Calcium in PDB 5sbb: Tubulin-Maytansinoid-4C-Complex

The structure of Tubulin-Maytansinoid-4C-Complex, PDB code: 5sbb 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)	49.54 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.615, 157.484, 180.633, 90, 90, 90
R / Rfree (%)	18.3 / 22.8

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

Calcium binding site 1 out of 4 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.4 occ:1.00 O A:GLY44 2.3 68.4 1.0 O A:THR41 2.4 80.2 1.0 O A:HOH611 2.4 73.5 1.0 OD2 A:ASP39 2.5 73.5 1.0 OG1 A:THR41 2.5 73.8 1.0 OD1 A:ASP39 2.5 70.4 1.0 OE1 A:GLU55 2.6 77.5 1.0 OE2 A:GLU55 2.6 67.9 1.0 CG A:ASP39 2.8 73.7 1.0 CD A:GLU55 2.9 72.6 1.0 C A:THR41 3.4 82.6 1.0 CB A:THR41 3.5 74.7 1.0 C A:GLY44 3.5 77.5 1.0 CA A:THR41 3.9 78.0 1.0 CZ A:PHE49 4.2 62.3 1.0 N A:THR41 4.2 80.7 1.0 N A:GLY44 4.3 78.6 1.0 CA A:GLY45 4.3 76.3 1.0 O A:HOH616 4.3 76.7 1.0 N A:GLY45 4.3 85.6 1.0 CB A:ASP39 4.3 66.1 1.0 CG A:GLU55 4.4 68.2 1.0 OD2 A:ASP47 4.4 76.6 1.0 CA A:GLY44 4.5 75.4 1.0 OD1 A:ASN50 4.6 68.3 1.0 N A:ILE42 4.6 82.1 1.0 CE1 A:PHE49 4.8 59.2 1.0 NE2 A:HIS61 4.8 63.4 1.0 CG2 A:THR41 4.8 69.9 1.0 ND2 A:ASN50 4.8 62.0 1.0

Calcium binding site 2 out of 4 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:92.9 occ:1.00 OE1 B:GLU113 2.9 81.2 1.0 CD B:GLU113 3.7 81.1 1.0 OE2 B:GLU113 3.7 80.2 1.0 OE1 B:GLU110 4.9 45.9 1.0

Calcium binding site 3 out of 4 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:53.0 occ:1.00 O C:THR41 2.4 60.2 1.0 O C:HOH612 2.4 47.0 1.0 O C:GLY44 2.4 54.5 1.0 OD2 C:ASP39 2.4 53.7 1.0 OG1 C:THR41 2.4 53.5 1.0 OE2 C:GLU55 2.5 50.9 1.0 OD1 C:ASP39 2.5 54.6 1.0 OE1 C:GLU55 2.5 48.0 1.0 CG C:ASP39 2.8 50.9 1.0 CD C:GLU55 2.8 44.7 1.0 C C:THR41 3.4 59.3 1.0 CB C:THR41 3.5 59.2 1.0 C C:GLY44 3.6 59.7 1.0 CA C:THR41 3.8 58.1 1.0 N C:THR41 4.0 50.5 1.0 O C:HOH604 4.1 50.5 1.0 CB C:ASP39 4.3 49.5 1.0 OD2 C:ASP47 4.3 57.4 1.0 CG C:GLU55 4.3 40.8 1.0 CA C:GLY45 4.3 56.6 1.0 N C:GLY45 4.4 62.7 1.0 N C:GLY44 4.4 55.0 1.0 OD1 C:ASN50 4.5 43.4 1.0 N C:ILE42 4.6 55.8 1.0 CA C:GLY44 4.6 63.2 1.0 CZ C:PHE49 4.6 40.8 1.0 NE2 C:HIS61 4.7 47.2 1.0 CG2 C:THR41 4.8 48.4 1.0 O C:HOH738 4.8 47.0 1.0 CE1 C:PHE49 4.9 43.9 1.0 ND2 C:ASN50 4.9 42.4 1.0

Calcium binding site 4 out of 4 in the Tubulin-Maytansinoid-4C-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-4C-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:98.8 occ:1.00 O A:HOH715 2.4 56.9 1.0 O A:HOH722 2.7 66.2 1.0 OD2 E:ASP44 3.2 94.2 1.0 O A:HOH713 3.6 53.0 1.0 OG A:SER158 4.3 58.5 1.0 O A:HOH726 4.3 59.8 1.0 CG E:ASP44 4.3 100.2 1.0 O A:GLY162 4.5 67.8 1.0 O A:GLU196 4.5 57.9 1.0 CB A:SER158 4.6 50.4 1.0 OD1 E:ASP44 4.7 96.7 1.0 NZ A:LYS166 4.9 53.0 1.0 O A:HOH608 5.0 50.6 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