Calcium in PDB 3d0y: Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5, PDB code: 3d0y was solved by T.Ostendorp, J.Diez, C.W.Heizmann, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.890, 58.150, 47.660, 90.00, 111.12, 90.00
R / Rfree (%)	20.6 / 26.1

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5 (pdb code 3d0y). 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 S100B in the Calcium and Zinc Loaded State at pH 6.5, PDB code: 3d0y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca92 b:29.1 occ:1.00 OD1 A:ASP61 2.2 17.5 1.0 OD2 A:ASP63 2.2 21.2 1.0 O A:GLU67 2.3 9.0 1.0 OD1 A:ASP65 2.3 16.9 1.0 O A:HOH96 2.4 39.1 1.0 OE1 A:GLU72 2.5 14.4 1.0 OE2 A:GLU72 2.6 14.1 1.0 CD A:GLU72 2.9 15.6 1.0 CG A:ASP63 3.2 20.0 1.0 CG A:ASP61 3.3 19.2 1.0 CG A:ASP65 3.3 19.4 1.0 C A:GLU67 3.5 11.4 1.0 OD1 A:ASP63 3.6 22.1 1.0 OD2 A:ASP65 3.7 18.9 1.0 N A:GLU67 4.1 14.0 1.0 CB A:ASP61 4.1 20.9 1.0 OD2 A:ASP61 4.1 20.2 1.0 CA A:ASP61 4.2 20.9 1.0 N A:ASP65 4.2 18.7 1.0 N A:ASP63 4.2 21.3 1.0 CA A:GLU67 4.3 12.6 1.0 N A:CYS68 4.4 10.8 1.0 CG A:GLU72 4.4 13.5 1.0 CB A:ASP63 4.4 20.1 1.0 N A:ASP69 4.5 12.5 1.0 N A:GLY64 4.5 20.6 1.0 CA A:CYS68 4.5 11.6 1.0 CB A:ASP65 4.5 17.7 1.0 C A:ASP61 4.5 21.5 1.0 N A:ASN62 4.6 22.5 1.0 CA A:ASP63 4.6 20.6 1.0 C A:ASP63 4.7 20.4 1.0 CA A:ASP65 4.7 18.1 1.0 N A:GLY66 4.8 16.2 1.0 CB A:GLU67 4.9 12.1 1.0 O A:HOH144 4.9 35.5 1.0 CG A:ASP69 4.9 13.7 1.0 C A:ASP65 4.9 17.4 1.0 OD2 A:ASP69 4.9 16.6 1.0 C A:CYS68 5.0 11.3 0.5 C A:CYS68 5.0 11.4 0.5

Calcium binding site 2 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca93 b:32.1 occ:1.00 O A:GLU21 2.2 14.1 1.0 O A:ASP23 2.3 21.8 1.0 O A:SER18 2.3 16.0 1.0 O A:LYS26 2.3 15.2 1.0 OE1 A:GLU31 2.4 18.0 1.0 OE2 A:GLU31 2.5 16.9 1.0 CD A:GLU31 2.8 14.4 1.0 C A:SER18 3.3 15.5 1.0 C A:ASP23 3.4 21.2 1.0 C A:GLU21 3.5 17.8 1.0 C A:LYS26 3.6 16.4 1.0 CA A:SER18 3.9 15.1 1.0 N A:GLU21 4.1 17.6 1.0 N A:ASP23 4.1 21.1 1.0 CG A:GLU31 4.3 17.1 1.0 CA A:ASP23 4.3 21.4 1.0 C A:GLY22 4.3 20.8 1.0 N A:LYS24 4.4 21.6 1.0 CA A:GLU21 4.4 18.2 1.0 N A:LYS28 4.4 17.1 1.0 N A:LEU27 4.5 15.9 1.0 N A:GLY19 4.5 15.8 1.0 N A:GLY22 4.5 19.0 1.0 N A:LYS26 4.5 16.9 1.0 CA A:LYS24 4.5 21.0 1.0 CA A:LEU27 4.5 17.1 1.0 CA A:LYS26 4.6 15.9 1.0 CB A:SER18 4.6 14.5 1.0 O A:TYR17 4.6 15.2 1.0 OE1 A:GLU67 4.7 18.0 1.0 CA A:GLY22 4.7 20.0 1.0 N A:ARG20 4.7 16.5 1.0 CB A:ASP23 4.7 21.2 1.0 O A:GLY22 4.8 20.8 1.0 C A:LYS24 4.8 20.7 1.0 C A:LEU27 4.8 16.8 1.0 CA A:GLY19 4.9 15.7 1.0 O A:HOH149 4.9 53.6 1.0 C A:GLY19 5.0 16.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca92 b:31.7 occ:1.00 O B:ASP23 2.2 18.8 1.0 OE1 B:GLU31 2.3 11.9 1.0 O B:LYS26 2.4 12.4 1.0 O B:SER18 2.4 14.4 1.0 O B:HOH95 2.5 34.0 1.0 OE2 B:GLU31 2.5 15.0 1.0 O B:GLU21 2.6 19.3 1.0 CD B:GLU31 2.7 13.2 1.0 C B:ASP23 3.4 19.1 1.0 C B:SER18 3.4 13.9 1.0 C B:LYS26 3.6 13.1 1.0 C B:GLU21 3.7 19.3 1.0 CA B:SER18 3.9 13.1 1.0 N B:GLU21 4.1 18.3 1.0 N B:ASP23 4.1 20.3 1.0 CA B:ASP23 4.2 19.8 1.0 OE1 B:GLU67 4.2 22.8 1.0 CG B:GLU31 4.2 13.0 1.0 N B:LYS28 4.3 13.7 1.0 N B:LYS24 4.3 18.3 1.0 N B:LYS26 4.4 14.3 1.0 N B:LEU27 4.4 12.6 1.0 CA B:GLU21 4.5 20.0 1.0 CA B:LEU27 4.5 12.9 1.0 C B:GLY22 4.5 20.0 1.0 CA B:LYS24 4.5 16.7 1.0 CB B:ASP23 4.5 20.4 1.0 N B:GLY19 4.5 15.1 1.0 O B:TYR17 4.5 12.4 1.0 CA B:LYS26 4.6 14.0 1.0 CB B:SER18 4.6 13.4 1.0 CG B:LYS28 4.7 13.8 1.0 N B:ARG20 4.7 15.4 1.0 C B:LYS24 4.7 16.3 1.0 N B:GLY22 4.7 19.9 1.0 O B:HOH172 4.8 44.5 1.0 C B:LEU27 4.8 12.7 1.0 O B:GLY22 4.8 21.0 1.0 N B:HIS25 4.9 16.2 1.0 CB B:GLU21 4.9 20.1 1.0 NZ B:LYS28 4.9 20.6 1.0 CA B:GLY22 4.9 19.6 1.0 CA B:GLY19 5.0 14.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca93 b:36.0 occ:1.00 O B:HOH141 1.4 26.9 1.0 OD1 B:ASP61 1.9 21.0 1.0 OD1 B:ASP63 2.3 26.7 1.0 O B:GLU67 2.4 13.8 1.0 OD1 B:ASP65 2.5 20.9 1.0 OE1 B:GLU72 2.6 10.6 1.0 OE2 B:GLU72 2.7 11.0 1.0 CD B:GLU72 3.0 10.1 1.0 CG B:ASP61 3.1 23.0 1.0 CG B:ASP63 3.3 27.9 1.0 C B:GLU67 3.6 14.6 1.0 CG B:ASP65 3.6 22.6 1.0 CA B:ASP61 3.8 23.3 1.0 CB B:ASP61 3.8 23.3 1.0 OD2 B:ASP63 3.9 29.8 1.0 N B:ASP65 3.9 23.1 1.0 OD2 B:ASP61 4.0 21.2 1.0 N B:ASP63 4.1 25.2 1.0 OD2 B:ASP65 4.2 23.8 1.0 C B:ASP61 4.2 23.6 1.0 N B:GLU67 4.2 18.3 1.0 N B:GLY64 4.2 24.1 1.0 N B:ASN62 4.4 24.6 1.0 CA B:GLU67 4.4 16.1 1.0 CB B:ASP63 4.5 25.6 1.0 CG B:GLU72 4.5 8.4 1.0 N B:CYS68 4.5 13.1 1.0 CA B:ASP63 4.6 25.4 1.0 C B:ASP63 4.6 24.9 1.0 CB B:ASP65 4.6 22.2 1.0 CA B:CYS68 4.6 12.1 1.0 N B:GLY66 4.6 21.7 1.0 CA B:ASP65 4.6 22.6 1.0 N B:ASP69 4.7 11.1 1.0 O B:ASP61 4.7 23.5 1.0 C B:ASP65 4.9 22.0 1.0 C B:GLY64 4.9 23.6 1.0 CA B:GLY64 4.9 24.1 1.0 O B:HOH173 5.0 41.5 1.0

T.Ostendorp, J.Diez, C.W.Heizmann, G.Fritz. The Crystal Structures of Human S100B in the Zinc- and Calcium-Loaded State at Three pH Values Reveal Zinc Ligand Swapping. Biochim.Biophys.Acta V.1813 1083 2011.
ISSN: ISSN 0006-3002
PubMed: 20950652
DOI: 10.1016/J.BBAMCR.2010.10.006