Calcium in PDB 5sbc: Tubulin-Maytansinoid-5A-Complex

The structure of Tubulin-Maytansinoid-5A-Complex, PDB code: 5sbc 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)	48.02 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.911, 157.908, 181.461, 90, 90, 90
R / Rfree (%)	18.6 / 22.8

The structure of Tubulin-Maytansinoid-5A-Complex also contains other interesting chemical elements:

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

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

Calcium binding site 1 out of 4 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:75.3 occ:1.00 O A:GLY44 2.4 88.6 1.0 O A:THR41 2.4 83.1 1.0 OE2 A:GLU55 2.4 72.1 1.0 OG1 A:THR41 2.5 82.4 1.0 O A:HOH656 2.5 82.0 1.0 OD1 A:ASP39 2.5 76.5 1.0 OE1 A:GLU55 2.6 95.4 1.0 OD2 A:ASP39 2.6 79.2 1.0 CD A:GLU55 2.8 82.2 1.0 CG A:ASP39 2.9 83.1 1.0 C A:THR41 3.4 91.7 1.0 CB A:THR41 3.5 87.5 1.0 C A:GLY44 3.5 86.1 1.0 CA A:THR41 3.9 87.3 1.0 N A:THR41 4.2 89.8 1.0 CZ A:PHE49 4.2 67.8 1.0 CA A:GLY45 4.3 91.8 1.0 N A:GLY45 4.3 93.9 1.0 CG A:GLU55 4.3 81.9 1.0 N A:GLY44 4.4 93.1 1.0 CB A:ASP39 4.4 80.1 1.0 CA A:GLY44 4.5 91.1 1.0 O A:HOH690 4.5 75.2 1.0 OD1 A:ASN50 4.6 77.0 1.0 N A:ILE42 4.6 86.3 1.0 ND2 A:ASN50 4.7 70.9 1.0 NE2 A:HIS61 4.7 79.1 1.0 CG2 A:THR41 4.8 83.3 1.0 CE1 A:PHE49 4.8 65.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:99.7 occ:1.00 OE1 B:GLU113 2.8 98.1 1.0 CD B:GLU113 3.7 81.6 1.0 OE2 B:GLU113 3.8 90.3 1.0 OE1 B:GLU110 4.4 57.5 1.0 OE2 B:GLU110 4.9 78.8 1.0

Calcium binding site 3 out of 4 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:62.3 occ:1.00 O C:THR41 2.4 72.9 1.0 O C:HOH615 2.4 48.7 1.0 OE2 C:GLU55 2.4 62.3 1.0 OG1 C:THR41 2.5 59.2 1.0 OE1 C:GLU55 2.5 52.9 1.0 O C:GLY44 2.5 64.7 1.0 OD2 C:ASP39 2.6 61.4 1.0 OD1 C:ASP39 2.7 69.6 1.0 CD C:GLU55 2.8 59.7 1.0 CG C:ASP39 3.0 58.3 1.0 C C:THR41 3.4 71.8 1.0 C C:GLY44 3.4 72.1 1.0 CB C:THR41 3.4 64.4 1.0 CA C:THR41 3.8 63.5 1.0 O C:HOH602 4.0 56.2 1.0 N C:GLY45 4.2 72.7 1.0 N C:THR41 4.2 59.8 1.0 CA C:GLY45 4.2 60.8 1.0 N C:GLY44 4.2 72.5 1.0 CG C:GLU55 4.3 56.0 1.0 CA C:GLY44 4.3 68.9 1.0 OD2 C:ASP47 4.3 75.5 1.0 CB C:ASP39 4.5 65.8 1.0 N C:ILE42 4.5 71.7 1.0 OD1 C:ASN50 4.6 51.9 1.0 CZ C:PHE49 4.8 46.3 1.0 CG2 C:THR41 4.8 55.4 1.0 NE2 C:HIS61 4.8 51.8 1.0 CE1 C:PHE49 4.9 52.3 1.0 ND2 C:ASN50 4.9 55.1 1.0 CA C:ILE42 5.0 65.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Maytansinoid-5A-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-5A-Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:99.2 occ:1.00 OD2 E:ASP44 3.0 103.2 1.0 O A:HOH693 3.0 64.1 1.0 O A:HOH702 3.0 66.3 1.0 OG A:SER158 4.0 65.6 1.0 CG E:ASP44 4.1 106.4 1.0 O A:GLY162 4.2 75.0 1.0 CB A:SER158 4.3 61.7 1.0 OD1 E:ASP44 4.4 102.7 1.0 O A:HOH721 4.6 62.9 1.0 NZ A:LYS166 4.6 60.3 1.0 O A:GLU196 4.6 76.1 1.0 CA A:SER158 5.0 68.0 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