Calcium in PDB 5sb8: Tubulin-Maytansinoid-3-Complex

The structure of Tubulin-Maytansinoid-3-Complex, PDB code: 5sb8 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)	49.66 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.664, 157.491, 181.511, 90, 90, 90
R / Rfree (%)	19.3 / 23

The structure of Tubulin-Maytansinoid-3-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-3-Complex (pdb code 5sb8). 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-3-Complex, PDB code: 5sb8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:77.2 occ:1.00 O A:GLY44 2.4 83.4 1.0 O A:THR41 2.4 86.0 1.0 OE2 A:GLU55 2.4 75.5 1.0 OD1 A:ASP39 2.5 72.4 1.0 OG1 A:THR41 2.5 79.5 1.0 OD2 A:ASP39 2.6 79.1 1.0 OE1 A:GLU55 2.7 88.5 1.0 CG A:ASP39 2.9 81.6 1.0 CD A:GLU55 2.9 79.7 1.0 C A:THR41 3.4 84.4 1.0 CB A:THR41 3.4 87.9 1.0 C A:GLY44 3.4 81.8 1.0 CA A:THR41 3.8 84.5 1.0 CA A:GLY45 4.2 82.0 1.0 N A:THR41 4.2 83.2 1.0 N A:GLY45 4.2 86.5 1.0 N A:GLY44 4.3 87.3 1.0 CZ A:PHE49 4.3 72.2 1.0 CB A:ASP39 4.4 78.5 1.0 CG A:GLU55 4.4 83.2 1.0 OD1 A:ASN50 4.4 80.5 1.0 CA A:GLY44 4.5 81.0 1.0 N A:ILE42 4.6 88.7 1.0 ND2 A:ASN50 4.7 71.8 1.0 NE2 A:HIS61 4.7 78.7 1.0 OD2 A:ASP47 4.8 87.8 1.0 CG2 A:THR41 4.8 76.7 1.0 O A:HOH666 4.9 80.7 1.0

Calcium binding site 2 out of 3 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:97.1 occ:1.00 OE1 B:GLU113 2.8 89.5 1.0 CD B:GLU113 3.6 83.3 1.0 OE2 B:GLU113 3.7 84.4 1.0 OE1 B:GLU110 4.5 52.1 1.0

Calcium binding site 3 out of 3 in the Tubulin-Maytansinoid-3-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-3-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:63.3 occ:1.00 O C:HOH601 2.3 77.8 1.0 O C:GLY44 2.3 63.2 1.0 OE1 C:GLU55 2.4 53.4 1.0 O C:THR41 2.4 65.7 1.0 OE2 C:GLU55 2.4 56.1 1.0 OD2 C:ASP39 2.5 61.0 1.0 OG1 C:THR41 2.6 61.2 1.0 OD1 C:ASP39 2.7 58.7 1.0 CD C:GLU55 2.7 59.2 1.0 CG C:ASP39 2.9 60.5 1.0 C C:GLY44 3.3 69.0 1.0 C C:THR41 3.5 67.8 1.0 CB C:THR41 3.6 64.7 1.0 O C:HOH603 3.9 57.6 1.0 CA C:THR41 4.0 61.8 1.0 N C:GLY45 4.1 67.2 1.0 CA C:GLY45 4.1 62.6 1.0 N C:GLY44 4.2 67.5 1.0 CG C:GLU55 4.3 52.4 1.0 N C:THR41 4.3 58.5 1.0 CA C:GLY44 4.3 70.2 1.0 OD2 C:ASP47 4.3 75.9 1.0 CB C:ASP39 4.4 61.3 1.0 OD1 C:ASN50 4.5 55.6 1.0 N C:ILE42 4.6 66.3 1.0 NE2 C:HIS61 4.7 50.0 1.0 CZ C:PHE49 4.8 46.4 1.0 ND2 C:ASN50 4.8 51.1 1.0 CG2 C:THR41 4.9 55.8 1.0 CE1 C:PHE49 4.9 49.0 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