Calcium in PDB 7nl6: Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand

The structure of Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand, PDB code: 7nl6 was solved by R.P.Jakob, J.Cramer, A.Lakkaichi, B.Aliu, I.Cattaneo, S.Klein, X.Jiang, S.Rabbani, O.Schwardt, B.Ernst, T.Maier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.26 / 2.20
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.473, 59.473, 73.939, 90, 90, 120
R / Rfree (%)	19.4 / 22.9

The binding sites of Calcium atom in the Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand (pdb code 7nl6). 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 Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand, PDB code: 7nl6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand


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 Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:31.2 occ:1.00 O A:HOH635 2.4 30.0 1.0 OD2 A:ASP320 2.5 34.7 1.0 OE1 A:GLU324 2.6 43.9 1.0 O A:GLU354 2.6 26.5 1.0 OD1 A:ASP355 2.6 30.7 1.0 OD1 A:ASN350 2.7 29.6 1.0 HA A:ASP355 2.8 31.9 1.0 OD1 A:ASP320 2.9 37.7 1.0 OE2 A:GLU324 2.9 42.9 1.0 CG A:ASP320 3.0 33.9 1.0 CD A:GLU324 3.1 45.6 1.0 CG A:ASN350 3.3 32.6 1.0 C A:GLU354 3.5 28.9 1.0 HB2 A:ASN350 3.5 39.9 1.0 CA A:ASP355 3.7 26.6 1.0 CG A:ASP355 3.7 32.3 1.0 CA A:CA503 3.9 33.8 1.0 CB A:ASN350 3.9 33.3 1.0 N A:ASP355 4.0 27.6 1.0 ND2 A:ASN350 4.0 31.2 1.0 H A:GLU354 4.0 40.4 1.0 HD21 A:ASN350 4.1 37.4 1.0 HZ2 A:TRP327 4.1 33.7 1.0 HA A:ASN350 4.2 39.0 1.0 HA A:GLU324 4.2 46.4 1.0 CB A:ASP355 4.3 26.2 1.0 OE2 A:GLU353 4.3 42.7 1.0 H A:GLY325 4.3 46.1 1.0 HH2 A:TRP327 4.4 34.6 1.0 N A:GLU354 4.5 33.7 1.0 CZ2 A:TRP327 4.5 28.1 1.0 CG A:GLU324 4.5 44.8 1.0 CB A:ASP320 4.5 29.8 1.0 CA A:GLU354 4.6 30.7 1.0 HB3 A:ASP355 4.6 31.4 1.0 HD22 A:ASN350 4.6 37.4 1.0 CA A:ASN350 4.7 32.5 1.0 CH2 A:TRP327 4.7 28.9 1.0 OD2 A:ASP355 4.7 34.5 1.0 HB3 A:ASN350 4.7 39.9 1.0 HB2 A:GLU324 4.8 48.8 1.0 OD2 A:ASP366 4.8 29.1 1.0 HB2 A:ASP366 4.8 31.2 1.0 HB2 A:ASP320 4.8 35.7 1.0 H A:ASP355 4.8 33.1 1.0 C A:ASP355 4.8 27.9 1.0 O A:HOH619 4.9 23.3 1.0 HB2 A:GLU354 4.9 35.8 1.0 HA A:GLU353 4.9 45.4 1.0 HB3 A:ASP320 4.9 35.7 1.0 HG3 A:GLU324 5.0 53.7 1.0 N A:GLY325 5.0 38.4 1.0 O A:ASP320 5.0 28.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand


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 Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:24.3 occ:1.00 H16 A:UH8504 2.0 31.2 1.0 OD1 A:ASP366 2.3 29.9 1.0 OD1 A:ASN349 2.4 25.3 1.0 OD1 A:ASN365 2.4 24.6 1.0 O3 A:UH8504 2.5 26.1 1.0 O A:ASP366 2.5 28.1 1.0 OE1 A:GLU347 2.6 29.0 1.0 O4 A:UH8504 2.7 27.6 1.0 OE1 A:GLU354 2.8 30.0 1.0 CG A:ASP366 3.2 29.4 1.0 H A:ASP366 3.3 26.7 1.0 C12 A:UH8504 3.3 22.2 1.0 CG A:ASN349 3.3 27.1 1.0 H A:ASN349 3.3 36.2 1.0 H17 A:UH8504 3.4 33.1 1.0 CG A:ASN365 3.4 22.0 1.0 H3 A:UH8504 3.4 26.6 1.0 HD21 A:ASN349 3.4 33.2 1.0 HD21 A:ASN365 3.4 24.7 1.0 CD A:GLU347 3.4 29.4 1.0 C13 A:UH8504 3.5 24.0 1.0 C A:ASP366 3.6 21.3 1.0 CD A:GLU354 3.7 32.8 1.0 ND2 A:ASN349 3.7 27.7 1.0 H4 A:UH8504 3.8 28.7 1.0 ND2 A:ASN365 3.8 20.6 1.0 OE2 A:GLU347 3.8 27.0 1.0 N A:ASP366 3.8 22.3 1.0 OD2 A:ASP366 3.8 29.1 1.0 OE2 A:GLU354 3.9 29.4 1.0 HG22 A:VAL351 3.9 45.7 1.0 H A:ASN350 4.0 36.7 1.0 CA A:ASP366 4.1 21.9 1.0 N A:ASN349 4.2 30.2 1.0 CB A:ASP366 4.2 26.1 1.0 HA A:PRO348 4.3 30.6 1.0 H A:VAL351 4.4 41.9 1.0 HB3 A:GLU347 4.5 30.5 1.0 HB2 A:GLU354 4.5 35.8 1.0 HA A:ASN365 4.5 29.0 1.0 HD22 A:ASN349 4.5 33.2 1.0 HA A:ASP367 4.6 31.3 1.0 HD22 A:ASN365 4.6 24.7 1.0 CB A:ASN349 4.6 25.4 1.0 N A:ASN350 4.6 30.6 1.0 CG A:GLU347 4.6 26.1 1.0 CB A:ASN365 4.7 21.8 1.0 C A:ASN365 4.7 24.7 1.0 HG3 A:GLU347 4.7 31.3 1.0 C4 A:UH8504 4.7 21.2 1.0 HB2 A:ASP366 4.8 31.2 1.0 HB3 A:GLU354 4.8 35.8 1.0 N A:ASP367 4.8 22.3 1.0 HA A:GLU347 4.8 31.7 1.0 CG2 A:VAL351 4.8 38.1 1.0 CA A:ASN349 4.8 25.3 1.0 C1 A:UH8504 4.9 24.3 1.0 CA A:ASN365 4.9 24.2 1.0 HG21 A:VAL351 4.9 45.7 1.0 CG A:GLU354 4.9 35.4 1.0 HB3 A:ASP366 4.9 31.2 1.0 CB A:GLU354 5.0 29.9 1.0 HB3 A:ASN349 5.0 30.4 1.0 H A:UH8504 5.0 29.1 1.0 HB2 A:ASN365 5.0 26.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand


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 Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:33.8 occ:1.00 O A:HOH619 2.3 23.3 1.0 OE2 A:GLU353 2.5 42.7 1.0 OE1 A:GLU324 2.6 43.9 1.0 O A:HOH662 2.6 31.4 1.0 OD1 A:ASP355 2.6 30.7 1.0 O A:HOH677 2.7 32.5 1.0 OD2 A:ASP355 2.9 34.5 1.0 CG A:ASP355 3.1 32.3 1.0 HB2 A:GLU324 3.1 48.8 1.0 CD A:GLU353 3.4 42.2 1.0 HG3 A:GLU353 3.4 48.9 1.0 CD A:GLU324 3.8 45.6 1.0 CA A:CA501 3.9 31.2 1.0 CG A:GLU353 3.9 40.8 1.0 HD21 A:ASN350 4.0 37.4 1.0 CB A:GLU324 4.0 40.7 1.0 HA A:GLU324 4.2 46.4 1.0 HG2 A:GLU353 4.2 48.9 1.0 CG A:GLU324 4.3 44.8 1.0 OE1 A:GLU353 4.3 42.6 1.0 OD1 A:ASN350 4.4 29.6 1.0 HG2 A:GLU324 4.4 53.7 1.0 CB A:ASP355 4.6 26.2 1.0 ND2 A:ASN350 4.6 31.2 1.0 CA A:GLU324 4.6 38.7 1.0 O A:ASP320 4.7 28.7 1.0 O A:HOH610 4.7 34.3 1.0 OD1 A:ASP320 4.7 37.7 1.0 HB3 A:GLU324 4.7 48.8 1.0 HA A:LEU321 4.7 38.8 1.0 OE2 A:GLU324 4.8 42.9 1.0 HB3 A:ASP355 4.8 31.4 1.0 HA A:GLU353 4.8 45.4 1.0 CG A:ASN350 4.9 32.6 1.0 HA A:ASP355 5.0 31.9 1.0

J.Cramer, A.Lakkaichi, B.Aliu, R.P.Jakob, S.Klein, I.Cattaneo, X.Jiang, S.Rabbani, O.Schwardt, G.Zimmer, M.Ciancaglini, T.Abreu Mota, T.Maier, B.Ernst. Sweet Drugs For Bad Bugs: A Glycomimetic Strategy Against the Dc-Sign-Mediated Dissemination of Sars-Cov-2. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 34652144
DOI: 10.1021/JACS.1C06778