Calcium in PDB 9qwj: Crystal Structure of S2C Tcr in Complex with CD1C

The structure of Crystal Structure of S2C Tcr in Complex with CD1C, PDB code: 9qwj was solved by V.Karuppiah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.03 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.373, 122.068, 108.696, 90, 110.03, 90
R / Rfree (%)	20 / 23.5

The binding sites of Calcium atom in the Crystal Structure of S2C Tcr in Complex with CD1C (pdb code 9qwj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of S2C Tcr in Complex with CD1C, PDB code: 9qwj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of S2C Tcr in Complex with CD1C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of S2C Tcr in Complex with CD1C within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:41.4 occ:1.00 O D:HOH302 2.1 47.5 1.0 O D:GLU15 2.3 39.9 1.0 O D:HOH342 2.3 39.0 1.0 OG D:SER14 2.4 35.9 1.0 OD2 D:ASP114 2.5 42.3 1.0 O D:HOH347 2.5 35.8 1.0 OD1 D:ASP114 2.6 41.8 1.0 CG D:ASP114 2.8 41.0 1.0 CB D:SER14 3.4 36.0 1.0 C D:GLU15 3.5 37.3 1.0 N D:GLU15 4.0 35.8 1.0 C D:SER14 4.0 37.1 1.0 CA D:GLU15 4.1 37.0 1.0 CA D:SER14 4.3 36.1 1.0 CB D:GLU15 4.3 41.5 1.0 OE2 D:GLU16 4.3 49.1 1.0 CB D:ASP114 4.4 38.7 1.0 O D:SER14 4.4 37.9 1.0 CB D:GLU16 4.5 43.3 1.0 N D:GLU16 4.5 37.3 1.0 CG D:GLU16 4.7 45.6 1.0 CA D:GLU16 4.9 39.8 1.0 CD D:GLU16 5.0 49.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of S2C Tcr in Complex with CD1C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of S2C Tcr in Complex with CD1C within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca202 b:36.6 occ:1.00 O U:HOH308 2.3 34.5 1.0 O T:ASP127 2.3 37.3 1.0 OD1 T:ASP127 2.3 40.1 1.0 O U:VAL128 2.4 33.0 1.0 O U:HOH338 2.5 40.1 1.0 C T:ASP127 3.3 38.4 1.0 CG T:ASP127 3.4 39.8 1.0 C U:VAL128 3.5 31.0 1.0 CA T:ASP127 3.8 38.6 1.0 N U:VAL128 4.0 29.9 1.0 O U:GLU239 4.1 35.6 1.0 CB T:ASP127 4.1 38.9 1.0 CA U:VAL128 4.2 30.6 1.0 OD2 T:ASP127 4.3 43.8 1.0 OE2 U:GLU130 4.3 42.9 1.0 CB U:VAL128 4.4 31.1 1.0 N T:SER128 4.5 39.5 1.0 N U:PHE129 4.6 28.4 1.0 CB T:SER128 4.9 42.4 1.0 CA U:PHE129 4.9 29.2 1.0 CG1 U:VAL128 4.9 31.2 1.0 CG U:GLU130 4.9 39.4 1.0 CA T:SER128 4.9 42.9 1.0 O U:HOH344 4.9 32.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of S2C Tcr in Complex with CD1C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of S2C Tcr in Complex with CD1C within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca203 b:43.4 occ:1.00 O T:HOH350 2.2 41.4 1.0 O T:GLU15 2.3 37.2 1.0 O T:HOH340 2.3 40.5 1.0 O T:HOH303 2.5 40.6 1.0 OD2 T:ASP114 2.5 48.7 1.0 OG T:SER14 2.5 36.3 1.0 OD1 T:ASP114 2.6 41.9 1.0 CG T:ASP114 2.8 42.9 1.0 C T:GLU15 3.5 36.0 1.0 CB T:SER14 3.5 35.3 1.0 N T:GLU15 4.1 35.9 1.0 C T:SER14 4.1 36.0 1.0 CA T:GLU15 4.2 36.5 1.0 CB T:GLU15 4.3 40.1 1.0 CB T:ASP114 4.4 40.9 1.0 CA T:SER14 4.4 35.2 1.0 CB T:GLU16 4.5 38.3 1.0 O T:SER14 4.5 37.9 1.0 N T:GLU16 4.6 36.8 1.0 OE2 T:GLU16 4.6 46.8 1.0 O T:HOH326 4.6 33.6 1.0 CG T:GLU16 4.7 41.2 1.0 O T:HOH356 4.7 48.3 1.0 CA T:GLU16 4.9 39.0 1.0

R.Szoke-Kovacs, S.Khakoo, V.L.Rangel, P.Della Cristina, J.Pentier, R.Khanolkar, S.El-Ajouz, R.Simmons, D.K.Cole, P.Gogolak, M.Salio, V.Karuppiah. A CD1C Lipid Agnostic T Cell Receptor Bispecific Engager Redirects T Cells Against CD1C + Cells. Front Immunol V. 16 14610 2025.
ISSN: ESSN 1664-3224
PubMed: 40777002
DOI: 10.3389/FIMMU.2025.1614610