Calcium in PDB 6dxl: Linked Amidobenzimidazole Sting Agonist

Protein crystallography data

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

Calcium Binding Sites:

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 6dxl

Go back to Calcium Binding Sites List in 6dxl
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 6dxl

Go back to Calcium Binding Sites List in 6dxl
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

Reference:

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
Page generated: Sat Dec 12 06:03:48 2020

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