Calcium in PDB 5csn: S100B-RSK1 Crystal Structure C

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

The structure of S100B-RSK1 Crystal Structure C, PDB code: 5csn 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)	44.59 / 2.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.790, 39.930, 178.340, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 27.9

The binding sites of Calcium atom in the S100B-RSK1 Crystal Structure C (pdb code 5csn). 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 C, PDB code: 5csn:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:98.2 occ:1.00 O A:ASP23 2.3 0.9 1.0 OE1 A:GLU31 2.3 0.7 1.0 OE2 A:GLU31 2.3 0.5 1.0 O A:GLU21 2.4 0.5 1.0 O A:SER18 2.4 1.0 1.0 O A:LYS26 2.5 0.3 1.0 CD A:GLU31 2.6 0.8 1.0 C A:ASP23 3.4 0.4 1.0 C A:SER18 3.4 0.0 1.0 C A:GLU21 3.6 0.6 1.0 C A:LYS26 3.7 0.9 1.0 CA A:SER18 3.8 0.1 1.0 N A:ASP23 3.9 0.8 1.0 CG A:GLU31 4.1 0.6 1.0 C A:GLY22 4.2 0.3 1.0 CA A:ASP23 4.2 0.0 1.0 N A:GLU21 4.2 0.1 1.0 N A:LYS24 4.3 0.1 1.0 N A:LYS28 4.4 0.4 1.0 CA A:LYS24 4.4 0.9 1.0 CA A:LEU27 4.4 0.4 1.0 CB A:SER18 4.4 0.5 1.0 N A:LYS26 4.5 0.2 1.0 CA A:GLU21 4.5 0.7 1.0 N A:LEU27 4.5 0.9 1.0 N A:GLY22 4.6 0.8 1.0 O A:GLY22 4.6 0.5 1.0 N A:GLY19 4.6 0.7 1.0 CA A:LYS26 4.6 97.0 1.0 CA A:GLY22 4.7 0.6 1.0 CB A:ASP23 4.7 0.2 1.0 O A:TYR17 4.7 0.6 1.0 C A:LYS24 4.7 0.8 1.0 N A:ARG20 4.8 0.8 1.0 CB A:GLU31 4.9 98.6 1.0 C A:LEU27 4.9 0.4 1.0

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


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 C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:0.3 occ:1.00 OD1 A:ASP65 2.3 0.3 1.0 OE2 A:GLU72 2.3 0.7 1.0 OE1 A:GLU72 2.3 0.0 1.0 OD1 A:ASP61 2.3 0.2 1.0 O A:GLU67 2.4 0.6 1.0 OD1 A:ASP63 2.4 0.3 1.0 CD A:GLU72 2.7 0.0 1.0 CG A:ASP65 3.2 0.6 1.0 CG A:ASP63 3.2 0.6 1.0 OD2 A:ASP63 3.3 0.3 1.0 CG A:ASP61 3.4 0.2 1.0 OD2 A:ASP65 3.4 0.5 1.0 C A:GLU67 3.6 0.8 1.0 OD2 A:ASP61 4.0 0.4 1.0 OD1 A:ASP69 4.0 0.8 1.0 N A:GLU67 4.1 0.1 1.0 CG A:GLU72 4.2 1.0 1.0 CB A:ASP61 4.3 0.8 1.0 N A:ASP65 4.3 0.2 1.0 CA A:GLU67 4.4 0.8 1.0 CA A:ASP61 4.5 0.5 1.0 CB A:ASP65 4.5 0.1 1.0 N A:CYS68 4.5 0.2 1.0 CA A:CYS68 4.5 0.5 1.0 N A:ASP69 4.5 1.0 1.0 CB A:ASP63 4.7 0.9 1.0 N A:GLY66 4.7 0.6 1.0 CA A:ASP65 4.8 0.3 1.0 N A:ASP63 4.8 0.1 1.0 N A:GLY64 4.8 0.7 1.0 CB A:GLU72 5.0 0.2 1.0 C A:ASP65 5.0 0.8 1.0

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


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 C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:44.5 occ:1.00 O B:ASP23 2.3 56.0 1.0 OE1 B:GLU31 2.4 50.9 1.0 O B:GLU21 2.4 50.6 1.0 O B:LYS26 2.4 44.7 1.0 OE2 B:GLU31 2.4 54.7 1.0 O B:SER18 2.5 55.7 1.0 CD B:GLU31 2.7 39.3 1.0 C B:ASP23 3.4 51.1 1.0 C B:SER18 3.5 44.9 1.0 C B:GLU21 3.6 48.6 1.0 C B:LYS26 3.6 57.5 1.0 CA B:SER18 3.9 46.5 1.0 N B:ASP23 4.1 49.5 1.0 N B:GLU21 4.1 51.8 1.0 CG B:GLU31 4.2 45.3 1.0 C B:GLY22 4.3 41.2 1.0 N B:LYS28 4.3 41.7 1.0 CA B:ASP23 4.3 48.7 1.0 N B:LYS24 4.3 49.2 1.0 CD B:LYS28 4.3 44.1 1.0 CA B:LEU27 4.4 35.8 1.0 CA B:GLU21 4.4 52.5 1.0 CA B:LYS24 4.4 30.8 1.0 OE1 B:GLU67 4.4 80.7 1.0 N B:LEU27 4.5 49.3 1.0 CG B:LYS28 4.5 45.1 1.0 N B:LYS26 4.5 50.5 1.0 N B:GLY22 4.5 57.4 1.0 CB B:SER18 4.6 34.2 1.0 N B:GLY19 4.6 39.0 1.0 O B:GLY22 4.6 57.4 1.0 CA B:LYS26 4.6 42.4 1.0 N B:ARG20 4.7 52.1 1.0 CA B:GLY22 4.7 40.8 1.0 O B:TYR17 4.8 53.3 1.0 C B:LYS24 4.8 43.4 1.0 CB B:ASP23 4.8 55.0 1.0 C B:LEU27 4.8 40.9 1.0

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


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 C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:72.5 occ:1.00 OD1 B:ASP63 2.3 83.8 1.0 OD1 B:ASP65 2.3 86.3 1.0 O B:GLU67 2.4 60.8 1.0 OE1 B:GLU72 2.4 61.8 1.0 OE2 B:GLU72 2.5 77.1 1.0 OD1 B:ASP61 2.5 73.7 1.0 OD2 B:ASP65 2.6 76.9 1.0 CG B:ASP65 2.7 79.8 1.0 CD B:GLU72 2.8 56.5 1.0 CG B:ASP63 3.0 90.4 1.0 OD2 B:ASP63 3.0 0.3 1.0 C B:GLU67 3.5 62.7 1.0 CG B:ASP61 3.7 73.1 1.0 N B:ASP69 4.1 55.6 1.0 CB B:ASP65 4.1 52.8 1.0 N B:GLU67 4.3 64.5 1.0 CG B:GLU72 4.3 60.7 1.0 CA B:CYS68 4.3 53.4 1.0 N B:CYS68 4.3 60.1 1.0 OD2 B:ASP61 4.3 70.3 1.0 CA B:GLU67 4.4 53.3 1.0 N B:ASP65 4.4 87.6 1.0 CB B:ASP63 4.4 84.8 1.0 C B:CYS68 4.6 50.7 1.0 OD1 B:ASP69 4.6 64.5 1.0 CG B:ASP69 4.7 58.2 1.0 CB B:ASP61 4.7 68.9 1.0 N B:ASP63 4.7 81.9 1.0 CA B:ASP61 4.7 67.9 1.0 CA B:ASP65 4.8 63.3 1.0 CB B:ASP69 4.8 53.6 1.0 CB B:GLU67 4.9 67.5 1.0 N B:GLY64 4.9 76.7 1.0 CA B:ASP63 5.0 84.5 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