Calcium in PDB 8r5m: E-Selectin Complexed with Glycomimetic Ligand DS0567

The structure of E-Selectin Complexed with Glycomimetic Ligand DS0567, PDB code: 8r5m 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)	52.09 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.45, 73.22, 52.24, 90, 94.38, 90
R / Rfree (%)	21 / 23.9

The binding sites of Calcium atom in the E-Selectin Complexed with Glycomimetic Ligand DS0567 (pdb code 8r5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the E-Selectin Complexed with Glycomimetic Ligand DS0567, PDB code: 8r5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the E-Selectin Complexed with Glycomimetic Ligand DS0567


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 DS0567 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca309 b:79.1 occ:1.00 OE1 A:GLU88 2.3 68.4 1.0 OBO A:Y6O308 2.4 81.6 1.0 OD1 A:ASN82 2.4 95.0 1.0 OD1 A:ASP106 2.5 70.4 1.0 OD1 A:ASN105 2.6 67.2 1.0 O A:ASP106 2.6 64.5 1.0 OE2 A:GLU80 2.7 95.0 1.0 OBM A:Y6O308 2.8 83.2 1.0 CG A:ASP106 3.3 69.2 1.0 CBN A:Y6O308 3.4 83.2 1.0 CD A:GLU88 3.4 82.0 1.0 CG A:ASN82 3.5 90.6 1.0 CG A:ASN105 3.6 75.3 1.0 C A:ASP106 3.6 64.5 1.0 CBL A:Y6O308 3.7 83.0 1.0 CD A:GLU80 3.7 105.5 1.0 N A:ASP106 3.8 59.9 1.0 CBP A:Y6O308 3.9 84.0 1.0 ND2 A:ASN105 3.9 72.0 1.0 OE2 A:GLU88 3.9 80.9 1.0 OD2 A:ASP106 4.0 70.2 1.0 ND2 A:ASN82 4.1 74.6 1.0 OE1 A:GLU80 4.1 103.5 1.0 CA A:ASP106 4.1 59.9 1.0 CB A:ASP106 4.2 62.5 1.0 N A:ASN83 4.2 73.9 1.0 N A:ASN82 4.3 77.4 1.0 OBQ A:Y6O308 4.5 83.8 1.0 CB A:ASN82 4.6 74.0 1.0 CG A:GLU88 4.7 70.1 1.0 C A:ASN105 4.7 62.1 1.0 CA A:ASN82 4.8 76.4 1.0 N A:GLU107 4.8 61.0 1.0 C A:ASN82 4.8 79.0 1.0 N A:ARG84 4.8 77.3 1.0 CB A:ASN105 4.9 63.3 1.0 CG A:GLU80 4.9 88.1 1.0 OE2 A:GLU107 4.9 73.0 1.0 CA A:ASN83 4.9 73.4 1.0 CB A:GLU88 5.0 70.9 1.0

Calcium binding site 2 out of 2 in the E-Selectin Complexed with Glycomimetic Ligand DS0567


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E-Selectin Complexed with Glycomimetic Ligand DS0567 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca310 b:97.2 occ:1.00 O A:GLY168 2.9 77.5 1.0 O A:HOH446 3.3 65.7 1.0 C A:GLY168 3.5 77.2 1.0 O A:HOH438 3.9 75.2 1.0 N A:GLY168 4.0 71.8 1.0 N A:SER169 4.2 74.1 1.0 CA A:GLY168 4.2 71.4 1.0 CB A:SER169 4.3 78.7 1.0 OD2 A:ASP190 4.3 92.0 1.0 OE2 A:GLU166 4.4 103.4 1.0 OD1 A:ASP190 4.4 86.9 1.0 CA A:SER169 4.5 73.4 1.0 O A:PRO165 4.6 79.7 1.0 CG A:ASP190 4.8 85.6 1.0 N A:HIS167 4.9 75.4 1.0 OE1 A:GLU166 4.9 131.0 1.0 CD A:GLU166 5.0 120.3 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