Calcium in PDB 3czt: Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9, PDB code: 3czt 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)	17.80 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	34.980, 89.260, 59.580, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.2

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9 (pdb code 3czt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9, PDB code: 3czt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca92 b:15.2 occ:1.00 O X:HOH120 2.3 16.5 1.0 O X:SER18 2.4 17.3 0.5 O X:GLU21 2.4 18.7 1.0 O X:SER18 2.4 17.5 0.5 O X:LYS26 2.4 12.4 1.0 OE1 X:GLU31 2.4 15.0 1.0 O X:ASP23 2.5 19.1 1.0 OE2 X:GLU31 2.5 16.8 1.0 CD X:GLU31 2.9 13.0 1.0 C X:SER18 3.4 12.0 0.5 C X:SER18 3.4 11.9 0.5 C X:LYS26 3.6 12.4 1.0 C X:GLU21 3.6 19.5 1.0 C X:ASP23 3.6 19.7 1.0 CA X:SER18 3.9 13.2 0.5 CA X:SER18 3.9 13.0 0.5 N X:GLU21 4.1 19.0 1.0 N X:ASP23 4.2 20.5 1.0 C X:GLY22 4.2 20.0 1.0 CG X:GLU31 4.4 13.0 1.0 N X:LYS28 4.4 13.9 1.0 CA X:GLU21 4.4 20.4 1.0 N X:LYS26 4.4 13.8 1.0 N X:LEU27 4.4 11.6 1.0 OE1 X:GLU67 4.4 19.5 1.0 CB X:SER18 4.5 14.8 0.5 CA X:ASP23 4.5 19.5 1.0 CA X:LEU27 4.5 11.8 1.0 N X:LYS24 4.5 18.1 1.0 CA X:LYS24 4.5 18.6 1.0 CA X:LYS26 4.5 13.1 1.0 CB X:SER18 4.5 14.5 0.5 N X:GLY22 4.6 18.9 1.0 N X:GLY19 4.6 15.1 1.0 CA X:GLY22 4.6 19.5 1.0 O X:GLY22 4.6 22.1 1.0 O X:TYR17 4.7 13.4 1.0 O X:HOH156 4.7 27.8 1.0 N X:ARG20 4.7 16.3 1.0 C X:LYS24 4.9 18.4 1.0 C X:LEU27 4.9 13.0 1.0 CB X:GLU21 4.9 21.9 1.0 CB X:ASP23 5.0 19.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca93 b:14.3 occ:1.00 OD1 X:ASP61 2.3 15.8 1.0 OD2 X:ASP63 2.3 19.9 1.0 O X:GLU67 2.4 13.2 1.0 OD1 X:ASP65 2.4 13.4 1.0 OE1 X:GLU72 2.5 13.8 1.0 O X:HOH104 2.5 21.0 1.0 OE2 X:GLU72 2.6 14.2 1.0 CD X:GLU72 2.9 13.4 1.0 CG X:ASP65 3.3 18.3 1.0 CG X:ASP63 3.4 20.8 1.0 CG X:ASP61 3.4 16.4 1.0 C X:GLU67 3.5 11.4 1.0 OD2 X:ASP65 3.8 23.2 1.0 OD1 X:ASP63 3.9 27.2 1.0 N X:GLU67 4.2 13.2 1.0 N X:ASP65 4.2 18.1 1.0 OD2 X:ASP61 4.2 18.4 1.0 N X:ASP63 4.3 20.9 1.0 CA X:ASP61 4.3 16.8 1.0 CB X:ASP61 4.3 17.5 1.0 CG X:GLU72 4.4 12.6 1.0 N X:CYS68 4.4 12.6 1.0 CA X:GLU67 4.4 12.8 1.0 N X:ASP69 4.4 11.8 1.0 CB X:ASP65 4.4 17.9 1.0 CA X:CYS68 4.5 12.4 1.0 CB X:ASP63 4.5 20.5 1.0 C X:ASP61 4.5 18.8 1.0 O X:HOH262 4.5 29.5 1.0 N X:GLY64 4.5 19.2 1.0 N X:ASN62 4.6 19.8 1.0 CA X:ASP63 4.7 20.9 1.0 CA X:ASP65 4.7 17.6 1.0 C X:ASP63 4.7 20.8 1.0 N X:GLY66 4.7 15.5 1.0 CG X:ASP69 4.9 16.5 1.0 C X:CYS68 4.9 12.1 1.0 O X:HOH111 4.9 25.9 1.0 OD2 X:ASP69 4.9 20.2 1.0 C X:ASP65 5.0 17.2 1.0 CB X:GLU67 5.0 12.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca94 b:18.9 occ:0.45 O X:HOH161 2.4 24.3 1.0 O X:HOH135 2.5 20.9 1.0 O X:HOH223 3.7 21.2 0.5 O X:GLY19 4.1 18.6 1.0 O X:HOH186 4.7 29.5 1.0 NZ X:LYS24 4.7 30.1 1.0 O X:HOH125 4.8 18.8 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