Calcium in PDB 4pe4: Crystal Structure of Calcium-Loaded S100B Bound to SC1475

The structure of Crystal Structure of Calcium-Loaded S100B Bound to SC1475, PDB code: 4pe4 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)	35.40 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.015, 58.087, 47.891, 90.00, 111.23, 90.00
R / Rfree (%)	20.9 / 25.1

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded S100B Bound to SC1475 (pdb code 4pe4). 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 SC1475, PDB code: 4pe4:
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 SC1475


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 SC1475 within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca102 b:38.1 occ:1.00 O X:LYS26 2.4 39.0 1.0 O X:SER18 2.4 44.6 1.0 OE2 X:GLU31 2.4 45.9 1.0 OE1 X:GLU31 2.4 38.9 1.0 O X:ASP23 2.5 47.0 1.0 O X:GLU21 2.5 50.5 1.0 O X:HOH203 2.7 42.2 1.0 CD X:GLU31 2.8 41.5 1.0 C X:SER18 3.4 48.5 1.0 C X:ASP23 3.6 53.4 1.0 C X:LYS26 3.6 42.2 1.0 C X:GLU21 3.7 50.6 1.0 CA X:SER18 3.8 44.6 1.0 N X:GLU21 4.1 50.7 1.0 CG X:GLU31 4.3 35.6 1.0 N X:LYS26 4.3 49.6 1.0 N X:LYS28 4.4 36.3 1.0 CA X:LYS24 4.4 53.9 1.0 N X:LYS24 4.4 49.7 1.0 N X:ASP23 4.4 49.1 1.0 OE1 X:GLU67 4.4 53.2 1.0 N X:LEU27 4.5 41.5 1.0 C X:GLY22 4.5 49.1 1.0 CA X:LEU27 4.5 39.4 1.0 CA X:GLU21 4.5 46.8 1.0 CA X:LYS26 4.5 45.4 1.0 CA X:ASP23 4.5 52.7 1.0 O X:TYR17 4.5 36.7 1.0 CB X:SER18 4.5 40.1 1.0 N X:GLY19 4.6 49.6 1.0 C X:LYS24 4.7 53.9 1.0 N X:GLY22 4.7 44.0 1.0 N X:ARG20 4.8 50.3 1.0 O X:GLY22 4.8 48.4 1.0 CG X:LYS28 4.8 44.3 1.0 CA X:GLY22 4.9 45.1 1.0 C X:LEU27 4.9 35.0 1.0 CB X:ASP23 4.9 58.3 1.0 C X:GLY19 4.9 53.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC1475


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 SC1475 within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca103 b:47.6 occ:1.00 O X:HOH202 2.3 52.5 1.0 O X:GLU67 2.3 39.0 1.0 OD1 X:ASP61 2.3 58.8 1.0 OD1 X:ASP63 2.3 56.5 1.0 OD1 X:ASP65 2.4 53.7 1.0 OE2 X:GLU72 2.4 48.8 1.0 OE1 X:GLU72 2.4 38.8 1.0 CD X:GLU72 2.8 48.6 1.0 CG X:ASP65 3.3 62.9 1.0 CG X:ASP63 3.4 64.5 1.0 C X:GLU67 3.4 41.4 1.0 CG X:ASP61 3.5 59.2 1.0 OD2 X:ASP63 3.7 66.5 1.0 OD2 X:ASP65 3.7 58.7 1.0 N X:GLU67 4.1 50.1 1.0 N X:ASP69 4.2 37.1 1.0 N X:ASP65 4.2 61.0 1.0 CA X:ASP61 4.2 47.8 1.0 CA X:CYS68 4.2 42.5 1.0 N X:CYS68 4.2 34.7 1.0 OD2 X:ASP61 4.3 56.6 1.0 CG X:GLU72 4.3 43.2 1.0 CA X:GLU67 4.3 46.5 1.0 CB X:ASP61 4.3 52.2 1.0 CB X:ASP65 4.5 59.9 1.0 N X:ASP63 4.5 61.5 1.0 C X:ASP61 4.6 57.2 1.0 N X:GLY64 4.6 59.7 1.0 N X:SER62 4.6 61.7 1.0 OD2 X:ASP69 4.7 50.5 1.0 CB X:ASP63 4.7 64.3 1.0 C X:CYS68 4.7 35.8 1.0 CA X:ASP65 4.7 53.6 1.0 CG X:ASP69 4.8 39.2 1.0 N X:GLY66 4.9 56.5 1.0 C X:ASP65 4.9 50.7 1.0 CB X:GLU67 4.9 34.6 1.0 CA X:ASP63 4.9 58.4 1.0 C X:ASP63 5.0 70.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC1475


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 SC1475 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:46.9 occ:1.00 OD1 A:ASP63 2.3 62.6 1.0 OD1 A:ASP65 2.3 56.4 1.0 OD1 A:ASP61 2.4 56.2 1.0 O A:GLU67 2.4 40.9 1.0 OE1 A:GLU72 2.5 40.6 1.0 OE2 A:GLU72 2.5 49.1 1.0 CD A:GLU72 2.8 48.4 1.0 O A:HOH208 2.8 56.0 1.0 CG A:ASP65 3.2 63.4 1.0 CG A:ASP63 3.3 64.8 1.0 C A:GLU67 3.5 41.2 1.0 CG A:ASP61 3.5 58.9 1.0 OD2 A:ASP63 3.6 64.7 1.0 OD2 A:ASP65 3.6 57.6 1.0 N A:ASP65 4.1 62.3 1.0 N A:GLU67 4.2 45.7 1.0 N A:ASP69 4.2 38.9 1.0 N A:CYS68 4.3 36.1 1.0 CA A:CYS68 4.3 42.8 1.0 OD2 A:ASP61 4.3 58.4 1.0 CA A:ASP61 4.3 47.7 1.0 CG A:GLU72 4.3 41.4 1.0 CA A:GLU67 4.4 47.4 1.0 CB A:ASP61 4.4 51.2 1.0 CB A:ASP65 4.4 60.4 1.0 N A:ASP63 4.5 63.0 1.0 N A:GLY64 4.6 60.3 1.0 CB A:ASP63 4.6 64.4 1.0 CA A:ASP65 4.6 51.2 1.0 OD2 A:ASP69 4.7 51.4 1.0 C A:ASP61 4.7 60.4 1.0 N A:SER62 4.7 59.7 1.0 C A:CYS68 4.7 36.9 1.0 CG A:ASP69 4.8 41.2 1.0 N A:GLY66 4.8 58.5 1.0 C A:ASP65 4.9 55.4 1.0 CA A:ASP63 4.9 60.8 1.0 C A:ASP63 4.9 70.1 1.0 CB A:GLU67 4.9 41.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Loaded S100B Bound to SC1475


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 SC1475 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:43.4 occ:1.00 O A:LYS26 2.4 45.1 1.0 O A:SER18 2.4 44.7 1.0 OE2 A:GLU31 2.4 46.1 1.0 OE1 A:GLU31 2.4 42.8 1.0 O A:HOH203 2.4 44.6 1.0 O A:GLU21 2.5 53.3 1.0 O A:ASP23 2.5 46.9 1.0 CD A:GLU31 2.7 43.7 1.0 C A:SER18 3.4 49.9 1.0 C A:LYS26 3.6 44.0 1.0 C A:ASP23 3.6 52.3 1.0 C A:GLU21 3.7 52.9 1.0 CA A:SER18 3.8 45.7 1.0 N A:GLU21 4.1 53.3 1.0 CG A:GLU31 4.2 35.2 1.0 N A:LYS28 4.3 38.8 1.0 N A:LYS26 4.4 53.1 1.0 N A:ASP23 4.4 55.9 1.0 OE1 A:GLU67 4.4 52.9 1.0 CA A:LYS24 4.4 56.2 1.0 N A:LYS24 4.4 47.1 1.0 CA A:GLU21 4.5 44.5 1.0 CA A:LEU27 4.5 41.1 1.0 O A:TYR17 4.5 40.2 1.0 N A:LEU27 4.5 41.7 1.0 C A:GLY22 4.5 51.6 1.0 CA A:LYS26 4.5 45.3 1.0 N A:GLY19 4.5 50.6 1.0 CB A:SER18 4.6 43.8 1.0 CA A:ASP23 4.6 50.9 1.0 N A:GLY22 4.7 46.8 1.0 N A:ARG20 4.7 48.1 1.0 C A:LYS24 4.8 56.5 1.0 CG A:LYS28 4.8 42.5 1.0 O A:GLY22 4.8 48.5 1.0 C A:LEU27 4.9 38.9 1.0 CA A:GLY22 4.9 47.1 1.0 C A:GLY19 4.9 55.8 1.0 CB A:GLU31 5.0 35.2 1.0 CA A:GLY19 5.0 50.3 1.0 CB A:ASP23 5.0 60.7 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