Calcium in PDB 5sba: Tubulin-Maytansinoid-4B-Complex

The structure of Tubulin-Maytansinoid-4B-Complex, PDB code: 5sba was solved by P.Marzullo, Z.Boiarska, H.Perez-Pena, A.-C.Abel, B.Alvarez-Bernad, D.Lucena-Agell, F.Vasile, M.Sironi, M.O.Steinmetz, A.E.Prota, J.F.Diaz, S.Pieraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.174, 156.45, 180.827, 90, 90, 90
R / Rfree (%)	18.4 / 22.7

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

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

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

Calcium binding site 1 out of 3 in the Tubulin-Maytansinoid-4B-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Maytansinoid-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:68.7 occ:1.00 O A:THR41 2.4 90.9 1.0 O A:HOH632 2.4 68.6 1.0 OE2 A:GLU55 2.4 69.9 1.0 O A:GLY44 2.4 79.1 1.0 OE1 A:GLU55 2.5 82.7 1.0 OD2 A:ASP39 2.5 72.0 1.0 OG1 A:THR41 2.6 71.8 1.0 OD1 A:ASP39 2.6 72.7 1.0 CD A:GLU55 2.8 72.6 1.0 CG A:ASP39 2.9 72.3 1.0 C A:THR41 3.3 85.0 1.0 CB A:THR41 3.4 79.7 1.0 C A:GLY44 3.4 82.1 1.0 CA A:THR41 3.8 78.8 1.0 O A:HOH609 4.1 79.9 1.0 CA A:GLY45 4.1 86.7 1.0 N A:GLY45 4.2 87.5 1.0 N A:THR41 4.2 82.2 1.0 N A:GLY44 4.3 79.4 1.0 CG A:GLU55 4.3 75.9 1.0 CB A:ASP39 4.4 73.3 1.0 CA A:GLY44 4.4 80.4 1.0 CZ A:PHE49 4.4 60.0 1.0 N A:ILE42 4.5 89.2 1.0 OD1 A:ASN50 4.7 71.2 1.0 CG2 A:THR41 4.7 76.9 1.0 OD2 A:ASP47 4.7 66.6 1.0 ND2 A:ASN50 4.8 65.8 1.0 CE1 A:PHE49 4.9 60.6 1.0 NE2 A:HIS61 4.9 73.0 1.0 CA A:ILE42 4.9 87.5 1.0

Calcium binding site 2 out of 3 in the Tubulin-Maytansinoid-4B-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Maytansinoid-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:57.4 occ:1.00 O C:THR41 2.3 65.0 1.0 OD2 C:ASP39 2.4 56.6 1.0 OG1 C:THR41 2.4 60.0 1.0 O C:GLY44 2.4 60.2 1.0 OE2 C:GLU55 2.4 55.2 1.0 O C:HOH607 2.5 49.6 1.0 OE1 C:GLU55 2.5 47.8 1.0 OD1 C:ASP39 2.5 57.1 1.0 CG C:ASP39 2.8 52.6 1.0 CD C:GLU55 2.8 51.4 1.0 C C:THR41 3.3 65.4 1.0 CB C:THR41 3.4 64.0 1.0 C C:GLY44 3.6 66.4 1.0 CA C:THR41 3.8 60.4 1.0 N C:THR41 4.0 58.5 1.0 O C:HOH618 4.2 46.2 1.0 CB C:ASP39 4.3 47.6 1.0 OD2 C:ASP47 4.3 56.1 1.0 CG C:GLU55 4.3 48.9 1.0 CA C:GLY45 4.4 64.4 1.0 N C:GLY45 4.5 66.8 1.0 N C:GLY44 4.5 63.1 1.0 N C:ILE42 4.5 68.8 1.0 OD1 C:ASN50 4.5 46.4 1.0 CZ C:PHE49 4.6 45.7 1.0 NE2 C:HIS61 4.6 47.9 1.0 CA C:GLY44 4.6 64.7 1.0 CG2 C:THR41 4.7 50.8 1.0 O C:HOH786 4.8 49.1 1.0 CE1 C:PHE49 4.9 47.3 1.0 ND2 C:ASN50 4.9 40.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Maytansinoid-4B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:97.7 occ:1.00 O E:HOH336 2.4 84.3 1.0 O A:HOH690 2.9 63.4 1.0 OD2 E:ASP44 3.4 103.7 1.0 OG A:SER158 3.9 60.0 1.0 O A:HOH716 4.0 68.3 1.0 O A:GLY162 4.1 71.5 1.0 NZ A:LYS166 4.2 59.0 1.0 CB A:SER158 4.3 55.4 1.0 O A:HOH605 4.5 56.9 1.0 CG E:ASP44 4.6 92.7 1.0 O A:GLU196 4.8 65.8 1.0 CA A:SER158 4.9 54.5 1.0 O A:LYS164 5.0 66.9 1.0 O A:HIS197 5.0 52.5 1.0

P.Marzullo, Z.Boiarska, H.Perez-Pena, A.C.Abel, B.Alvarez-Bernad, D.Lucena-Agell, F.Vasile, M.Sironi, K.H.Altmann, A.E.Prota, J.F.Diaz, S.Pieraccini, D.Passarella. Maytansinol Derivatives: Side Reactions As A Chance For New Tubulin Binders. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 34788896
DOI: 10.1002/CHEM.202103520