Calcium in PDB 8b7a: Tubulin - Maytansinoid - 4 Complex

The structure of Tubulin - Maytansinoid - 4 Complex, PDB code: 8b7a 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, F.J.Diaz, M.O.Steinmetz, A.E.Prota, S.Piaraccini, D.Passarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.15 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.271, 158.55, 181.846, 90, 90, 90
R / Rfree (%)	18.1 / 22.3

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

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Tubulin - Maytansinoid - 4 Complex (pdb code 8b7a). 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 - 4 Complex, PDB code: 8b7a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:75.8 occ:1.00 O A:GLY44 2.4 97.6 1.0 O A:THR41 2.4 91.8 1.0 OD1 A:ASP39 2.4 83.8 1.0 OD2 A:ASP39 2.4 83.8 1.0 OE2 A:GLU55 2.5 79.6 1.0 OE1 A:GLU55 2.6 85.5 1.0 OG1 A:THR41 2.7 81.5 1.0 O A:HOH631 2.7 80.7 1.0 CG A:ASP39 2.7 86.4 1.0 CD A:GLU55 2.9 80.9 1.0 C A:THR41 3.4 95.7 1.0 CB A:THR41 3.4 92.1 1.0 C A:GLY44 3.5 101.2 1.0 CA A:THR41 3.8 91.3 1.0 N A:THR41 4.1 95.8 1.0 CB A:ASP39 4.3 84.7 1.0 N A:GLY44 4.3 101.3 1.0 CA A:GLY45 4.3 106.5 1.0 N A:GLY45 4.3 108.1 1.0 CZ A:PHE49 4.4 79.7 1.0 CG A:GLU55 4.4 82.1 1.0 CA A:GLY44 4.5 102.5 1.0 N A:ILE42 4.6 93.5 1.0 OD1 A:ASN50 4.6 68.9 1.0 NE2 A:HIS61 4.7 80.0 1.0 ND2 A:ASN50 4.8 73.4 1.0 CG2 A:THR41 4.8 86.8 1.0 OD2 A:ASP47 4.9 99.2 1.0 CE1 A:PHE49 5.0 82.0 1.0

Calcium binding site 2 out of 5 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:109.0 occ:1.00 O B:HOH662 2.5 75.9 1.0 OE1 B:GLU113 2.7 91.5 1.0 OE2 B:GLU113 3.1 94.4 1.0 CD B:GLU113 3.2 90.2 1.0 CG B:GLU113 4.7 74.1 1.0

Calcium binding site 3 out of 5 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:112.8 occ:1.00 OD2 B:ASP120 3.4 70.2 1.0 OD1 B:ASP120 3.8 73.6 1.0 CG B:ASP120 4.0 75.1 1.0 CB B:ASP116 4.6 56.3 1.0 O B:ASP116 4.8 65.0 1.0 OD2 B:ASP116 4.9 79.7 1.0

Calcium binding site 4 out of 5 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:62.6 occ:1.00 OE2 C:GLU55 2.4 66.4 1.0 O C:THR41 2.4 79.4 1.0 O C:HOH628 2.5 54.4 1.0 O C:GLY44 2.5 66.1 1.0 OD2 C:ASP39 2.5 66.2 1.0 OG1 C:THR41 2.5 74.6 1.0 OE1 C:GLU55 2.6 56.2 1.0 OD1 C:ASP39 2.6 63.5 1.0 CD C:GLU55 2.8 60.3 1.0 CG C:ASP39 2.9 67.5 1.0 C C:THR41 3.4 77.2 1.0 C C:GLY44 3.4 74.4 1.0 CB C:THR41 3.5 67.2 1.0 CA C:THR41 3.9 71.3 1.0 N C:GLY45 4.2 73.7 1.0 CA C:GLY45 4.2 66.0 1.0 N C:THR41 4.3 65.9 1.0 O C:HOH624 4.3 67.8 1.0 CG C:GLU55 4.3 54.7 1.0 N C:GLY44 4.3 79.0 1.0 O C:HOH631 4.3 79.7 1.0 CA C:GLY44 4.4 76.8 1.0 CB C:ASP39 4.4 71.0 1.0 OD2 C:ASP47 4.5 76.8 1.0 N C:ILE42 4.6 75.2 1.0 OD1 C:ASN50 4.6 54.6 1.0 NE2 C:HIS61 4.6 51.1 1.0 CZ C:PHE49 4.8 49.1 1.0 CG2 C:THR41 4.9 63.0 1.0 ND2 C:ASN50 4.9 53.5 1.0 CE1 C:PHE49 4.9 44.5 1.0

Calcium binding site 5 out of 5 in the Tubulin - Maytansinoid - 4 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 - 4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:112.2 occ:1.00 O A:HOH720 2.7 73.6 1.0 OD2 E:ASP44 3.1 99.2 1.0 O A:HOH717 3.3 70.9 1.0 CG E:ASP44 4.0 99.5 1.0 OD1 E:ASP44 4.1 92.3 1.0 MG A:MG505 4.2 95.4 1.0 O A:GLU196 4.3 70.5 1.0 OG A:SER158 4.3 69.7 1.0 O A:GLY162 4.5 78.0 1.0 CB A:SER158 4.7 61.1 1.0 NZ A:LYS166 4.7 62.2 1.0 OD1 A:ASP199 5.0 60.3 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