 CB D:GLU293 5.0 18.6 1.0 CA D:ASN307 5.0 12.5 1.0 O2 D:JMI403 5.0 23.0 0.8 CB D:GLU285 5.0 17.8 1.0

K.Wangkanont, K.Wangkanont. N/A N/A.