Calcium in PDB 3gk4: X-Ray Structure of Bovine SBI523,Ca(2+)-S100B

The structure of X-Ray Structure of Bovine SBI523,Ca(2+)-S100B, PDB code: 3gk4 was solved by T.H.Charpentier, D.J.Weber, E.A.Toth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.77 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	34.459, 89.532, 59.234, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 22.8

The binding sites of Calcium atom in the X-Ray Structure of Bovine SBI523,Ca(2+)-S100B (pdb code 3gk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Structure of Bovine SBI523,Ca(2+)-S100B, PDB code: 3gk4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Structure of Bovine SBI523,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Bovine SBI523,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca92 b:42.5 occ:1.00 O X:SER18 2.3 44.0 1.0 O X:ASP23 2.3 48.0 1.0 O X:GLU21 2.3 45.2 1.0 O X:HOH117 2.4 44.9 1.0 OE1 X:GLU31 2.4 40.6 1.0 O X:LYS26 2.5 45.0 1.0 OE2 X:GLU31 2.6 42.0 1.0 CD X:GLU31 2.9 38.9 1.0 C X:SER18 3.4 44.2 1.0 C X:ASP23 3.5 48.0 1.0 C X:GLU21 3.5 46.2 1.0 C X:LYS26 3.7 45.2 1.0 CA X:SER18 3.9 43.5 1.0 N X:GLU21 4.0 44.9 1.0 N X:ASP23 4.2 47.1 1.0 N X:LYS28 4.2 43.2 1.0 CA X:LYS24 4.3 48.4 1.0 CA X:GLU21 4.3 46.3 1.0 N X:LYS24 4.3 48.1 1.0 C X:GLY22 4.3 46.4 1.0 CG X:GLU31 4.4 43.5 1.0 CA X:ASP23 4.4 47.7 1.0 CG X:LYS28 4.4 45.5 1.0 N X:LYS26 4.5 46.3 1.0 CA X:LEU27 4.5 43.7 1.0 N X:LEU27 4.5 43.1 1.0 CB X:SER18 4.5 43.7 1.0 OE1 X:GLU67 4.5 45.9 1.0 N X:GLY19 4.6 43.2 1.0 O X:GLY22 4.6 45.6 1.0 N X:GLY22 4.6 45.6 1.0 CA X:LYS26 4.7 45.0 1.0 O X:TYR17 4.7 44.7 1.0 CA X:GLY22 4.8 46.1 1.0 C X:LEU27 4.8 43.8 1.0 N X:ARG20 4.8 44.1 1.0 C X:LYS24 4.8 48.2 1.0 NZ X:LYS28 4.9 57.6 1.0 CB X:GLU21 4.9 47.1 1.0 CB X:ASP23 4.9 47.8 1.0 CA X:GLY19 5.0 43.9 1.0

Calcium binding site 2 out of 2 in the X-Ray Structure of Bovine SBI523,Ca(2+)-S100B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Bovine SBI523,Ca(2+)-S100B within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca93 b:42.6 occ:1.00 O X:HOH113 2.2 41.7 1.0 OD1 X:ASP61 2.2 46.5 1.0 OD1 X:ASP65 2.3 47.2 1.0 OD1 X:ASP63 2.4 48.5 1.0 O X:GLU67 2.4 45.5 1.0 OE1 X:GLU72 2.4 43.3 1.0 OE2 X:GLU72 2.7 46.0 1.0 CD X:GLU72 2.9 47.2 1.0 CG X:ASP65 3.2 46.4 1.0 CG X:ASP63 3.3 47.9 1.0 CG X:ASP61 3.4 46.0 1.0 C X:GLU67 3.6 45.0 1.0 OD2 X:ASP63 3.6 49.4 1.0 OD2 X:ASP65 3.6 47.2 1.0 N X:ASP65 4.1 45.6 1.0 CA X:ASP61 4.1 44.8 1.0 N X:GLU67 4.2 45.3 1.0 CB X:ASP61 4.2 43.6 1.0 OD2 X:ASP61 4.3 46.2 1.0 N X:ASP63 4.3 45.7 1.0 CB X:ASP65 4.4 45.4 1.0 N X:GLY64 4.4 45.9 1.0 N X:ASP69 4.4 44.9 1.0 N X:CYS68 4.4 45.3 1.0 CA X:GLU67 4.4 45.3 1.0 CG X:GLU72 4.4 45.5 1.0 C X:ASP61 4.5 44.6 1.0 CA X:CYS68 4.5 45.0 1.0 CB X:ASP63 4.5 46.5 1.0 CA X:ASP65 4.6 45.5 1.0 CA X:ASP63 4.7 46.5 1.0 N X:SER62 4.7 45.0 1.0 N X:GLY66 4.7 45.2 1.0 C X:ASP63 4.7 46.1 1.0 OD2 X:ASP69 4.9 44.0 1.0 C X:ASP65 4.9 45.4 1.0 CG X:ASP69 4.9 46.2 1.0 C X:CYS68 4.9 45.0 1.0 O X:ASP61 5.0 44.2 1.0

T.H.Charpentier, P.T.Wilder, M.A.Liriano, K.M.Varney, S.Zhong, A.Coop, E.Pozharski, A.D.Mackerell, E.A.Toth, D.J.Weber. Small Molecules Bound to Unique Sites in the Target Protein Binding Cleft of Calcium-Bound S100B As Characterized By Nuclear Magnetic Resonance and X-Ray Crystallography. Biochemistry V. 48 6202 2009.
ISSN: ISSN 0006-2960
PubMed: 19469484
DOI: 10.1021/BI9005754