Calcium in PDB 4pdz: Crystal Structure of Calcium-Loaded S100B Bound to SBI4172

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SBI4172, PDB code: 4pdz 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)	35.26 / 1.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.988, 57.119, 47.998, 90.00, 110.97, 90.00
R / Rfree (%)	22.8 / 26.8

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4172 (pdb code 4pdz). 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 SBI4172, PDB code: 4pdz:
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 SBI4172


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 SBI4172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:34.3 occ:1.00 O A:GLU21 2.3 37.5 1.0 O A:SER18 2.3 36.5 1.0 OE1 A:GLU31 2.4 35.5 1.0 O A:ASP23 2.4 45.0 1.0 OE2 A:GLU31 2.4 39.5 1.0 O A:HOH217 2.5 39.4 1.0 O A:LYS26 2.6 36.5 1.0 CD A:GLU31 2.8 33.0 1.0 C A:SER18 3.4 37.1 1.0 C A:GLU21 3.5 42.4 1.0 C A:ASP23 3.5 45.0 1.0 C A:LYS26 3.8 38.8 1.0 N A:GLU21 3.8 40.2 1.0 CA A:SER18 3.9 38.8 1.0 CA A:GLU21 4.2 42.9 1.0 CG A:GLU31 4.3 34.9 1.0 N A:ASP23 4.4 45.4 1.0 N A:LYS24 4.4 43.9 1.0 CA A:LYS24 4.4 44.7 1.0 C A:GLY22 4.4 44.4 1.0 N A:LYS28 4.4 38.4 1.0 O A:TYR17 4.5 34.3 1.0 N A:GLY19 4.5 38.1 1.0 CA A:ASP23 4.5 45.3 1.0 N A:ARG20 4.5 36.3 1.0 CA A:LEU27 4.6 31.1 1.0 N A:GLY22 4.6 44.7 1.0 O A:HOH223 4.6 48.8 1.0 N A:LYS26 4.6 40.5 1.0 CB A:SER18 4.6 37.5 1.0 N A:LEU27 4.6 31.1 1.0 OE1 A:GLU67 4.7 46.9 1.0 O A:GLY22 4.7 44.8 1.0 C A:LYS24 4.7 41.5 1.0 CB A:GLU21 4.7 42.5 1.0 CA A:LYS26 4.8 37.2 1.0 CA A:GLY22 4.8 44.7 1.0 CA A:GLY19 4.9 40.0 1.0 CB A:ASP23 4.9 44.2 1.0 CG A:LYS28 4.9 37.4 1.0 C A:ARG20 4.9 39.5 1.0 C A:LEU27 5.0 29.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4172


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 SBI4172 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:44.0 occ:1.00 OD1 A:ASP61 1.8 50.4 1.0 OD1 A:ASP65 2.4 45.8 1.0 O A:GLU67 2.4 41.3 1.0 OD1 A:ASP63 2.4 54.8 1.0 O A:HOH237 2.5 46.1 1.0 OE1 A:GLU72 2.5 45.0 1.0 CG A:ASP61 2.7 48.0 1.0 OD2 A:ASP61 3.1 52.4 1.0 OE2 A:GLU72 3.1 45.7 1.0 CG A:ASP63 3.2 54.1 1.0 CD A:GLU72 3.2 45.8 1.0 CG A:ASP65 3.3 50.8 1.0 OD2 A:ASP63 3.4 56.9 1.0 C A:GLU67 3.4 40.1 1.0 OD2 A:ASP65 3.7 47.4 1.0 CB A:ASP61 3.9 47.0 1.0 N A:ASP65 4.1 53.1 1.0 N A:GLU67 4.1 46.1 1.0 N A:GLY64 4.3 54.1 1.0 N A:CYS68 4.3 38.5 1.0 CA A:ASP61 4.3 45.3 1.0 N A:ASP69 4.3 36.9 1.0 CA A:GLU67 4.3 43.0 1.0 CA A:CYS68 4.3 33.9 1.0 CB A:ASP65 4.5 51.0 1.0 N A:ASP63 4.5 51.2 1.0 CB A:ASP63 4.5 55.2 1.0 CA A:ASP65 4.6 48.2 1.0 OD2 A:ASP69 4.6 49.2 1.0 CG A:GLU72 4.7 43.5 1.0 N A:GLY66 4.7 47.4 1.0 C A:ASP61 4.7 49.5 1.0 CG A:ASP69 4.8 43.1 1.0 C A:CYS68 4.8 33.9 1.0 C A:ASP65 4.8 48.0 1.0 CA A:ASP63 4.9 54.5 1.0 CB A:GLU67 4.9 43.9 1.0 N A:SER62 4.9 50.3 1.0 C A:GLY64 5.0 52.6 1.0 C A:ASP63 5.0 55.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4172


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 SBI4172 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:34.0 occ:1.00 O B:HOH209 2.3 35.0 1.0 O B:GLU21 2.3 36.4 1.0 OE1 B:GLU31 2.3 36.7 1.0 O B:SER18 2.4 36.4 1.0 O B:LYS26 2.4 35.6 1.0 O B:ASP23 2.5 38.0 1.0 OE2 B:GLU31 2.5 36.0 1.0 CD B:GLU31 2.8 37.8 1.0 C B:SER18 3.4 35.2 1.0 C B:GLU21 3.5 42.8 1.0 C B:LYS26 3.6 36.2 1.0 C B:ASP23 3.7 40.2 1.0 CA B:SER18 3.9 37.5 1.0 N B:GLU21 4.0 35.6 1.0 CG B:GLU31 4.3 34.3 1.0 CA B:GLU21 4.3 41.1 1.0 N B:LYS28 4.4 34.4 1.0 N B:ASP23 4.4 33.1 1.0 N B:LYS26 4.4 35.1 1.0 C B:GLY22 4.5 40.7 1.0 N B:LYS24 4.5 40.0 1.0 CA B:LYS24 4.5 38.7 1.0 CA B:LEU27 4.5 34.3 1.0 CB B:SER18 4.5 34.8 1.0 N B:LEU27 4.5 33.8 1.0 N B:GLY22 4.5 42.1 1.0 CA B:ASP23 4.6 40.3 1.0 N B:GLY19 4.6 34.0 1.0 CA B:LYS26 4.6 33.2 1.0 O B:TYR17 4.6 36.3 1.0 OE1 B:GLU67 4.7 41.0 1.0 N B:ARG20 4.7 34.1 1.0 CA B:GLY22 4.7 38.1 1.0 CB B:GLU21 4.7 42.0 1.0 C B:LYS24 4.8 38.8 1.0 O B:GLY22 4.8 43.1 1.0 CG B:LYS28 4.8 31.8 1.0 C B:LEU27 4.9 33.5 1.0 CB B:GLU31 5.0 31.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SBI4172


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 SBI4172 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:41.2 occ:1.00 O B:HOH220 2.2 41.3 1.0 O B:GLU67 2.3 36.9 1.0 OD1 B:ASP61 2.3 47.2 1.0 OD1 B:ASP63 2.4 52.6 1.0 OD1 B:ASP65 2.4 45.5 1.0 OE1 B:GLU72 2.5 42.1 1.0 OE2 B:GLU72 2.6 45.1 1.0 CD B:GLU72 2.9 41.9 1.0 CG B:ASP63 3.0 50.8 1.0 OD2 B:ASP63 3.0 53.4 1.0 CG B:ASP65 3.3 46.7 1.0 C B:GLU67 3.4 39.2 1.0 CG B:ASP61 3.4 46.2 1.0 OD2 B:ASP65 3.8 44.1 1.0 N B:GLU67 4.1 42.5 1.0 N B:ASP69 4.2 38.0 1.0 OD2 B:ASP61 4.2 43.1 1.0 N B:ASP65 4.3 49.5 1.0 CA B:GLU67 4.3 37.6 1.0 N B:CYS68 4.3 36.4 1.0 CA B:CYS68 4.3 37.4 1.0 CB B:ASP65 4.4 46.6 1.0 CB B:ASP61 4.4 44.0 1.0 CA B:ASP61 4.4 45.8 1.0 CG B:GLU72 4.4 40.5 1.0 OD2 B:ASP69 4.5 42.1 1.0 CB B:ASP63 4.5 53.5 1.0 CG B:ASP69 4.6 41.6 1.0 N B:ASP63 4.6 52.4 1.0 N B:GLY64 4.6 50.2 1.0 CA B:ASP65 4.7 49.1 1.0 C B:CYS68 4.7 35.3 1.0 CB B:GLU67 4.8 39.6 1.0 N B:GLY66 4.8 45.9 1.0 C B:ASP61 4.9 49.0 1.0 C B:ASP65 4.9 46.0 1.0 CB B:ASP69 4.9 36.1 1.0 N B:SER62 4.9 47.2 1.0 CA B:ASP63 4.9 48.5 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