Calcium in PDB 3hcm: Crystal Structure of Human S100B in Complex with S45

The structure of Crystal Structure of Human S100B in Complex with S45, PDB code: 3hcm was solved by S.Mangani, L.Cesari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.63 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.257, 57.797, 47.745, 90.00, 111.41, 90.00
R / Rfree (%)	22.7 / 31.1

The structure of Crystal Structure of Human S100B in Complex with S45 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human S100B in Complex with S45 (pdb code 3hcm). 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 Human S100B in Complex with S45, PDB code: 3hcm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human S100B in Complex with S45


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 Human S100B in Complex with S45 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca92 b:34.9 occ:1.00 O A:SER18 2.2 34.6 1.0 O A:LYS26 2.3 28.8 1.0 OE1 A:GLU31 2.4 23.7 1.0 O A:ASP23 2.4 41.3 1.0 OE2 A:GLU31 2.6 29.6 1.0 O A:GLU21 2.7 42.7 1.0 CD A:GLU31 2.9 25.9 1.0 C A:SER18 3.2 33.1 1.0 C A:LYS26 3.5 30.7 1.0 C A:ASP23 3.6 40.5 1.0 CA A:SER18 3.7 32.6 1.0 C A:GLU21 3.9 42.3 1.0 N A:LYS26 4.3 32.9 1.0 N A:GLU21 4.3 41.1 1.0 N A:GLY19 4.3 34.7 1.0 CG A:GLU31 4.4 26.2 1.0 CB A:SER18 4.4 32.0 1.0 N A:LEU27 4.4 27.6 1.0 O A:TYR17 4.4 30.2 1.0 CA A:LEU27 4.4 26.5 1.0 N A:ASP23 4.4 40.9 1.0 CA A:LYS26 4.5 31.9 1.0 CA A:ASP23 4.5 40.9 1.0 N A:LYS28 4.5 24.2 1.0 N A:LYS24 4.5 39.8 1.0 OE1 A:GLU67 4.5 38.2 1.0 C A:LYS24 4.5 37.9 1.0 N A:ARG20 4.6 38.8 1.0 CA A:LYS24 4.6 38.8 1.0 C A:GLY22 4.6 41.3 1.0 O A:LYS24 4.7 39.0 1.0 CG A:LYS28 4.7 28.0 1.0 CB A:ASP23 4.7 40.8 1.0 CA A:GLU21 4.7 42.3 1.0 CA A:GLY19 4.8 37.2 1.0 O A:GLY22 4.8 41.7 1.0 N A:HIS25 4.9 37.5 1.0 CB A:LYS26 4.9 32.8 1.0 C A:LEU27 4.9 25.3 1.0 N A:GLY22 4.9 41.8 1.0 N A:SER18 5.0 31.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human S100B in Complex with S45


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 Human S100B in Complex with S45 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca93 b:37.0 occ:1.00 OD1 A:ASP61 2.2 34.4 1.0 OD1 A:ASP63 2.3 39.9 1.0 O A:HOH139 2.4 34.5 1.0 OE1 A:GLU72 2.4 29.8 1.0 O A:GLU67 2.5 30.5 1.0 OD1 A:ASP65 2.6 39.7 1.0 OE2 A:GLU72 2.7 32.8 1.0 CD A:GLU72 2.9 30.0 1.0 CG A:ASP63 3.3 42.2 1.0 CG A:ASP65 3.3 40.2 1.0 CG A:ASP61 3.4 31.9 1.0 C A:GLU67 3.5 31.6 1.0 OD2 A:ASP65 3.6 38.5 1.0 OD2 A:ASP63 3.6 46.7 1.0 OD2 A:ASP61 4.1 31.0 1.0 OD2 A:ASP69 4.3 42.9 1.0 N A:ASP69 4.3 30.7 1.0 CA A:ASP61 4.3 34.3 1.0 N A:GLU67 4.3 35.2 1.0 CB A:ASP61 4.3 34.4 1.0 N A:CYS68 4.3 28.9 1.0 CA A:CYS68 4.4 29.3 1.0 CG A:GLU72 4.4 28.3 1.0 N A:ASP63 4.4 40.2 1.0 CA A:GLU67 4.4 32.5 1.0 N A:ASP65 4.5 40.4 1.0 CB A:ASP65 4.5 39.7 1.0 N A:ASN62 4.6 38.0 1.0 CB A:ASP63 4.6 41.4 1.0 N A:GLY64 4.8 41.7 1.0 C A:ASP61 4.8 36.3 1.0 C A:CYS68 4.8 29.6 1.0 O A:HOH98 4.8 45.5 1.0 CA A:ASP63 4.9 41.6 1.0 CB A:ASP69 4.9 33.8 1.0 CA A:ASP65 4.9 40.2 1.0 N A:GLY66 5.0 39.5 1.0 CB A:GLU67 5.0 33.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human S100B in Complex with S45


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 Human S100B in Complex with S45 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca92 b:35.7 occ:1.00 O B:ASP23 2.2 38.0 1.0 O B:SER18 2.3 32.4 1.0 O B:GLU21 2.4 38.4 1.0 O B:HOH123 2.4 31.7 1.0 O B:LYS26 2.5 30.6 1.0 OE2 B:GLU31 2.7 34.1 1.0 OE1 B:GLU31 2.8 29.9 1.0 CD B:GLU31 3.0 30.1 1.0 C B:ASP23 3.3 38.4 1.0 C B:SER18 3.4 32.7 1.0 C B:GLU21 3.6 38.0 1.0 C B:LYS26 3.8 31.3 1.0 CA B:SER18 3.9 32.4 1.0 N B:GLU21 4.0 36.5 1.0 OE1 B:GLU67 4.0 40.5 1.0 N B:ASP23 4.2 38.9 1.0 N B:LYS24 4.2 36.8 1.0 CA B:ASP23 4.2 38.7 1.0 CA B:LYS24 4.3 36.3 1.0 CA B:GLU21 4.3 38.2 1.0 C B:GLY22 4.3 38.7 1.0 CB B:SER18 4.4 32.8 1.0 CG B:GLU31 4.5 27.6 1.0 N B:LYS26 4.5 33.3 1.0 N B:GLY19 4.5 32.5 1.0 O B:GLY22 4.6 39.7 1.0 C B:LYS24 4.6 35.3 1.0 N B:ARG20 4.6 34.1 1.0 N B:GLY22 4.6 38.1 1.0 N B:LYS28 4.6 29.3 1.0 N B:LEU27 4.7 29.4 1.0 CB B:ASP23 4.7 39.7 1.0 CA B:LEU27 4.7 29.1 1.0 CA B:LYS26 4.7 31.8 1.0 O B:TYR17 4.8 32.7 1.0 CA B:GLY22 4.8 38.3 1.0 CA B:GLY19 4.9 33.2 1.0 CB B:GLU21 4.9 37.9 1.0 C B:GLY19 4.9 33.1 1.0 N B:HIS25 5.0 35.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human S100B in Complex with S45


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 Human S100B in Complex with S45 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca93 b:32.9 occ:1.00 O B:HOH131 2.3 39.0 1.0 OE1 B:GLU72 2.3 25.6 1.0 O B:GLU67 2.3 26.9 1.0 OD1 B:ASP61 2.4 32.0 1.0 OD1 B:ASP63 2.5 38.5 1.0 OE2 B:GLU72 2.5 24.3 1.0 OD1 B:ASP65 2.7 34.1 1.0 CD B:GLU72 2.8 21.6 1.0 CG B:ASP63 3.3 37.8 1.0 C B:GLU67 3.5 28.0 1.0 CG B:ASP65 3.5 34.8 1.0 CG B:ASP61 3.6 31.1 1.0 OD2 B:ASP63 3.6 35.2 1.0 OD2 B:ASP65 3.8 30.8 1.0 CA B:ASP61 4.2 31.2 1.0 N B:ASP63 4.2 38.4 1.0 CG B:GLU72 4.2 26.3 1.0 N B:GLU67 4.3 29.1 1.0 CB B:ASP61 4.3 29.7 1.0 N B:ASP69 4.3 26.9 1.0 N B:CYS68 4.3 27.7 1.0 CA B:GLU67 4.4 28.8 1.0 CA B:CYS68 4.4 28.2 1.0 N B:ASN62 4.4 33.9 1.0 OD2 B:ASP69 4.4 34.2 1.0 N B:ASP65 4.5 36.5 1.0 OD2 B:ASP61 4.5 26.6 1.0 CB B:ASP63 4.6 38.2 1.0 C B:ASP61 4.6 32.2 1.0 N B:GLY64 4.6 38.3 1.0 CG B:ASP69 4.7 28.7 1.0 CA B:ASP63 4.7 38.2 1.0 CB B:ASP65 4.8 34.0 1.0 C B:CYS68 4.8 26.3 1.0 CA B:ASP65 5.0 34.6 1.0 N B:GLY66 5.0 32.7 1.0 CB B:GLU72 5.0 24.9 1.0 CB B:GLU67 5.0 28.6 1.0

M.Agamennone, L.Cesari, D.Lalli, E.Turlizzi, R.Del Conte, P.Turano, S.Mangani, A.Padova. Fragmenting the S100B-P53 Interaction: Combined Virtual/Biophysical Screening Approaches to Identify Ligands Chemmedchem V. 5 428 2010.
ISSN: ISSN 1860-7179
PubMed: 20077460
DOI: 10.1002/CMDC.200900393