Calcium in PDB 5s4o: Tubulin-Z48847594-Complex

The structure of Tubulin-Z48847594-Complex, PDB code: 5s4o was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.744, 158.001, 178.586, 90, 90, 90
R / Rfree (%)	21.6 / 26.2

The structure of Tubulin-Z48847594-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z48847594-Complex (pdb code 5s4o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-Z48847594-Complex, PDB code: 5s4o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.3 occ:1.00 O A:GLY44 2.3 57.7 1.0 OD2 A:ASP39 2.4 55.1 1.0 O A:HOH617 2.4 56.3 1.0 O A:THR41 2.4 61.6 1.0 OG1 A:THR41 2.5 60.9 1.0 OD1 A:ASP39 2.5 54.5 1.0 OE1 A:GLU55 2.6 63.3 1.0 OE2 A:GLU55 2.6 57.0 1.0 CG A:ASP39 2.8 55.9 1.0 CD A:GLU55 3.0 61.6 1.0 CB A:THR41 3.4 57.2 1.0 C A:THR41 3.4 65.5 1.0 C A:GLY44 3.5 64.6 1.0 CA A:THR41 3.8 62.3 1.0 N A:THR41 4.1 62.2 1.0 CA A:GLY45 4.2 68.6 1.0 CB A:ASP39 4.3 55.5 1.0 N A:GLY45 4.3 61.0 1.0 N A:GLY44 4.4 56.9 1.0 CG A:GLU55 4.5 60.4 1.0 CZ A:PHE49 4.5 53.5 1.0 OD2 A:ASP47 4.5 60.4 1.0 OD1 A:ASN50 4.5 61.9 1.0 O A:HOH667 4.6 55.9 1.0 CA A:GLY44 4.6 56.1 1.0 N A:ILE42 4.6 64.0 1.0 CG2 A:THR41 4.8 55.9 1.0 NE2 A:HIS61 4.8 58.6 1.0 ND2 A:ASN50 4.9 49.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:76.7 occ:1.00 OE1 B:GLU113 2.6 59.5 1.0 CD B:GLU113 3.6 57.2 1.0 OE2 B:GLU113 3.8 59.6 1.0 OE1 B:GLU110 4.3 32.6 1.0 CG B:GLU113 5.0 43.5 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:43.4 occ:1.00 O C:THR41 2.3 47.0 1.0 O C:GLY44 2.4 41.6 1.0 OD2 C:ASP39 2.4 45.4 1.0 O C:HOH607 2.4 36.0 1.0 OE2 C:GLU55 2.4 37.4 1.0 OD1 C:ASP39 2.5 43.7 1.0 OG1 C:THR41 2.5 48.1 1.0 OE1 C:GLU55 2.5 41.7 1.0 CG C:ASP39 2.8 48.1 1.0 CD C:GLU55 2.8 43.0 1.0 C C:THR41 3.4 47.2 1.0 CB C:THR41 3.5 45.0 1.0 C C:GLY44 3.5 43.8 1.0 CA C:THR41 3.8 42.1 1.0 N C:THR41 4.1 40.6 1.0 CA C:GLY45 4.2 43.2 1.0 CB C:ASP39 4.3 49.3 1.0 N C:GLY45 4.3 41.2 1.0 OD2 C:ASP47 4.3 48.0 1.0 CG C:GLU55 4.3 40.7 1.0 N C:GLY44 4.5 48.4 1.0 CZ C:PHE49 4.5 41.9 1.0 N C:ILE42 4.5 44.7 1.0 CA C:GLY44 4.6 41.4 1.0 OD1 C:ASN50 4.7 34.9 1.0 NE2 C:HIS61 4.7 37.0 1.0 CG2 C:THR41 4.8 36.5 1.0 CE1 C:PHE49 4.9 41.3 1.0 ND2 C:ASN50 4.9 29.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:74.8 occ:1.00 O A:HOH675 2.5 50.9 1.0 O A:HOH672 2.8 56.9 1.0 OD2 E:ASP44 3.3 63.8 1.0 O A:GLU196 3.8 49.3 1.0 O A:HOH651 3.9 40.4 1.0 OG A:SER158 4.0 41.8 1.0 O A:HOH676 4.3 47.8 1.0 CG E:ASP44 4.4 70.1 1.0 CB A:SER158 4.5 37.7 1.0 CA A:HIS197 4.5 35.5 1.0 NZ A:LYS166 4.6 36.2 1.0 OD1 E:ASP44 4.8 68.1 1.0 ND1 A:HIS197 4.8 47.7 1.0 O A:HIS197 4.8 34.5 1.0 C A:GLU196 4.9 43.2 1.0 C A:HIS197 4.9 35.0 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273