Calcium in PDB 5ks9: BEL502-DQ8-Glia-ALPHA1 Complex

The structure of BEL502-DQ8-Glia-ALPHA1 Complex, PDB code: 5ks9 was solved by J.Petersen, J.Rossjohn, H.H.Reid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.560, 56.870, 232.050, 90.00, 92.77, 90.00
R / Rfree (%)	19.9 / 22.4

The binding sites of Calcium atom in the BEL502-DQ8-Glia-ALPHA1 Complex (pdb code 5ks9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the BEL502-DQ8-Glia-ALPHA1 Complex, PDB code: 5ks9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:75.2 occ:1.00 OE1 A:GLN44 2.5 62.2 1.0 O A:HOH450 2.8 34.7 1.0 O A:GLU134 3.7 29.7 1.0 CD A:GLN44 3.7 64.3 1.0 O B:HOH1143 4.2 44.3 1.0 CA A:THR135 4.2 22.7 1.0 C A:GLU134 4.2 29.7 1.0 N A:THR135 4.5 24.4 1.0 NE2 A:GLN44 4.5 50.9 1.0 OE1 A:GLU30 4.5 46.3 1.0 CG2 A:THR135 4.7 25.1 1.0 CG A:GLN44 4.8 46.8 1.0 CB A:THR135 4.9 24.4 1.0

Calcium binding site 2 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:66.0 occ:1.00 OE1 C:GLN44 2.8 42.9 1.0 O C:GLU134 3.4 29.6 1.0 CD C:GLN44 3.8 45.8 1.0 C C:GLU134 4.1 29.9 1.0 CA C:THR135 4.1 22.2 1.0 N C:THR135 4.4 24.8 1.0 NE2 C:GLN44 4.5 31.5 1.0 O C:HOH431 4.5 46.3 1.0 O D:HOH1157 4.6 47.9 1.0 OE1 C:GLU30 4.8 34.8 1.0 CG2 C:THR135 4.8 29.6 1.0 CG C:GLN44 4.8 35.6 1.0 CB C:THR135 4.9 27.9 1.0

Calcium binding site 3 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:66.5 occ:1.00 OE1 E:GLN164 2.2 83.1 1.0 OD1 E:ASP174 2.4 54.0 1.0 CD E:GLN164 3.2 89.5 1.0 CG E:ASP174 3.4 51.2 1.0 O E:HOH464 3.6 25.5 1.0 CG E:GLN164 3.7 71.5 1.0 OD2 E:ASP174 4.0 57.5 1.0 O E:HOH472 4.0 33.7 1.0 O E:VAL162 4.1 55.7 1.0 CA E:ASP174 4.3 33.5 1.0 NE2 E:GLN164 4.3 83.3 1.0 CB E:ASP174 4.4 35.4 1.0 N E:GLN164 4.7 59.7 1.0 N E:ASP174 4.7 32.8 1.0 O E:THR173 4.7 35.7 1.0 C E:SER163 4.8 61.5 1.0 C E:THR173 4.9 34.9 1.0 CB E:GLN164 4.9 61.6 1.0 CA E:GLN164 5.0 59.8 1.0

Calcium binding site 4 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca301 b:0.3 occ:1.00 OD1 G:ASP174 2.1 58.0 1.0 NE2 G:GLN164 2.5 77.3 1.0 O G:HOH408 2.6 41.0 1.0 OE1 G:GLN164 2.9 80.2 1.0 CD G:GLN164 3.0 86.6 1.0 CG G:ASP174 3.2 56.3 1.0 OD2 G:ASP174 3.6 63.9 1.0 O G:HOH439 4.3 33.3 1.0 CG G:GLN164 4.3 73.3 1.0 CB G:ASP174 4.4 40.6 1.0 N G:ASP174 4.6 37.3 1.0 CA G:ASP174 4.8 38.3 1.0 O H:HOH350 4.8 27.5 1.0 O G:ILE172 5.0 33.2 1.0

J.Petersen, Y.Kooy-Winkelaar, K.L.Loh, M.Tran, J.Van Bergen, F.Koning, J.Rossjohn, H.H.Reid. Diverse T Cell Receptor Gene Usage in Hla-DQ8-Associated Celiac Disease Converges Into A Consensus Binding Solution. Structure V. 24 1643 2016.
ISSN: ISSN 0969-2126
PubMed: 27568928
DOI: 10.1016/J.STR.2016.07.010