Calcium in PDB 5csf: S100B-RSK1 Crystal Structure A

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

The structure of S100B-RSK1 Crystal Structure A, PDB code: 5csf 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)	43.21 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.300, 39.240, 172.820, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 29.1

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

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


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 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:91.6 occ:1.00 OE2 A:GLU31 2.4 85.5 1.0 O A:GLU21 2.5 95.6 1.0 O A:HOH201 2.5 87.8 1.0 O A:ASP23 2.5 89.0 1.0 O A:LYS26 2.5 84.3 1.0 OE1 A:GLU31 2.5 86.9 1.0 O A:SER18 2.6 82.8 1.0 CD A:GLU31 2.8 84.2 1.0 C A:SER18 3.5 85.4 1.0 C A:ASP23 3.6 88.8 1.0 C A:GLU21 3.7 97.9 1.0 C A:LYS26 3.7 83.0 1.0 CA A:SER18 3.9 84.8 1.0 N A:GLU21 4.0 92.8 1.0 N A:ASP23 4.1 87.8 1.0 CG A:GLU31 4.3 79.8 1.0 N A:LYS28 4.3 78.2 1.0 C A:GLY22 4.3 90.1 1.0 CA A:ASP23 4.4 91.5 1.0 CA A:LEU27 4.4 80.0 1.0 CA A:GLU21 4.5 93.8 1.0 N A:LEU27 4.5 84.3 1.0 N A:LYS24 4.5 85.5 1.0 O A:TYR17 4.5 84.1 1.0 N A:ARG20 4.5 86.6 1.0 OE2 A:GLU67 4.6 86.0 1.0 N A:GLY19 4.6 84.6 1.0 CA A:LYS24 4.6 89.1 1.0 CB A:SER18 4.6 81.6 1.0 N A:LYS26 4.6 85.6 1.0 N A:GLY22 4.6 96.5 1.0 O A:GLY22 4.7 85.8 1.0 CA A:LYS26 4.7 84.5 1.0 CA A:GLY22 4.8 95.3 1.0 C A:LEU27 4.8 85.3 1.0 CB A:ASP23 4.9 87.1 1.0 C A:GLY19 4.9 90.4 1.0 C A:LYS24 5.0 91.5 1.0 CB A:GLU31 5.0 81.7 1.0

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


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 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:84.1 occ:1.00 OD1 A:ASP63 2.3 86.4 1.0 OD1 A:ASP65 2.3 82.1 1.0 O A:GLU67 2.3 79.2 1.0 OD1 A:ASP61 2.4 86.6 1.0 O A:HOH202 2.4 84.6 1.0 OE1 A:GLU72 2.7 79.6 1.0 OE2 A:GLU72 3.0 85.3 1.0 CG A:ASP65 3.2 84.8 1.0 CD A:GLU72 3.2 83.7 1.0 CG A:ASP63 3.2 88.0 1.0 C A:GLU67 3.4 82.1 1.0 CG A:ASP61 3.5 88.8 1.0 OD2 A:ASP63 3.5 85.9 1.0 OD2 A:ASP65 3.5 79.4 1.0 OD2 A:ASP61 4.1 92.4 1.0 N A:GLU67 4.2 88.6 1.0 N A:ASP65 4.2 92.3 1.0 N A:ASP69 4.2 72.8 1.0 N A:CYS68 4.3 85.2 1.0 CA A:CYS68 4.3 75.4 1.0 CA A:GLU67 4.4 83.9 1.0 CB A:ASP65 4.4 90.6 1.0 CB A:ASP61 4.5 89.0 1.0 N A:GLY64 4.6 94.0 1.0 CB A:ASP63 4.6 87.7 1.0 CA A:ASP61 4.6 90.8 1.0 N A:ASP63 4.6 93.1 1.0 CG A:GLU72 4.7 79.4 1.0 C A:CYS68 4.7 74.1 1.0 CA A:ASP65 4.7 88.0 1.0 N A:GLY66 4.7 86.6 1.0 C A:ASP63 4.9 94.1 1.0 CB A:GLU67 4.9 84.0 1.0 CA A:ASP63 4.9 91.8 1.0 N A:ASN62 4.9 91.2 1.0 C A:ASP65 4.9 87.1 1.0

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


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 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:54.1 occ:1.00 O B:GLU21 2.2 52.4 1.0 O B:HOH202 2.3 52.9 1.0 O B:SER18 2.4 51.5 1.0 O B:ASP23 2.4 54.9 1.0 OE1 B:GLU31 2.4 52.7 1.0 O B:LYS26 2.4 48.3 1.0 OE2 B:GLU31 2.5 52.9 1.0 CD B:GLU31 2.8 52.8 1.0 C B:SER18 3.4 49.0 1.0 C B:ASP23 3.4 52.7 1.0 C B:GLU21 3.5 52.4 1.0 C B:LYS26 3.7 49.8 1.0 CA B:SER18 3.9 48.6 1.0 N B:ASP23 4.1 49.8 1.0 N B:GLU21 4.1 52.4 1.0 C B:GLY22 4.2 52.7 1.0 N B:LYS24 4.3 50.3 1.0 CA B:ASP23 4.3 55.4 1.0 CA B:GLU21 4.3 50.2 1.0 CA B:LYS24 4.3 55.2 1.0 CG B:GLU31 4.3 49.2 1.0 N B:LYS26 4.4 55.8 1.0 N B:GLY22 4.4 49.3 1.0 N B:GLY19 4.5 47.1 1.0 CB B:SER18 4.6 47.6 1.0 O B:GLY22 4.6 49.5 1.0 N B:LYS28 4.6 54.7 1.0 CA B:LYS26 4.6 52.6 1.0 CA B:GLY22 4.6 46.0 1.0 N B:LEU27 4.6 49.2 1.0 O B:TYR17 4.6 48.6 1.0 CA B:LEU27 4.6 54.6 1.0 OE1 B:GLU67 4.6 62.9 1.0 C B:LYS24 4.7 55.8 1.0 N B:ARG20 4.8 45.2 1.0 CB B:ASP23 4.8 50.0 1.0 CB B:GLU21 4.8 57.0 1.0 CD B:LYS28 4.9 60.9 1.0 CA B:GLY19 4.9 47.0 1.0 C B:GLY19 5.0 51.1 1.0

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


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 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:57.6 occ:1.00 OD1 B:ASP63 2.3 67.5 1.0 OD1 B:ASP61 2.4 61.9 1.0 O B:HOH201 2.4 57.7 1.0 O B:GLU67 2.4 62.2 1.0 OD1 B:ASP65 2.5 61.9 1.0 OE1 B:GLU72 2.5 62.0 1.0 OE2 B:GLU72 2.6 63.9 1.0 CD B:GLU72 2.9 65.3 1.0 CG B:ASP63 3.2 68.2 1.0 CG B:ASP65 3.2 62.2 1.0 OD2 B:ASP63 3.4 63.4 1.0 OD2 B:ASP65 3.4 61.2 1.0 C B:GLU67 3.5 61.6 1.0 CG B:ASP61 3.6 68.6 1.0 N B:GLU67 4.2 65.1 1.0 N B:ASP69 4.3 55.8 1.0 N B:CYS68 4.3 63.8 1.0 N B:ASP65 4.3 69.0 1.0 CA B:ASP61 4.4 69.0 1.0 CA B:GLU67 4.4 61.4 1.0 CA B:CYS68 4.4 57.9 1.0 CB B:ASP61 4.4 69.6 1.0 CB B:ASP65 4.4 66.6 1.0 N B:ASP63 4.5 75.7 1.0 CG B:GLU72 4.5 56.7 1.0 OD2 B:ASP61 4.5 66.9 1.0 CB B:ASP63 4.6 70.7 1.0 OD2 B:ASP69 4.6 60.6 1.0 N B:ASN62 4.8 67.7 1.0 N B:GLY64 4.8 71.0 1.0 CA B:ASP65 4.8 66.0 1.0 C B:CYS68 4.8 53.8 1.0 N B:GLY66 4.9 64.7 1.0 C B:ASP61 4.9 69.4 1.0 CG B:ASP69 4.9 62.0 1.0 CA B:ASP63 4.9 72.2 1.0 CB B:GLU67 4.9 62.9 1.0 C B:ASP63 5.0 69.5 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