Calcium in PDB 5dkn: Crystal Structure of Calcium-Loaded S100B Bound to SBI4225

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SBI4225, PDB code: 5dkn was solved by M.C.Cavalier, M.I.Ansari, A.D.Pierce, P.T.Wilder, L.E.Mcknight, E.P.Raman, D.B.Neau, P.Bezawada, M.J.Alasady, K.M.Varney, E.A.Toth, A.D.Mackerelljr., A.Coop, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.80 / 1.53
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.046, 64.046, 47.563, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.8

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4225 (pdb code 5dkn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4225, PDB code: 5dkn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4225


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 Calcium-Loaded S100B Bound to SBI4225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:12.7 occ:1.00 O A:HOH240 2.3 13.8 1.0 O A:SER18 2.3 14.2 1.0 O A:ASP23 2.4 14.8 1.0 O A:GLU21 2.4 13.7 1.0 O A:LYS26 2.4 12.2 1.0 OE1 A:GLU31 2.4 12.8 1.0 OE2 A:GLU31 2.6 13.1 1.0 CD A:GLU31 2.9 14.3 1.0 C A:SER18 3.4 15.8 1.0 C A:ASP23 3.5 14.7 1.0 C A:GLU21 3.6 17.9 1.0 C A:LYS26 3.6 10.8 1.0 CA A:SER18 3.9 12.6 1.0 N A:GLU21 4.2 16.0 1.0 N A:ASP23 4.2 16.8 1.0 C A:GLY22 4.3 14.7 1.0 CA A:ASP23 4.3 17.9 1.0 CG A:GLU31 4.3 11.6 1.0 CA A:GLU21 4.4 16.4 1.0 N A:LYS28 4.4 11.2 1.0 N A:LYS24 4.4 18.2 1.0 N A:LYS26 4.4 12.7 1.0 CA A:LEU27 4.5 10.7 1.0 CA A:LYS24 4.5 16.3 1.0 N A:LEU27 4.5 11.2 1.0 N A:GLY19 4.5 16.5 1.0 OE1 A:GLU67 4.6 15.1 1.0 CA A:LYS26 4.6 12.5 1.0 CB A:SER18 4.6 14.1 1.0 N A:GLY22 4.6 16.0 1.0 CB A:GLU21 4.7 13.9 1.0 O A:GLY22 4.7 17.4 1.0 O A:TYR17 4.7 15.4 1.0 CB A:ASP23 4.7 17.5 1.0 C A:LYS24 4.7 15.5 1.0 CA A:GLY22 4.7 15.6 1.0 O A:HOH224 4.8 16.0 1.0 CG A:LYS28 4.8 13.3 1.0 C A:LEU27 4.9 11.1 1.0 N A:ARG20 4.9 16.1 1.0 CA A:GLY19 4.9 17.7 1.0 C A:GLY19 5.0 19.2 1.0 CD A:LYS28 5.0 15.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4225


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 Calcium-Loaded S100B Bound to SBI4225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:11.2 occ:1.00 OD1 A:ASP61 2.3 13.8 1.0 OD1 A:ASP63 2.3 14.5 1.0 OD1 A:ASP65 2.3 14.7 1.0 O A:GLU67 2.4 14.4 1.0 O A:HOH220 2.4 15.0 1.0 OE1 A:GLU72 2.4 11.1 1.0 OE2 A:GLU72 2.5 11.7 1.0 CD A:GLU72 2.8 11.0 1.0 CG A:ASP65 3.3 17.0 1.0 CG A:ASP61 3.4 14.8 1.0 CG A:ASP63 3.4 18.2 1.0 C A:GLU67 3.5 12.5 1.0 OD2 A:ASP65 3.7 21.6 1.0 OD2 A:ASP63 3.9 20.0 1.0 CA A:ASP61 4.2 13.7 1.0 CB A:ASP61 4.2 13.8 1.0 N A:ASP63 4.2 16.2 1.0 N A:GLU67 4.2 13.6 1.0 OD2 A:ASP61 4.3 15.5 1.0 N A:ASP65 4.3 18.8 1.0 CG A:GLU72 4.4 9.9 1.0 N A:CYS68 4.4 10.7 1.0 CA A:GLU67 4.4 13.0 1.0 N A:ASP69 4.4 11.3 1.0 CB A:ASP65 4.5 18.2 1.0 CA A:CYS68 4.5 10.8 1.0 N A:SER62 4.5 13.0 1.0 C A:ASP61 4.6 15.1 1.0 CB A:ASP63 4.6 15.5 1.0 N A:GLY64 4.6 18.1 1.0 CA A:ASP63 4.7 16.6 1.0 CA A:ASP65 4.8 17.1 1.0 N A:GLY66 4.8 14.7 1.0 C A:ASP63 4.8 19.1 1.0 OD2 A:ASP69 4.8 16.3 1.0 CG A:ASP69 4.8 13.7 1.0 C A:CYS68 4.9 11.1 1.0 O A:HOH253 4.9 17.2 1.0 CB A:GLU67 5.0 13.7 1.0

M.C.Cavalier, M.I.Ansari, A.D.Pierce, P.T.Wilder, L.E.Mcknight, E.P.Raman, D.B.Neau, P.Bezawada, M.J.Alasady, T.H.Charpentier, K.M.Varney, E.A.Toth, A.D.Mackerell, A.Coop, D.J.Weber. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. J.Med.Chem. V. 59 592 2016.
ISSN: ISSN 0022-2623
PubMed: 26727270
DOI: 10.1021/ACS.JMEDCHEM.5B01369