Calcium in PDB 5dkq: Crystal Structure of Calcium-Loaded S100B Bound to SBI4214

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SBI4214, PDB code: 5dkq 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)	38.43 / 1.59
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.485, 63.485, 48.275, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4214 (pdb code 5dkq). 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 SBI4214, PDB code: 5dkq:
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 SBI4214


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 SBI4214 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:25.4 occ:1.00 O A:ASP23 2.2 27.5 1.0 O A:HOH250 2.3 26.8 1.0 O A:SER18 2.4 28.1 1.0 O A:LYS26 2.4 24.8 1.0 O A:GLU21 2.4 26.2 1.0 OE1 A:GLU31 2.5 26.6 1.0 OE2 A:GLU31 2.6 27.7 1.0 CD A:GLU31 2.9 30.9 1.0 C A:ASP23 3.4 27.1 1.0 C A:SER18 3.4 27.9 1.0 C A:LYS26 3.6 25.1 1.0 C A:GLU21 3.6 32.3 1.0 CA A:SER18 4.0 24.5 1.0 N A:ASP23 4.1 30.6 1.0 N A:GLU21 4.2 26.9 1.0 CA A:ASP23 4.3 28.2 1.0 N A:LYS24 4.3 30.1 1.0 C A:GLY22 4.3 28.0 1.0 N A:LYS26 4.3 25.2 1.0 CA A:LYS24 4.3 28.3 1.0 N A:LYS28 4.4 25.7 1.0 CG A:GLU31 4.4 24.2 1.0 CA A:GLU21 4.4 31.0 1.0 N A:LEU27 4.5 24.2 1.0 CA A:LEU27 4.5 20.5 1.0 CA A:LYS26 4.5 24.7 1.0 N A:GLY19 4.5 26.4 1.0 C A:LYS24 4.6 27.5 1.0 OE1 A:GLU67 4.6 29.1 1.0 N A:GLY22 4.6 32.5 1.0 CB A:SER18 4.6 26.7 1.0 CB A:ASP23 4.6 29.6 1.0 O A:GLY22 4.7 29.1 1.0 CB A:GLU21 4.7 28.5 1.0 CA A:GLY22 4.8 30.1 1.0 O A:TYR17 4.8 24.4 1.0 O A:HOH220 4.8 31.5 1.0 N A:ARG20 4.9 27.7 1.0 CG A:LYS28 4.9 26.4 1.0 C A:LEU27 4.9 25.2 1.0 N A:HIS25 4.9 29.2 1.0 CA A:GLY19 4.9 33.0 1.0 O A:LYS24 5.0 30.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4214


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 SBI4214 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:25.6 occ:1.00 OD1 A:ASP61 2.3 26.4 1.0 OD1 A:ASP63 2.3 26.0 1.0 OD1 A:ASP65 2.4 27.3 1.0 O A:HOH219 2.4 27.8 1.0 O A:GLU67 2.4 25.5 1.0 OE1 A:GLU72 2.4 22.5 1.0 OE2 A:GLU72 2.6 25.4 1.0 CD A:GLU72 2.9 27.9 1.0 CG A:ASP65 3.2 27.9 1.0 CG A:ASP61 3.4 31.0 1.0 CG A:ASP63 3.4 30.8 1.0 C A:GLU67 3.6 28.7 1.0 OD2 A:ASP65 3.6 32.0 1.0 OD2 A:ASP63 3.8 32.7 1.0 CA A:ASP61 4.1 29.8 1.0 CB A:ASP61 4.1 25.7 1.0 N A:GLU67 4.2 27.6 1.0 OD2 A:ASP61 4.2 30.4 1.0 N A:ASP63 4.2 27.3 1.0 N A:ASP65 4.3 31.9 1.0 CG A:GLU72 4.4 24.8 1.0 N A:ASP69 4.4 23.8 1.0 CB A:ASP65 4.4 29.2 1.0 CA A:GLU67 4.4 27.6 1.0 C A:ASP61 4.5 31.1 1.0 N A:CYS68 4.5 23.9 1.0 N A:SER62 4.5 25.8 1.0 CA A:CYS68 4.5 21.2 1.0 CB A:ASP63 4.6 25.9 1.0 N A:GLY64 4.7 31.8 1.0 CA A:ASP63 4.7 28.2 1.0 CA A:ASP65 4.8 32.8 1.0 N A:GLY66 4.8 27.1 1.0 C A:ASP63 4.8 33.2 1.0 CG A:ASP69 4.9 26.5 1.0 O A:HOH224 4.9 29.9 1.0 C A:CYS68 4.9 23.2 1.0 CB A:GLU67 4.9 27.3 1.0 OD2 A:ASP69 4.9 30.0 1.0 C A:ASP65 5.0 30.9 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