Calcium in PDB 5sb5: Tubulin-Todalam-9-Complex

The structure of Tubulin-Todalam-9-Complex, PDB code: 5sb5 was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.81, 157.711, 180.536, 90, 90, 90
R / Rfree (%)	18.8 / 22

The structure of Tubulin-Todalam-9-Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Fluorine	(F)	1 atom

The binding sites of Calcium atom in the Tubulin-Todalam-9-Complex (pdb code 5sb5). 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-Todalam-9-Complex, PDB code: 5sb5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-9-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Todalam-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:64.4 occ:1.00 O A:GLY44 2.4 68.6 1.0 O A:THR41 2.4 76.0 1.0 OD1 A:ASP39 2.4 68.5 1.0 OD2 A:ASP39 2.5 68.2 1.0 OE2 A:GLU55 2.5 59.8 1.0 OG1 A:THR41 2.5 72.3 1.0 OE1 A:GLU55 2.7 68.6 1.0 CG A:ASP39 2.8 68.3 1.0 CD A:GLU55 2.9 67.9 1.0 CB A:THR41 3.4 72.4 1.0 C A:THR41 3.4 77.2 1.0 C A:GLY44 3.6 73.4 1.0 CA A:THR41 3.8 76.8 1.0 N A:THR41 4.1 77.1 1.0 CA A:GLY45 4.3 73.0 1.0 CB A:ASP39 4.3 65.9 1.0 N A:GLY45 4.4 73.4 1.0 CZ A:PHE49 4.4 56.2 1.0 N A:GLY44 4.4 73.9 1.0 CG A:GLU55 4.4 64.1 1.0 OD2 A:ASP47 4.5 70.8 1.0 OD1 A:ASN50 4.5 62.1 1.0 N A:ILE42 4.6 77.7 1.0 CA A:GLY44 4.6 71.2 1.0 NE2 A:HIS61 4.7 68.8 1.0 CG2 A:THR41 4.7 67.1 1.0 ND2 A:ASN50 4.8 61.8 1.0 CE1 A:PHE49 4.9 55.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-9-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Todalam-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:84.7 occ:1.00 O B:HOH626 2.4 51.0 1.0 OE1 B:GLU113 2.8 72.6 1.0 OE2 B:GLU113 3.5 70.4 1.0 CD B:GLU113 3.5 68.6 1.0 CG B:GLU113 5.0 62.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-9-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Todalam-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:52.8 occ:1.00 O C:GLY44 2.4 53.6 1.0 OE1 C:GLU55 2.4 49.0 1.0 OE2 C:GLU55 2.4 52.5 1.0 O C:THR41 2.4 58.5 1.0 O C:HOH641 2.5 44.4 1.0 OG1 C:THR41 2.5 57.9 1.0 OD2 C:ASP39 2.6 45.3 1.0 OD1 C:ASP39 2.6 53.0 1.0 CD C:GLU55 2.7 48.7 1.0 CG C:ASP39 2.9 50.6 1.0 C C:THR41 3.4 58.2 1.0 C C:GLY44 3.5 56.6 1.0 CB C:THR41 3.5 57.5 1.0 CA C:THR41 3.9 55.8 1.0 CA C:GLY45 4.2 54.4 1.0 N C:THR41 4.2 55.1 1.0 O C:HOH612 4.2 45.3 1.0 N C:GLY45 4.2 57.9 1.0 CG C:GLU55 4.2 45.0 1.0 N C:GLY44 4.4 55.4 1.0 CB C:ASP39 4.4 51.3 1.0 OD1 C:ASN50 4.5 44.2 1.0 CA C:GLY44 4.5 57.1 1.0 CZ C:PHE49 4.5 42.7 1.0 N C:ILE42 4.6 56.5 1.0 NE2 C:HIS61 4.6 42.9 1.0 OD2 C:ASP47 4.6 52.2 1.0 CE1 C:PHE49 4.8 40.8 1.0 ND2 C:ASN50 4.8 39.8 1.0 CG2 C:THR41 4.8 47.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-9-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Todalam-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:84.0 occ:1.00 O A:HOH712 2.5 59.5 1.0 O E:HOH335 2.7 63.3 1.0 O A:HOH688 2.9 54.4 1.0 OD2 E:ASP44 3.4 85.3 1.0 O A:HOH702 3.4 50.1 1.0 O A:GLU196 4.0 56.1 1.0 OG A:SER158 4.1 54.3 1.0 CG E:ASP44 4.4 83.6 1.0 OD1 E:ASP44 4.5 76.1 1.0 CB A:SER158 4.7 51.7 1.0 CA A:HIS197 4.7 46.5 1.0 NZ A:LYS166 4.8 48.3 1.0 OD1 A:ASP199 4.8 48.7 1.0 O A:HIS197 4.9 47.5 1.0 O A:GLY162 4.9 63.2 1.0

T.Muhlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz. Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052