Calcium in PDB 4pe1: Crystal Structure of Calcium-Loaded S100B Bound to SC124

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SC124, PDB code: 4pe1 was solved by M.C.Cavalier, A.D.Pierce, P.T.Wilder, D.Neau, E.A.Toth, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.35 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.649, 56.463, 48.269, 90.00, 110.10, 90.00
R / Rfree (%)	21.3 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SC124 (pdb code 4pe1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded S100B Bound to SC124, PDB code: 4pe1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC124


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 SC124 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:21.3 occ:1.00 O A:HOH247 2.3 26.6 1.0 O A:GLU21 2.3 21.7 1.0 O A:SER18 2.3 23.7 1.0 O A:ASP23 2.4 23.4 1.0 OE1 A:GLU31 2.4 20.2 1.0 O A:LYS26 2.5 20.3 1.0 OE2 A:GLU31 2.6 24.0 1.0 CD A:GLU31 2.9 21.3 1.0 C A:SER18 3.4 22.6 1.0 C A:ASP23 3.5 27.2 1.0 C A:GLU21 3.5 30.5 1.0 C A:LYS26 3.7 24.0 1.0 CA A:SER18 3.9 17.9 1.0 N A:GLU21 4.0 23.3 1.0 N A:ASP23 4.2 27.5 1.0 CA A:GLU21 4.3 26.4 1.0 N A:LYS28 4.3 23.3 1.0 CG A:GLU31 4.4 24.1 1.0 N A:LYS24 4.4 24.0 1.0 C A:GLY22 4.4 30.1 1.0 CA A:ASP23 4.4 24.8 1.0 OE1 A:GLU67 4.4 27.5 1.0 CA A:LYS24 4.4 30.1 1.0 N A:LYS26 4.5 21.5 1.0 CA A:LEU27 4.5 20.7 1.0 N A:GLY19 4.5 21.2 1.0 N A:LEU27 4.5 20.2 1.0 N A:GLY22 4.6 23.4 1.0 CB A:SER18 4.6 20.7 1.0 CA A:LYS26 4.6 23.2 1.0 O A:TYR17 4.6 21.1 1.0 N A:ARG20 4.7 19.5 1.0 CA A:GLY22 4.8 28.1 1.0 C A:LYS24 4.8 29.6 1.0 CB A:ASP23 4.8 29.7 1.0 O A:GLY22 4.8 29.9 1.0 C A:LEU27 4.8 20.3 1.0 O A:HOH262 4.9 36.3 1.0 CB A:GLU21 4.9 24.0 1.0 CA A:GLY19 4.9 22.5 1.0 CG A:LYS28 4.9 23.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC124


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 SC124 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:24.0 occ:1.00 OD1 A:ASP63 2.4 25.6 1.0 OD1 A:ASP61 2.4 30.2 1.0 O A:GLU67 2.4 22.1 1.0 OD1 A:ASP65 2.4 26.6 1.0 O A:HOH249 2.4 33.4 1.0 OE1 A:GLU72 2.4 21.5 1.0 OE2 A:GLU72 2.6 26.4 1.0 CD A:GLU72 2.9 26.0 1.0 CG A:ASP63 3.3 33.3 1.0 CG A:ASP65 3.3 34.2 1.0 CG A:ASP61 3.5 27.6 1.0 C A:GLU67 3.5 18.6 1.0 OD2 A:ASP65 3.6 37.0 1.0 OD2 A:ASP63 3.7 37.5 1.0 CA A:ASP61 4.1 28.5 1.0 N A:ASP63 4.2 34.7 1.0 CB A:ASP61 4.2 24.6 1.0 N A:GLU67 4.2 25.5 1.0 N A:SER62 4.3 37.0 1.0 OD2 A:ASP61 4.3 23.7 1.0 N A:ASP65 4.3 33.4 1.0 N A:ASP69 4.3 19.5 1.0 CG A:GLU72 4.4 23.2 1.0 CA A:GLU67 4.4 20.2 1.0 N A:CYS68 4.4 19.1 1.0 CA A:CYS68 4.4 18.6 1.0 N A:GLY64 4.5 41.2 1.0 CB A:ASP63 4.6 39.2 1.0 C A:ASP61 4.6 31.2 1.0 OD2 A:ASP69 4.6 28.4 1.0 CA A:ASP63 4.7 38.2 1.0 CB A:ASP65 4.7 31.1 1.0 CG A:ASP69 4.7 25.1 1.0 C A:ASP63 4.8 43.8 1.0 C A:CYS68 4.9 19.3 1.0 N A:GLY66 4.9 24.7 1.0 CA A:ASP65 5.0 30.1 1.0 CB A:GLU67 5.0 22.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC124


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 Calcium-Loaded S100B Bound to SC124 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:29.9 occ:1.00 O B:ASP23 2.0 39.7 1.0 O B:LYS26 2.1 26.2 1.0 O B:SER18 2.3 24.0 1.0 O B:HOH273 2.3 35.3 1.0 OE1 B:GLU31 2.5 26.6 1.0 OE2 B:GLU31 2.7 34.1 1.0 O B:GLU21 3.0 35.4 1.0 CD B:GLU31 3.0 24.5 1.0 C B:ASP23 3.1 51.0 1.0 C B:SER18 3.3 25.8 1.0 C B:LYS26 3.3 25.3 1.0 CA B:LYS24 3.7 42.4 1.0 N B:LYS26 3.8 36.9 1.0 CA B:SER18 3.8 23.4 1.0 N B:LYS24 3.9 42.8 1.0 C B:LYS24 4.0 37.1 1.0 CA B:ASP23 4.1 44.5 1.0 N B:HIS25 4.1 50.7 1.0 CA B:LYS26 4.1 31.6 1.0 C B:GLU21 4.2 39.4 1.0 CB B:SER18 4.2 23.0 1.0 N B:ASP23 4.2 46.6 1.0 CB B:ASP23 4.3 40.6 1.0 N B:LEU27 4.3 23.9 1.0 OE1 B:GLU67 4.4 33.4 1.0 CA B:LEU27 4.5 20.9 1.0 N B:LYS28 4.5 23.3 1.0 N B:GLY19 4.5 25.1 1.0 C B:GLY22 4.5 31.9 1.0 O B:LYS24 4.5 39.4 1.0 CG B:GLU31 4.5 25.4 1.0 CB B:LYS26 4.7 30.0 1.0 N B:GLU21 4.7 22.7 1.0 C B:HIS25 4.8 37.4 1.0 CA B:GLY22 4.9 45.5 1.0 OD1 B:ASP23 4.9 43.5 1.0 C B:LEU27 4.9 17.1 1.0 CA B:GLY19 4.9 27.3 1.0 O B:TYR17 5.0 24.9 1.0 O B:GLY22 5.0 45.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC124


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium-Loaded S100B Bound to SC124 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:23.5 occ:1.00 OD1 B:ASP63 2.3 31.8 1.0 OD1 B:ASP61 2.3 23.8 1.0 O B:HOH249 2.4 26.7 1.0 O B:GLU67 2.4 20.7 1.0 OD1 B:ASP65 2.4 27.0 1.0 OE1 B:GLU72 2.4 20.2 1.0 OE2 B:GLU72 2.6 28.0 1.0 CD B:GLU72 2.9 23.8 1.0 CG B:ASP63 3.2 34.9 1.0 CG B:ASP65 3.4 36.8 1.0 CG B:ASP61 3.5 25.7 1.0 OD2 B:ASP63 3.5 41.8 1.0 C B:GLU67 3.5 17.7 1.0 OD2 B:ASP65 3.8 30.8 1.0 CA B:ASP61 4.2 24.2 1.0 N B:ASP65 4.2 32.6 1.0 N B:GLU67 4.2 26.6 1.0 CB B:ASP61 4.3 22.1 1.0 N B:ASP63 4.3 32.2 1.0 N B:ASP69 4.3 20.1 1.0 OD2 B:ASP61 4.3 27.1 1.0 N B:CYS68 4.4 18.3 1.0 CA B:CYS68 4.4 18.6 1.0 CG B:GLU72 4.4 23.3 1.0 N B:GLY64 4.4 31.9 1.0 CA B:GLU67 4.4 21.3 1.0 CB B:ASP63 4.4 31.7 1.0 C B:ASP61 4.5 32.4 1.0 CB B:ASP65 4.5 33.1 1.0 OD2 B:ASP69 4.6 35.6 1.0 N B:SER62 4.7 27.4 1.0 CA B:ASP63 4.7 39.5 1.0 CG B:ASP69 4.7 26.6 1.0 C B:ASP63 4.7 35.3 1.0 CA B:ASP65 4.8 27.3 1.0 N B:GLY66 4.8 27.2 1.0 C B:CYS68 4.8 16.5 1.0 C B:ASP65 5.0 27.2 1.0

M.C.Cavalier, A.D.Pierce, P.T.Wilder, M.J.Alasady, K.G.Hartman, D.B.Neau, T.L.Foley, A.Jadhav, D.J.Maloney, A.Simeonov, E.A.Toth, D.J.Weber. Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B. Biochemistry V. 53 6628 2014.
ISSN: ISSN 0006-2960
PubMed: 25268459
DOI: 10.1021/BI5005552