Calcium in PDB 6dxl: Linked Amidobenzimidazole Sting Agonist

The structure of Linked Amidobenzimidazole Sting Agonist, PDB code: 6dxl was solved by N.O.Concha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.26 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.140, 73.034, 60.275, 90.00, 96.08, 90.00
R / Rfree (%)	24.9 / 28.4

The binding sites of Calcium atom in the Linked Amidobenzimidazole Sting Agonist (pdb code 6dxl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Linked Amidobenzimidazole Sting Agonist, PDB code: 6dxl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Linked Amidobenzimidazole Sting Agonist


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Linked Amidobenzimidazole Sting Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:68.9 occ:1.00 O A:HOH504 2.3 65.6 1.0 OE2 A:GLU316 2.4 0.8 1.0 O A:HOH506 2.4 83.6 1.0 OD2 A:ASP205 2.5 66.1 1.0 CD A:GLU316 2.8 1.0 1.0 OE1 A:GLU316 2.9 0.5 1.0 CG A:ASP205 3.5 65.1 1.0 OD1 A:ASP205 3.8 80.1 1.0 HG3 A:GLU316 4.1 0.7 1.0 CG A:GLU316 4.1 0.9 1.0 HA3 A:GLY207 4.2 61.1 1.0 HE2 A:TYR314 4.4 88.1 1.0 HB2 A:PRO203 4.4 48.8 1.0 HB2 A:GLU316 4.5 0.5 1.0 HB3 A:PRO203 4.5 48.8 1.0 O A:GLY207 4.6 57.4 1.0 H A:GLY207 4.7 58.6 1.0 HG2 A:GLU316 4.8 0.7 1.0 CB A:GLU316 4.9 0.2 1.0 CB A:ASP205 4.9 61.2 1.0 HH A:TYR314 4.9 88.5 1.0 CB A:PRO203 5.0 44.2 1.0 CA A:GLY207 5.0 49.9 1.0

Calcium binding site 2 out of 2 in the Linked Amidobenzimidazole Sting Agonist


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Linked Amidobenzimidazole Sting Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:84.5 occ:1.00 O B:VAL341 2.1 79.6 1.0 O B:HOH505 2.1 84.1 1.0 O B:HOH502 2.3 49.7 1.0 O B:THR342 2.8 0.9 1.0 C B:VAL341 3.2 81.1 1.0 C B:THR342 3.5 0.7 1.0 HA B:THR342 3.7 0.6 1.0 HA B:VAL341 3.9 94.9 1.0 CA B:THR342 4.0 87.8 1.0 N B:THR342 4.0 82.9 1.0 CA B:VAL341 4.2 78.0 1.0 N B:VAL343 4.5 93.1 1.0 C B:VAL343 4.6 0.2 1.0 O B:GLU340 4.6 65.3 1.0 HB B:VAL341 4.7 96.1 1.0 HA B:VAL343 4.7 0.9 1.0 H B:THR342 4.9 0.7 1.0 CA B:VAL343 4.9 99.7 1.0

J.M.Ramanjulu, G.S.Pesiridis, J.Yang, N.Concha, R.Singhaus, S.Y.Zhang, J.L.Tran, P.Moore, S.Lehmann, H.C.Eberl, M.Muelbaier, J.L.Schneck, J.Clemens, M.Adam, J.Mehlmann, J.Romano, A.Morales, J.Kang, L.Leister, T.L.Graybill, A.K.Charnley, G.Ye, N.Nevins, K.Behnia, A.I.Wolf, V.Kasparcova, K.Nurse, L.Wang, Y.Li, M.Klein, C.B.Hopson, J.Guss, M.Bantscheff, G.Bergamini, M.A.Reilly, Y.Lian, K.J.Duffy, J.Adams, K.P.Foley, P.J.Gough, R.W.Marquis, J.Smothers, A.Hoos, J.Bertin. Design of Amidobenzimidazole Sting Receptor Agonists with Systemic Activity. Nature V. 564 439 2018.
ISSN: ESSN 1476-4687
PubMed: 30405246
DOI: 10.1038/S41586-018-0705-Y