Calcium in PDB 8b7c: Tubulin-Maytansinoid-12 Complex

The structure of Tubulin-Maytansinoid-12 Complex, PDB code: 8b7c was solved by Z.Boiarska, H.Perez-Pena, A.-C.Abel, P.Marzullo, B.Alvarez-Bernad, F.Bonato, B.Santini, D.Horvath, D.Lucena-Agell, F.Vasile, M.Sironi, J.F.Diaz, M.O.Steinmetz, A.E.Prota, S.Pieraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.866, 157.939, 180.57, 90, 90, 90
R / Rfree (%)	18.3 / 21.2

The structure of Tubulin-Maytansinoid-12 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-12 Complex (pdb code 8b7c). 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-12 Complex, PDB code: 8b7c:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:61.9 occ:1.00 O A:GLY44 2.3 68.3 1.0 O A:THR41 2.4 75.9 1.0 O A:HOH631 2.4 63.1 1.0 OE2 A:GLU55 2.4 55.3 1.0 OD2 A:ASP39 2.4 70.5 1.0 OD1 A:ASP39 2.5 72.8 1.0 OG1 A:THR41 2.5 60.5 1.0 OE1 A:GLU55 2.6 58.9 1.0 CG A:ASP39 2.8 74.3 1.0 CD A:GLU55 2.8 58.9 1.0 C A:THR41 3.4 75.3 1.0 C A:GLY44 3.5 72.8 1.0 CB A:THR41 3.5 74.9 1.0 CA A:THR41 3.9 74.7 1.0 N A:THR41 4.2 74.2 1.0 CA A:GLY45 4.3 76.0 1.0 N A:GLY44 4.3 71.8 1.0 N A:GLY45 4.3 81.8 1.0 CB A:ASP39 4.3 69.1 1.0 CG A:GLU55 4.3 55.0 1.0 CZ A:PHE49 4.4 59.8 1.0 O A:HOH715 4.5 56.8 1.0 CA A:GLY44 4.5 67.4 1.0 OD1 A:ASN50 4.5 57.6 1.0 N A:ILE42 4.6 77.6 1.0 NE2 A:HIS61 4.7 64.8 1.0 CE1 A:PHE49 4.8 56.1 1.0 CG2 A:THR41 4.8 64.9 1.0 ND2 A:ASN50 4.9 55.9 1.0

Calcium binding site 2 out of 4 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:87.6 occ:1.00 OE1 B:GLU113 2.4 66.0 1.0 O B:HOH696 2.5 60.4 1.0 OE2 B:GLU113 3.1 69.5 1.0 CD B:GLU113 3.1 63.1 1.0 CG B:GLU113 4.6 52.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:47.4 occ:1.00 OE1 C:GLU55 2.4 45.4 1.0 O C:THR41 2.4 50.5 1.0 O C:GLY44 2.4 53.3 1.0 OD2 C:ASP39 2.4 50.1 1.0 O C:HOH613 2.5 35.8 1.0 OE2 C:GLU55 2.5 44.5 1.0 OG1 C:THR41 2.5 50.9 1.0 OD1 C:ASP39 2.6 53.2 1.0 CD C:GLU55 2.7 43.2 1.0 CG C:ASP39 2.8 49.4 1.0 C C:THR41 3.4 58.9 1.0 C C:GLY44 3.5 64.2 1.0 CB C:THR41 3.6 56.0 1.0 CA C:THR41 3.9 57.2 1.0 N C:THR41 4.2 49.5 1.0 CG C:GLU55 4.3 39.7 1.0 O C:HOH618 4.3 56.1 1.0 N C:GLY45 4.3 63.0 1.0 CA C:GLY45 4.3 57.4 1.0 N C:GLY44 4.3 59.0 1.0 O C:HOH667 4.3 48.0 1.0 CB C:ASP39 4.4 46.6 1.0 CA C:GLY44 4.4 63.6 1.0 OD2 C:ASP47 4.5 54.6 1.0 OD1 C:ASN50 4.5 42.1 1.0 N C:ILE42 4.6 51.6 1.0 NE2 C:HIS61 4.6 39.7 1.0 CZ C:PHE49 4.6 41.6 1.0 CG2 C:THR41 4.9 53.4 1.0 ND2 C:ASN50 4.9 37.0 1.0 CE1 C:PHE49 4.9 43.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-Maytansinoid-12 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-12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:106.3 occ:1.00 O E:HOH355 2.8 84.2 1.0 O A:HOH770 3.2 66.1 1.0 O A:HOH738 3.3 50.5 1.0 OD2 E:ASP44 3.4 91.7 1.0 OG A:SER158 3.9 53.1 1.0 O A:GLY162 4.3 62.4 1.0 CB A:SER158 4.3 55.8 1.0 O A:HOH706 4.3 60.0 1.0 NZ A:LYS166 4.5 44.7 1.0 CG E:ASP44 4.5 90.0 1.0 O A:GLU196 4.6 55.3 1.0 OD1 E:ASP44 4.9 85.8 1.0 O A:HOH620 4.9 57.8 1.0 CA A:SER158 5.0 56.5 1.0

Z.Boiarska, H.Perez-Pena, A.C.Abel, P.Marzullo, B.Alvarez-Bernad, F.Bonato, B.Santini, D.Horvath, D.Lucena-Agell, F.Vasile, M.Sironi, J.F.Diaz, A.E.Prota, S.Pieraccini, D.Passarella. Maytansinol Functionalization: Towards Useful Probes For Studying Microtubule Dynamics. Chemistry V. 29 03431 2023.
ISSN: ISSN 0947-6539
PubMed: 36468686
DOI: 10.1002/CHEM.202203431