Calcium in PDB 5csj: S100B-RSK1 Crystal Structure B

All present enzymatic activity of S100B-RSK1 Crystal Structure B:
2.7.11.1;

The structure of S100B-RSK1 Crystal Structure B, PDB code: 5csj was solved by G.Gogl, L.Nyitray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.12 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.960, 68.930, 91.490, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 27.6

The structure of S100B-RSK1 Crystal Structure B also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the S100B-RSK1 Crystal Structure B (pdb code 5csj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the S100B-RSK1 Crystal Structure B, PDB code: 5csj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the S100B-RSK1 Crystal Structure B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of S100B-RSK1 Crystal Structure B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:52.7 occ:1.00 O A:ASP23 2.2 51.5 1.0 OE1 A:GLU31 2.3 51.3 1.0 O A:SER18 2.4 55.5 1.0 OE2 A:GLU31 2.4 55.8 1.0 O A:GLU21 2.4 65.3 1.0 O A:LYS26 2.5 51.0 1.0 CD A:GLU31 2.7 52.6 1.0 C A:ASP23 3.3 56.0 1.0 C A:SER18 3.4 53.3 1.0 C A:LYS26 3.6 48.1 1.0 C A:GLU21 3.6 62.2 1.0 CA A:SER18 3.9 53.9 1.0 N A:ASP23 4.0 63.7 1.0 N A:LYS24 4.2 60.5 1.0 CA A:ASP23 4.2 59.5 1.0 N A:GLU21 4.2 61.1 1.0 CG A:GLU31 4.2 51.7 1.0 C A:GLY22 4.3 57.9 1.0 CA A:LYS24 4.3 60.4 1.0 N A:LYS28 4.4 55.4 1.0 CA A:GLU21 4.5 62.7 1.0 N A:LYS26 4.5 57.8 1.0 N A:LEU27 4.5 49.5 1.0 CA A:LEU27 4.5 52.3 1.0 CB A:SER18 4.5 50.6 1.0 O A:GLY22 4.5 62.0 1.0 N A:GLY19 4.6 52.8 1.0 CA A:LYS26 4.6 52.9 1.0 N A:GLY22 4.6 62.0 1.0 OE2 A:GLU67 4.6 64.2 1.0 C A:LYS24 4.7 60.3 1.0 N A:ARG20 4.7 60.1 1.0 CB A:ASP23 4.7 60.8 1.0 O A:TYR17 4.8 52.5 1.0 CA A:GLY22 4.8 58.0 1.0 CG A:LYS28 4.9 59.8 1.0 C A:LEU27 4.9 53.7 1.0 CB A:LYS26 5.0 50.9 1.0 CA A:GLY19 5.0 52.9 1.0

Calcium binding site 2 out of 4 in the S100B-RSK1 Crystal Structure B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of S100B-RSK1 Crystal Structure B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:55.7 occ:1.00 OD1 A:ASP63 2.2 67.2 1.0 O A:GLU67 2.3 59.1 1.0 OD1 A:ASP65 2.4 68.8 1.0 OE1 A:GLU72 2.6 54.5 1.0 OD1 A:ASP61 2.6 60.8 1.0 OE2 A:GLU72 2.8 58.7 1.0 CG A:ASP63 3.0 64.9 1.0 CD A:GLU72 3.0 56.6 1.0 OD2 A:ASP63 3.1 65.7 1.0 CG A:ASP65 3.2 67.6 1.0 C A:GLU67 3.4 59.5 1.0 OD2 A:ASP65 3.6 67.5 1.0 CG A:ASP61 3.7 64.8 1.0 N A:GLU67 4.2 63.6 1.0 N A:ASP69 4.2 46.9 1.0 N A:CYS68 4.3 53.6 1.0 CA A:CYS68 4.3 49.8 1.0 CA A:GLU67 4.3 61.4 1.0 N A:ASP65 4.4 63.0 1.0 CB A:ASP63 4.5 61.9 1.0 CB A:ASP65 4.5 62.6 1.0 OD2 A:ASP61 4.5 67.3 1.0 CG A:GLU72 4.6 54.3 1.0 CA A:ASP61 4.6 57.3 1.0 CB A:ASP61 4.6 62.4 1.0 N A:ASP63 4.7 61.9 1.0 C A:CYS68 4.7 49.1 1.0 CB A:GLU67 4.9 58.6 1.0 N A:GLY64 4.9 70.7 1.0 OD1 A:ASP69 4.9 52.5 1.0 N A:ASN62 4.9 63.0 1.0 CA A:ASP65 4.9 61.7 1.0 CG A:ASP69 4.9 51.6 1.0 N A:GLY66 5.0 59.2 1.0 CA A:ASP63 5.0 63.4 1.0

Calcium binding site 3 out of 4 in the S100B-RSK1 Crystal Structure B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of S100B-RSK1 Crystal Structure B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:29.2 occ:1.00 O B:ASP23 2.2 30.8 1.0 O B:GLU21 2.3 37.8 1.0 O B:LYS26 2.4 35.8 1.0 O B:SER18 2.4 35.9 1.0 OE1 B:GLU31 2.4 36.2 1.0 OE2 B:GLU31 2.5 35.3 1.0 CD B:GLU31 2.8 36.3 1.0 C B:ASP23 3.3 33.0 1.0 C B:SER18 3.5 33.2 1.0 C B:GLU21 3.5 32.8 1.0 C B:LYS26 3.6 32.1 1.0 N B:ASP23 3.9 29.0 1.0 CA B:SER18 4.0 33.5 1.0 CA B:ASP23 4.1 32.9 1.0 C B:GLY22 4.1 30.7 1.0 N B:LYS26 4.3 31.8 1.0 N B:GLU21 4.3 34.8 1.0 N B:LYS24 4.3 31.4 1.0 CG B:GLU31 4.4 34.2 1.0 CA B:GLU21 4.4 31.5 1.0 CA B:LYS24 4.4 32.5 1.0 N B:LYS28 4.4 33.6 1.0 N B:LEU27 4.4 32.1 1.0 CA B:LEU27 4.5 31.5 1.0 CA B:LYS26 4.5 33.6 1.0 N B:GLY22 4.5 34.0 1.0 OE1 B:GLU67 4.5 50.5 1.0 CB B:ASP23 4.5 36.8 1.0 CA B:GLY22 4.5 31.8 1.0 O B:GLY22 4.6 30.2 1.0 N B:GLY19 4.6 27.4 1.0 O B:TYR17 4.7 31.6 1.0 C B:LYS24 4.7 35.6 1.0 CB B:SER18 4.7 29.8 1.0 CB B:GLU21 4.8 35.8 1.0 CD B:LYS28 4.8 40.7 1.0 C B:LEU27 4.9 30.3 1.0 CG B:LYS28 4.9 33.5 1.0 N B:ARG20 4.9 32.6 1.0 N B:HIS25 5.0 38.4 1.0

Calcium binding site 4 out of 4 in the S100B-RSK1 Crystal Structure B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of S100B-RSK1 Crystal Structure B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:42.7 occ:1.00 OD1 B:ASP63 2.2 50.4 1.0 OD1 B:ASP61 2.2 43.8 1.0 O B:HOH203 2.2 36.8 1.0 OE1 B:GLU72 2.3 44.9 1.0 OD1 B:ASP65 2.4 46.4 1.0 O B:GLU67 2.4 43.3 1.0 OE2 B:GLU72 2.6 46.6 1.0 CD B:GLU72 2.8 44.5 1.0 CG B:ASP63 3.2 51.3 1.0 CG B:ASP65 3.2 48.3 1.0 CG B:ASP61 3.4 46.4 1.0 OD2 B:ASP65 3.5 48.7 1.0 OD2 B:ASP63 3.5 51.9 1.0 C B:GLU67 3.5 40.8 1.0 OD2 B:ASP61 4.3 46.1 1.0 CB B:ASP61 4.3 42.9 1.0 N B:GLU67 4.3 42.0 1.0 CA B:ASP61 4.3 47.9 1.0 N B:CYS68 4.3 41.1 1.0 N B:ASP65 4.3 48.3 1.0 N B:ASP63 4.3 48.1 1.0 CG B:GLU72 4.3 41.8 1.0 CA B:CYS68 4.4 34.5 1.0 CB B:ASP65 4.4 47.6 1.0 N B:ASP69 4.4 36.5 1.0 CA B:GLU67 4.5 37.6 1.0 CB B:ASP63 4.5 50.7 1.0 N B:ASN62 4.6 42.3 1.0 OD2 B:ASP69 4.6 56.5 1.0 N B:GLY64 4.7 45.8 1.0 C B:ASP61 4.8 43.4 1.0 CA B:ASP65 4.8 43.2 1.0 CA B:ASP63 4.8 46.9 1.0 C B:CYS68 4.9 33.3 1.0 N B:GLY66 4.9 43.3 1.0 C B:ASP63 4.9 44.6 1.0 CG B:ASP69 5.0 51.1 1.0

G.Gogl, A.Alexa, B.Kiss, G.Katona, M.Kovacs, A.Bodor, A.Remenyi, L.Nyitray. Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition By S100B Protein: Modulation of the Extracellular Signal-Regulated Kinase (Erk) Signaling Cascade in A Calcium-Dependent Way. J.Biol.Chem. V. 291 11 2016.
ISSN: ESSN 1083-351X
PubMed: 26527685
DOI: 10.1074/JBC.M115.684928