Calcium in PDB 5sbd: Tubulin-Maytansinoid-5B-Complex

The structure of Tubulin-Maytansinoid-5B-Complex, PDB code: 5sbd 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)	49.58 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.075, 158.601, 180.439, 90, 90, 90
R / Rfree (%)	17.9 / 21.4

The structure of Tubulin-Maytansinoid-5B-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-5B-Complex (pdb code 5sbd). 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-Maytansinoid-5B-Complex, PDB code: 5sbd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.2 occ:1.00 O A:HOH611 2.4 59.9 1.0 O A:GLY44 2.4 71.7 1.0 O A:THR41 2.4 74.7 1.0 OD2 A:ASP39 2.5 67.6 1.0 OG1 A:THR41 2.5 65.5 1.0 OE1 A:GLU55 2.5 69.5 1.0 OD1 A:ASP39 2.5 70.1 1.0 OE2 A:GLU55 2.6 64.3 1.0 CD A:GLU55 2.9 65.0 1.0 CG A:ASP39 2.9 62.3 1.0 C A:THR41 3.4 77.4 1.0 C A:GLY44 3.4 69.0 1.0 CB A:THR41 3.5 71.8 1.0 CA A:THR41 3.9 73.4 1.0 N A:GLY44 4.2 73.8 1.0 N A:THR41 4.2 79.6 1.0 O A:HOH657 4.3 67.5 1.0 N A:GLY45 4.3 69.6 1.0 CZ A:PHE49 4.3 55.2 1.0 CA A:GLY45 4.3 72.0 1.0 CG A:GLU55 4.4 66.0 1.0 CA A:GLY44 4.4 79.2 1.0 CB A:ASP39 4.4 63.3 1.0 OD2 A:ASP47 4.5 72.2 1.0 OD1 A:ASN50 4.6 56.5 1.0 N A:ILE42 4.6 74.8 1.0 CE1 A:PHE49 4.7 58.3 1.0 NE2 A:HIS61 4.8 66.4 1.0 ND2 A:ASN50 4.8 60.8 1.0 CG2 A:THR41 4.8 66.9 1.0 N A:GLY43 5.0 74.3 1.0

Calcium binding site 2 out of 4 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:95.9 occ:1.00 OE1 B:GLU113 2.8 82.8 1.0 CD B:GLU113 3.7 74.6 1.0 OE2 B:GLU113 3.8 77.8 1.0 OE1 B:GLU110 4.3 39.6 1.0 OE2 B:GLU110 5.0 62.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Maytansinoid-5B-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-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:49.8 occ:1.00 O C:HOH604 2.3 37.2 1.0 O C:THR41 2.4 58.9 1.0 O C:GLY44 2.4 48.5 1.0 OG1 C:THR41 2.4 54.4 1.0 OD2 C:ASP39 2.4 52.0 1.0 OE1 C:GLU55 2.5 46.7 1.0 OE2 C:GLU55 2.5 48.9 1.0 OD1 C:ASP39 2.6 51.2 1.0 CD C:GLU55 2.9 47.6 1.0 CG C:ASP39 2.9 47.1 1.0 C C:THR41 3.4 61.3 1.0 C C:GLY44 3.5 65.6 1.0 CB C:THR41 3.5 60.7 1.0 CA C:THR41 3.9 62.6 1.0 N C:THR41 4.2 55.5 1.0 CA C:GLY45 4.2 59.8 1.0 N C:GLY45 4.3 65.9 1.0 OD2 C:ASP47 4.3 59.8 1.0 O C:HOH642 4.3 48.1 1.0 N C:GLY44 4.4 56.6 1.0 CG C:GLU55 4.4 39.2 1.0 CB C:ASP39 4.4 51.3 1.0 OD1 C:ASN50 4.5 45.1 1.0 CA C:GLY44 4.5 62.5 1.0 N C:ILE42 4.6 58.3 1.0 NE2 C:HIS61 4.6 45.6 1.0 CZ C:PHE49 4.7 46.1 1.0 CG2 C:THR41 4.8 49.2 1.0 ND2 C:ASN50 4.8 39.9 1.0 CE1 C:PHE49 4.9 41.9 1.0

Calcium binding site 4 out of 4 in the Tubulin-Maytansinoid-5B-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Maytansinoid-5B-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:92.0 occ:1.00 O A:HOH685 2.5 66.0 1.0 O A:HOH691 2.9 60.5 1.0 OD2 E:ASP44 3.2 88.5 1.0 O A:HOH716 3.4 57.5 1.0 OG A:SER158 4.1 55.2 1.0 O A:GLU196 4.1 66.8 1.0 CG E:ASP44 4.3 88.2 1.0 CB A:SER158 4.6 50.8 1.0 NZ A:LYS166 4.7 45.6 1.0 OD1 E:ASP44 4.7 82.7 1.0 O A:GLY162 4.8 66.0 1.0 CA A:HIS197 4.8 54.0 1.0 OD1 A:ASP199 5.0 47.3 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