Calcium in PDB 8b7b: Tubulin - Maytansinoid - 6 Complex

The structure of Tubulin - Maytansinoid - 6 Complex, PDB code: 8b7b 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)	47.83 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.085, 155.637, 181.924, 90, 90, 90
R / Rfree (%)	18.4 / 22.4

The structure of Tubulin - Maytansinoid - 6 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 - 6 Complex (pdb code 8b7b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tubulin - Maytansinoid - 6 Complex, PDB code: 8b7b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:79.6 occ:1.00 O A:GLY44 2.2 83.7 1.0 OD1 A:ASP39 2.4 74.0 1.0 OE2 A:GLU55 2.4 70.9 1.0 O A:THR41 2.5 84.6 1.0 OG1 A:THR41 2.6 76.4 1.0 OD2 A:ASP39 2.6 74.2 1.0 OE1 A:GLU55 2.7 86.7 1.0 CG A:ASP39 2.8 74.7 1.0 CD A:GLU55 2.9 77.0 1.0 C A:GLY44 3.4 86.2 1.0 C A:THR41 3.5 83.0 1.0 CB A:THR41 3.5 81.0 1.0 CA A:THR41 3.9 81.8 1.0 CA A:GLY45 4.1 89.4 1.0 N A:THR41 4.2 84.9 1.0 N A:GLY45 4.2 87.3 1.0 CZ A:PHE49 4.3 76.2 1.0 CB A:ASP39 4.3 73.0 1.0 N A:GLY44 4.3 87.2 1.0 OD1 A:ASN50 4.4 81.7 1.0 CG A:GLU55 4.4 76.6 1.0 CA A:GLY44 4.5 81.8 1.0 ND2 A:ASN50 4.5 73.3 1.0 N A:ILE42 4.7 81.3 1.0 CE1 A:PHE49 4.8 73.6 1.0 NE2 A:HIS61 4.8 80.8 1.0 OD2 A:ASP47 4.8 100.8 1.0 CG2 A:THR41 4.9 80.4 1.0 CG A:ASN50 4.9 73.4 1.0 OD1 A:ASP47 5.0 97.1 1.0

Calcium binding site 2 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:93.9 occ:1.00 O B:HOH654 2.2 65.7 1.0 OE1 B:GLU113 2.6 78.7 1.0 CD B:GLU113 3.4 76.1 1.0 OE2 B:GLU113 3.4 82.6 1.0 OE1 B:GLU110 4.7 46.8 1.0 CG B:GLU113 4.8 64.5 1.0 O B:HOH712 5.0 57.3 1.0

Calcium binding site 3 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:106.8 occ:1.00 O B:HOH732 2.3 84.1 1.0 OD2 B:ASP120 4.0 70.9 1.0 OD1 B:ASP120 4.2 68.0 1.0 O B:HOH662 4.3 65.8 1.0 OD2 B:ASP116 4.3 69.0 1.0 CB B:ASP116 4.4 53.2 1.0 CG B:ASP120 4.5 70.4 1.0 CG B:ASP116 4.6 55.4 1.0

Calcium binding site 4 out of 5 in the Tubulin - Maytansinoid - 6 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 - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.7 occ:1.00 O C:THR41 2.4 64.3 1.0 OG1 C:THR41 2.4 66.2 1.0 O C:GLY44 2.5 74.2 1.0 OD2 C:ASP39 2.5 55.7 1.0 OE2 C:GLU55 2.5 57.6 1.0 OE1 C:GLU55 2.5 59.1 1.0 OD1 C:ASP39 2.6 55.4 1.0 CD C:GLU55 2.8 61.6 1.0 CG C:ASP39 2.9 64.2 1.0 C C:THR41 3.4 70.8 1.0 CB C:THR41 3.5 69.3 1.0 C C:GLY44 3.6 78.0 1.0 CA C:THR41 3.9 67.4 1.0 O C:HOH609 4.1 64.0 1.0 OD2 C:ASP47 4.1 80.7 1.0 N C:THR41 4.2 72.4 1.0 CA C:GLY45 4.3 73.3 1.0 N C:GLY45 4.3 72.7 1.0 CG C:GLU55 4.3 53.8 1.0 CB C:ASP39 4.4 65.8 1.0 CZ C:PHE49 4.5 49.7 1.0 N C:ILE42 4.5 66.8 1.0 N C:GLY44 4.5 74.9 1.0 OD1 C:ASN50 4.6 58.1 1.0 CA C:GLY44 4.6 75.6 1.0 NE2 C:HIS61 4.7 51.6 1.0 CG2 C:THR41 4.8 59.9 1.0 CE1 C:PHE49 4.9 48.4 1.0 ND2 C:ASN50 5.0 48.4 1.0 CA C:ILE42 5.0 74.4 1.0

Calcium binding site 5 out of 5 in the Tubulin - Maytansinoid - 6 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin - Maytansinoid - 6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:106.9 occ:1.00 O A:HOH698 2.3 83.4 1.0 OD2 E:ASP44 3.1 105.1 1.0 O A:HOH645 3.4 75.9 1.0 O A:HOH705 3.9 73.1 1.0 O A:GLY162 4.1 75.8 1.0 CG E:ASP44 4.3 100.1 1.0 OG A:SER158 4.4 64.0 1.0 O A:GLU196 4.6 68.1 1.0 NZ A:LYS166 4.6 66.3 1.0 OD1 E:ASP44 4.7 88.8 1.0 CB A:SER158 4.7 62.4 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