Calcium in PDB 7nl7: 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: 7nl7 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)	51.39 / 2.10
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.346, 59.346, 75.18, 90, 90, 120
R / Rfree (%)	19.3 / 21.8

The binding sites of Calcium atom in the Crystal Structure of Dc-Sign in Complex with A Triazole-Based Glycomimetic Ligand (pdb code 7nl7). 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: 7nl7:
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:31.6 occ:1.00 OD1 A:ASN350 2.3 36.3 1.0 O A:HOH611 2.3 30.6 1.0 OE1 A:GLU324 2.4 38.7 1.0 O A:GLU354 2.4 32.2 1.0 OD2 A:ASP320 2.5 30.3 1.0 OD1 A:ASP355 2.5 35.2 1.0 OE2 A:GLU324 2.5 37.4 1.0 OD1 A:ASP320 2.6 33.1 1.0 CD A:GLU324 2.8 39.6 1.0 CG A:ASP320 2.9 32.3 1.0 HA A:ASP355 2.9 40.5 1.0 CG A:ASN350 3.1 38.2 1.0 C A:GLU354 3.4 33.6 1.0 HB2 A:ASN350 3.5 46.3 1.0 CG A:ASP355 3.6 37.0 1.0 CA A:ASP355 3.7 33.5 1.0 HZ2 A:TRP327 3.8 37.5 1.0 H A:GLU354 3.8 44.1 1.0 CB A:ASN350 3.9 38.4 1.0 ND2 A:ASN350 4.0 40.5 1.0 N A:ASP355 4.0 34.0 1.0 O A:HOH618 4.0 42.5 1.0 HD21 A:ASN350 4.1 48.8 1.0 HA A:ASN350 4.1 44.1 1.0 H A:GLY325 4.1 48.9 1.0 O A:HOH648 4.2 34.3 1.0 CZ2 A:TRP327 4.2 31.1 1.0 CB A:ASP355 4.2 33.7 1.0 HA A:GLU324 4.3 47.7 1.0 N A:GLU354 4.3 36.6 1.0 CG A:GLU324 4.3 40.2 1.0 CB A:ASP320 4.4 33.7 1.0 HH2 A:TRP327 4.4 35.8 1.0 OD2 A:ASP366 4.5 26.9 1.0 O A:HOH604 4.5 35.8 1.0 CA A:GLU354 4.5 34.3 1.0 CA A:ASN350 4.6 36.5 1.0 CH2 A:TRP327 4.6 29.6 1.0 HB3 A:ASP355 4.6 40.7 1.0 OD2 A:ASP355 4.6 36.3 1.0 HB3 A:ASN350 4.7 46.3 1.0 HD22 A:ASN350 4.7 48.8 1.0 HB2 A:ASP366 4.7 32.0 1.0 O A:ASP320 4.7 33.9 1.0 HG3 A:GLU324 4.7 48.4 1.0 HB2 A:ASP320 4.7 40.6 1.0 HG2 A:GLU324 4.7 48.4 1.0 HB2 A:GLU354 4.8 40.6 1.0 HB3 A:ASP320 4.8 40.6 1.0 HA A:GLU353 4.8 54.1 1.0 H A:ASP355 4.8 41.0 1.0 HB2 A:GLU324 4.9 46.4 1.0 C A:ASP355 4.9 32.9 1.0 N A:GLY325 4.9 40.5 1.0 H A:ASP320 4.9 36.4 1.0 CB A:GLU324 5.0 38.5 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:27.9 occ:1.00 H16 A:UH5504 2.0 32.3 1.0 OD1 A:ASP366 2.3 27.9 1.0 OD1 A:ASN365 2.3 24.5 1.0 OD1 A:ASN349 2.4 27.5 1.0 OE1 A:GLU347 2.4 33.1 1.0 O4 A:UH5504 2.5 26.8 1.0 O A:ASP366 2.5 27.6 1.0 OE1 A:GLU354 2.6 31.8 1.0 O3 A:UH5504 2.6 30.0 1.0 C7 A:UH5504 3.2 27.2 1.0 H A:ASP366 3.2 30.0 1.0 CD A:GLU347 3.3 33.8 1.0 HD21 A:ASN365 3.3 33.8 1.0 CG A:ASN365 3.3 28.3 1.0 H15 A:UH5504 3.3 32.9 1.0 CG A:ASP366 3.3 28.9 1.0 CG A:ASN349 3.3 33.2 1.0 H14 A:UH5504 3.3 36.2 1.0 H A:ASN349 3.4 38.4 1.0 C6 A:UH5504 3.4 28.8 1.0 HD21 A:ASN349 3.4 42.6 1.0 CD A:GLU354 3.5 34.6 1.0 OE2 A:GLU347 3.6 33.1 1.0 C A:ASP366 3.6 26.7 1.0 ND2 A:ASN365 3.7 27.9 1.0 H13 A:UH5504 3.7 34.7 1.0 ND2 A:ASN349 3.7 35.4 1.0 N A:ASP366 3.8 24.8 1.0 OE2 A:GLU354 3.8 32.7 1.0 H A:ASN350 4.0 39.9 1.0 OD2 A:ASP366 4.1 26.9 1.0 CA A:ASP366 4.1 28.9 1.0 N A:ASN349 4.2 31.8 1.0 H A:VAL351 4.3 47.8 1.0 CB A:ASP366 4.3 26.5 1.0 HA A:PRO348 4.3 36.5 1.0 HB3 A:GLU347 4.4 36.8 1.0 HB2 A:GLU354 4.4 40.6 1.0 HA A:ASP367 4.5 36.5 1.0 HD22 A:ASN365 4.5 33.8 1.0 CG A:GLU347 4.5 32.1 1.0 HD22 A:ASN349 4.5 42.6 1.0 HB3 A:GLU354 4.5 40.6 1.0 HA A:ASN365 4.6 32.4 1.0 N A:ASN350 4.6 33.1 1.0 CB A:ASN349 4.6 31.4 1.0 CB A:ASN365 4.6 24.1 1.0 C8 A:UH5504 4.7 30.9 1.0 CG A:GLU354 4.7 33.5 1.0 HG3 A:GLU347 4.7 38.8 1.0 C A:ASN365 4.7 26.6 1.0 N A:ASP367 4.8 29.3 1.0 C4 A:UH5504 4.8 30.9 1.0 CB A:GLU354 4.8 33.6 1.0 HB2 A:ASP366 4.8 32.0 1.0 CA A:ASN349 4.8 34.8 1.0 H9 A:UH5504 4.9 37.3 1.0 HA A:GLU347 4.9 38.8 1.0 CA A:ASN365 4.9 26.8 1.0 HB A:VAL351 4.9 48.1 1.0 CB A:GLU347 4.9 30.4 1.0 HG23 A:VAL351 4.9 49.3 1.0 HB3 A:ASP366 5.0 32.0 1.0 HB3 A:ASN349 5.0 37.9 1.0 HB2 A:ASN365 5.0 29.1 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:54.4 occ:1.00 O A:HOH679 2.1 48.1 1.0 O A:HOH623 2.2 41.0 1.0 O A:HOH604 2.2 35.8 1.0 O A:HOH629 2.3 47.2 1.0 OD2 A:ASP355 2.3 36.3 1.0 O A:HOH618 2.4 42.5 1.0 CG A:ASP355 3.2 37.0 1.0 OD1 A:ASP355 3.5 35.2 1.0 HB2 A:GLU324 3.9 46.4 1.0 OE1 A:GLU324 3.9 38.7 1.0 HA A:LEU321 4.0 43.3 1.0 HD23 A:LEU321 4.2 43.3 1.0 O A:LEU321 4.3 36.4 1.0 HB3 A:GLU353 4.3 61.0 1.0 O A:HOH670 4.4 40.6 1.0 O A:ASP320 4.5 33.9 1.0 CB A:ASP355 4.6 33.7 1.0 HB3 A:ASP355 4.6 40.7 1.0 CB A:GLU324 4.9 38.5 1.0 HB2 A:ASP355 4.9 40.7 1.0 CA A:LEU321 4.9 35.9 1.0 HA A:GLU324 5.0 47.7 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