Calcium in PDB 5sb3: Tubulin-Todalam-4-Complex

The structure of Tubulin-Todalam-4-Complex, PDB code: 5sb3 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)	49.46 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.65, 157.714, 180.188, 90, 90, 90
R / Rfree (%)	19.5 / 22.5

The structure of Tubulin-Todalam-4-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Todalam-4-Complex (pdb code 5sb3). 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-4-Complex, PDB code: 5sb3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:70.3 occ:1.00 O A:GLY44 2.4 76.1 1.0 O A:THR41 2.4 81.1 1.0 OG1 A:THR41 2.4 68.5 1.0 OD1 A:ASP39 2.4 74.7 1.0 OD2 A:ASP39 2.5 70.3 1.0 OE2 A:GLU55 2.5 67.3 1.0 OE1 A:GLU55 2.6 73.4 1.0 O A:HOH608 2.6 68.8 1.0 CG A:ASP39 2.8 75.0 1.0 CD A:GLU55 2.9 73.2 1.0 C A:THR41 3.4 81.4 1.0 CB A:THR41 3.4 80.1 1.0 C A:GLY44 3.6 78.3 1.0 CA A:THR41 3.8 84.2 1.0 N A:THR41 4.0 84.6 1.0 O A:HOH630 4.2 74.9 1.0 CA A:GLY45 4.3 77.4 1.0 CB A:ASP39 4.3 75.0 1.0 N A:GLY45 4.4 78.0 1.0 N A:GLY44 4.4 79.2 1.0 CG A:GLU55 4.4 71.3 1.0 CZ A:PHE49 4.4 66.0 1.0 OD1 A:ASN50 4.6 68.2 1.0 CA A:GLY44 4.6 78.1 1.0 N A:ILE42 4.6 84.1 1.0 OD2 A:ASP47 4.6 71.3 1.0 CG2 A:THR41 4.7 73.2 1.0 CE1 A:PHE49 4.8 64.3 1.0 NE2 A:HIS61 4.8 74.0 1.0 ND2 A:ASN50 5.0 64.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:94.3 occ:1.00 O B:HOH691 2.4 64.7 1.0 OE1 B:GLU113 2.6 77.6 1.0 OE2 B:GLU113 3.1 83.5 1.0 CD B:GLU113 3.2 76.8 1.0 CG B:GLU113 4.7 69.2 1.0

Calcium binding site 3 out of 4 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:60.0 occ:1.00 O C:GLY44 2.3 58.8 1.0 O C:THR41 2.4 65.5 1.0 OE2 C:GLU55 2.4 55.7 1.0 OE1 C:GLU55 2.4 54.5 1.0 OD2 C:ASP39 2.5 54.9 1.0 OG1 C:THR41 2.5 62.4 1.0 O C:HOH605 2.5 51.6 1.0 OD1 C:ASP39 2.6 58.6 1.0 CD C:GLU55 2.8 56.2 1.0 CG C:ASP39 2.9 54.5 1.0 C C:THR41 3.5 62.3 1.0 CB C:THR41 3.5 64.5 1.0 C C:GLY44 3.5 64.1 1.0 CA C:THR41 3.9 60.9 1.0 N C:THR41 4.2 58.5 1.0 O C:HOH617 4.3 51.7 1.0 CG C:GLU55 4.3 50.5 1.0 CA C:GLY45 4.3 63.5 1.0 N C:GLY45 4.4 65.4 1.0 OD2 C:ASP47 4.4 62.0 1.0 CB C:ASP39 4.4 55.0 1.0 N C:GLY44 4.5 63.2 1.0 OD1 C:ASN50 4.5 53.6 1.0 CA C:GLY44 4.6 62.3 1.0 NE2 C:HIS61 4.6 48.2 1.0 N C:ILE42 4.6 60.6 1.0 CZ C:PHE49 4.7 47.6 1.0 ND2 C:ASN50 4.8 44.1 1.0 CE1 C:PHE49 4.8 48.6 1.0 CG2 C:THR41 4.9 57.5 1.0

Calcium binding site 4 out of 4 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:105.2 occ:1.00 O A:HOH699 2.5 65.8 1.0 O A:HOH692 2.7 59.9 1.0 O E:HOH337 2.8 75.5 1.0 OD2 E:ASP44 3.4 95.1 1.0 O A:HOH685 3.6 53.7 1.0 O A:GLU196 4.1 57.4 1.0 OG A:SER158 4.3 60.5 1.0 CG E:ASP44 4.4 95.5 1.0 OD1 E:ASP44 4.6 93.2 1.0 OD1 A:ASP199 4.8 57.2 1.0 O A:GLY162 4.9 65.3 1.0 CA A:HIS197 4.9 53.0 1.0 CB A:SER158 4.9 57.7 1.0 NZ A:LYS166 4.9 53.8 1.0 O A:HIS197 5.0 54.1 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