Calcium in PDB 5sb9: Tubulin-Maytansinoid-4A-Complex

The structure of Tubulin-Maytansinoid-4A-Complex, PDB code: 5sb9 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)	47.92 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.539, 156.717, 181.697, 90, 90, 90
R / Rfree (%)	19.4 / 22.7

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

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

The binding sites of Calcium atom in the Tubulin-Maytansinoid-4A-Complex (pdb code 5sb9). 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-4A-Complex, PDB code: 5sb9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Maytansinoid-4A-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-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:84.1 occ:1.00 O A:THR41 2.3 86.5 1.0 OE2 A:GLU55 2.3 73.0 1.0 OD2 A:ASP39 2.4 78.0 1.0 OG1 A:THR41 2.6 86.0 1.0 OE1 A:GLU55 2.6 85.2 1.0 OD1 A:ASP39 2.6 76.2 1.0 O A:GLY44 2.7 76.4 1.0 CD A:GLU55 2.8 81.4 1.0 CG A:ASP39 2.9 78.8 1.0 C A:THR41 3.4 84.2 1.0 CB A:THR41 3.5 83.3 1.0 C A:GLY44 3.6 78.5 1.0 CA A:GLY45 3.8 82.0 1.0 CA A:THR41 3.9 80.6 1.0 N A:GLY45 4.1 80.2 1.0 CZ A:PHE49 4.2 72.4 1.0 N A:THR41 4.2 82.8 1.0 CG A:GLU55 4.3 76.6 1.0 CB A:ASP39 4.4 79.0 1.0 OD2 A:ASP47 4.4 77.7 1.0 OD1 A:ASN50 4.5 72.9 1.0 N A:ILE42 4.6 81.8 1.0 ND2 A:ASN50 4.6 70.6 1.0 NE2 A:HIS61 4.6 75.8 1.0 N A:GLY44 4.6 88.1 1.0 CA A:GLY44 4.8 87.5 1.0 CG2 A:THR41 4.9 74.5 1.0 CE2 A:PHE49 4.9 66.0 1.0 CA A:ILE42 5.0 96.9 1.0 CG A:ASN50 5.0 66.7 1.0

Calcium binding site 2 out of 3 in the Tubulin-Maytansinoid-4A-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-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:101.8 occ:1.00 O A:HOH643 3.7 64.3 1.0 OD2 E:ASP44 3.7 101.9 1.0 NZ A:LYS166 3.9 77.2 1.0 OD1 A:ASP199 4.3 58.1 1.0 OG A:SER158 4.3 65.6 1.0 O A:GLY162 4.3 74.4 1.0 O A:GLU196 4.7 68.8 1.0 CG E:ASP44 4.7 106.5 1.0 CB A:SER158 4.8 56.2 1.0 O A:LYS164 4.9 77.5 1.0 CE A:LYS166 4.9 55.9 1.0 O A:HIS197 4.9 55.8 1.0

Calcium binding site 3 out of 3 in the Tubulin-Maytansinoid-4A-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-4A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.9 occ:1.00 O C:THR41 2.3 72.4 1.0 OE2 C:GLU55 2.3 66.3 1.0 OG1 C:THR41 2.4 69.4 1.0 O C:HOH602 2.4 60.8 1.0 O C:GLY44 2.4 72.3 1.0 OD2 C:ASP39 2.5 70.9 1.0 OE1 C:GLU55 2.5 57.3 1.0 OD1 C:ASP39 2.7 68.2 1.0 CD C:GLU55 2.7 61.3 1.0 CG C:ASP39 2.9 62.9 1.0 C C:THR41 3.3 66.0 1.0 CB C:THR41 3.4 70.6 1.0 C C:GLY44 3.4 71.8 1.0 CA C:THR41 3.8 62.9 1.0 N C:THR41 4.2 63.8 1.0 N C:GLY45 4.2 73.9 1.0 CG C:GLU55 4.2 57.4 1.0 CA C:GLY45 4.2 76.3 1.0 OD2 C:ASP47 4.3 74.4 1.0 CA C:GLY44 4.4 72.8 1.0 N C:GLY44 4.4 79.4 1.0 CB C:ASP39 4.4 67.3 1.0 N C:ILE42 4.5 69.7 1.0 OD1 C:ASN50 4.5 59.7 1.0 O C:HOH690 4.6 58.2 1.0 CZ C:PHE49 4.7 47.4 1.0 CG2 C:THR41 4.7 61.9 1.0 NE2 C:HIS61 4.8 56.3 1.0 ND2 C:ASN50 4.8 50.0 1.0 CA C:ILE42 5.0 68.5 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