Calcium in PDB 8r5l: E-Selectin Complexed with Glycomimetic Ligand BW850

The structure of E-Selectin Complexed with Glycomimetic Ligand BW850, PDB code: 8r5l was solved by R.P.Jakob, B.Ernst, T.Maier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.1, 72.81, 52.53, 90, 94.11, 90
R / Rfree (%)	22 / 24.1

The binding sites of Calcium atom in the E-Selectin Complexed with Glycomimetic Ligand BW850 (pdb code 8r5l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the E-Selectin Complexed with Glycomimetic Ligand BW850, PDB code: 8r5l:

Calcium binding site 1 out of 1 in the E-Selectin Complexed with Glycomimetic Ligand BW850


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E-Selectin Complexed with Glycomimetic Ligand BW850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca308 b:82.9 occ:1.00 H12 A:Y6T309 1.5 103.2 1.0 OD1 A:ASP106 2.2 90.0 1.0 O3 A:Y6T309 2.3 103.5 1.0 OD1 A:ASN105 2.5 69.7 1.0 O A:ASP106 2.5 75.3 1.0 OE1 A:GLU88 2.7 67.3 1.0 OE1 A:GLU80 2.7 78.6 1.0 OD1 A:ASN82 3.0 96.7 1.0 H9 A:Y6T309 3.0 108.8 1.0 CG A:ASP106 3.1 88.9 1.0 O4 A:Y6T309 3.1 104.1 1.0 C7 A:Y6T309 3.3 105.1 1.0 H14 A:Y6T309 3.4 104.1 1.0 C A:ASP106 3.5 74.7 1.0 C6 A:Y6T309 3.6 108.6 1.0 CG A:ASN105 3.6 84.2 1.0 CD A:GLU88 3.7 94.7 1.0 OD2 A:ASP106 3.7 97.7 1.0 CD A:GLU80 3.8 111.6 1.0 C8 A:Y6T309 3.8 105.0 1.0 CG A:ASN82 3.8 108.5 1.0 N A:ASP106 3.8 71.3 1.0 CA A:ASP106 4.0 71.1 1.0 CB A:ASP106 4.1 73.8 1.0 O2 A:Y6T309 4.1 107.2 1.0 ND2 A:ASN105 4.1 76.0 1.0 H11 A:Y6T309 4.1 105.2 1.0 H13 A:Y6T309 4.2 104.9 1.0 H10 A:Y6T309 4.2 107.0 1.0 OE2 A:GLU80 4.2 107.3 1.0 N A:ASN83 4.2 94.4 1.0 N A:ASN82 4.3 93.8 1.0 OE2 A:GLU88 4.3 96.9 1.0 ND2 A:ASN82 4.3 100.0 1.0 N A:GLU107 4.6 69.7 1.0 C A:ASN105 4.6 73.2 1.0 CG A:GLU88 4.7 82.1 1.0 CB A:GLU88 4.7 77.7 1.0 OE2 A:GLU107 4.8 110.1 1.0 CA A:ASN82 4.8 94.1 1.0 CB A:ASN105 4.9 71.0 1.0 N A:ARG84 4.9 90.7 1.0 CB A:ASN82 4.9 94.1 1.0 C A:ASN82 4.9 99.1 1.0 CG A:GLU80 4.9 101.9 1.0 CA A:ASN83 4.9 93.2 1.0

B.Wagner, M.Smiesko, R.P.Jakob, T.Muhlethaler, J.Cramer, T.Maier, S.Rabbani, O.Schwardt, B.Ernst. Analogues of the Pan-Selectin Antagonist Rivipansel (Gmi-1070). Eur.J.Med.Chem. V. 272 16455 2024.
ISSN: ISSN 0223-5234
PubMed: 38728868
DOI: 10.1016/J.EJMECH.2024.116455