Calcium in PDB 5sbe: Tubulin-Maytansinoid-5C-Complex

The structure of Tubulin-Maytansinoid-5C-Complex, PDB code: 5sbe 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)	48.06 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.118, 158.404, 181.377, 90, 90, 90
R / Rfree (%)	19.2 / 23

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

Calcium binding site 1 out of 3 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:82.0 occ:1.00 OE2 A:GLU55 2.4 98.8 1.0 O A:GLY44 2.4 86.2 1.0 OG1 A:THR41 2.4 116.3 1.0 O A:THR41 2.6 107.1 1.0 OD1 A:ASP39 2.6 92.3 1.0 OE1 A:GLU55 2.6 102.8 1.0 OD2 A:ASP39 2.7 83.7 1.0 CD A:GLU55 2.8 94.3 1.0 CG A:ASP39 3.0 89.2 1.0 CB A:THR41 3.3 101.5 1.0 C A:GLY44 3.3 91.9 1.0 C A:THR41 3.5 109.2 1.0 CA A:THR41 3.9 100.8 1.0 CA A:GLY45 4.0 99.0 1.0 N A:GLY45 4.0 89.0 1.0 OD1 A:ASN50 4.3 94.2 1.0 N A:GLY44 4.3 95.9 1.0 N A:THR41 4.3 98.4 1.0 CZ A:PHE49 4.3 75.8 1.0 CA A:GLY44 4.3 92.5 1.0 CG A:GLU55 4.4 85.7 1.0 CB A:ASP39 4.5 87.4 1.0 ND2 A:ASN50 4.6 76.9 1.0 OD2 A:ASP47 4.6 92.6 1.0 CG2 A:THR41 4.7 97.2 1.0 N A:ILE42 4.7 100.0 1.0 NE2 A:HIS61 4.8 85.3 1.0 CG A:ASN50 4.9 84.8 1.0

Calcium binding site 2 out of 3 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:91.6 occ:1.00 OE1 B:GLU113 2.5 98.6 1.0 CD B:GLU113 3.4 94.5 1.0 OE2 B:GLU113 3.6 98.3 1.0 OE1 B:GLU110 4.0 64.8 1.0 OE2 B:GLU110 4.7 74.4 1.0 CD B:GLU110 4.7 59.2 1.0 CG B:GLU113 4.9 82.6 1.0

Calcium binding site 3 out of 3 in the Tubulin-Maytansinoid-5C-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-5C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:69.6 occ:1.00 OE2 C:GLU55 2.3 78.3 1.0 OG1 C:THR41 2.4 94.7 1.0 O C:GLY44 2.4 77.1 1.0 O C:THR41 2.5 84.9 1.0 OD2 C:ASP39 2.5 74.1 1.0 OD1 C:ASP39 2.5 84.4 1.0 O C:HOH609 2.6 70.9 1.0 OE1 C:GLU55 2.6 70.7 1.0 CD C:GLU55 2.8 70.9 1.0 CG C:ASP39 2.8 72.7 1.0 C C:THR41 3.5 81.9 1.0 CB C:THR41 3.5 84.2 1.0 C C:GLY44 3.6 81.0 1.0 CA C:THR41 3.9 84.6 1.0 N C:THR41 4.1 75.8 1.0 CA C:GLY45 4.3 86.3 1.0 N C:GLY45 4.3 89.9 1.0 CG C:GLU55 4.3 59.6 1.0 CB C:ASP39 4.3 77.3 1.0 OD2 C:ASP47 4.4 80.6 1.0 OD1 C:ASN50 4.5 66.0 1.0 CA C:GLY44 4.6 81.8 1.0 N C:GLY44 4.6 87.1 1.0 CZ C:PHE49 4.6 64.0 1.0 N C:ILE42 4.6 83.1 1.0 NE2 C:HIS61 4.7 58.0 1.0 CG2 C:THR41 4.8 83.0 1.0 ND2 C:ASN50 4.8 66.5 1.0 CE1 C:PHE49 4.8 59.6 1.0 O C:HOH718 4.9 66.0 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