Calcium in PDB 8bde: Tubulin-Baccatin III Complex

The structure of Tubulin-Baccatin III Complex, PDB code: 8bde was solved by A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muehlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.20 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.1, 157.15, 179.15, 90, 90, 90
R / Rfree (%)	19.2 / 21.8

The structure of Tubulin-Baccatin III Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Baccatin III Complex (pdb code 8bde). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-Baccatin III Complex, PDB code: 8bde:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:63.3 occ:1.00 O A:GLY44 2.3 75.7 1.0 OD2 A:ASP39 2.3 62.3 1.0 O A:THR41 2.4 79.0 1.0 O A:HOH638 2.5 50.9 1.0 OD1 A:ASP39 2.5 70.4 1.0 OE2 A:GLU55 2.5 54.2 1.0 OG1 A:THR41 2.6 62.5 1.0 OE1 A:GLU55 2.6 59.9 1.0 CG A:ASP39 2.7 62.7 1.0 CD A:GLU55 2.9 57.0 1.0 C A:THR41 3.4 81.6 1.0 C A:GLY44 3.4 79.0 1.0 CB A:THR41 3.6 72.0 1.0 CA A:THR41 3.9 77.0 1.0 N A:GLY44 4.2 79.9 1.0 N A:THR41 4.2 76.7 1.0 CB A:ASP39 4.2 66.9 1.0 N A:GLY45 4.3 86.2 1.0 CA A:GLY45 4.3 83.6 1.0 CA A:GLY44 4.4 82.2 1.0 CG A:GLU55 4.4 56.4 1.0 CZ A:PHE49 4.5 68.5 1.0 OD1 A:ASN50 4.5 56.1 1.0 N A:ILE42 4.6 80.0 1.0 OD2 A:ASP47 4.6 62.2 1.0 CE1 A:HIS61 4.7 61.9 1.0 CE1 A:PHE49 4.9 68.8 1.0 CG2 A:THR41 4.9 71.2 1.0 O A:HOH755 4.9 78.4 1.0 CA A:ILE42 4.9 80.2 1.0 N A:GLY43 4.9 75.7 1.0 ND2 A:ASN50 4.9 54.6 1.0

Calcium binding site 2 out of 2 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:51.7 occ:1.00 O C:GLY44 2.4 53.3 1.0 O C:THR41 2.4 49.0 1.0 O C:HOH619 2.5 44.2 1.0 OD2 C:ASP39 2.5 50.4 1.0 OG1 C:THR41 2.5 51.5 1.0 OE1 C:GLU55 2.5 47.1 1.0 OE2 C:GLU55 2.5 48.8 1.0 OD1 C:ASP39 2.6 48.0 1.0 CD C:GLU55 2.9 45.2 1.0 CG C:ASP39 2.9 51.1 1.0 CB C:THR41 3.4 57.9 1.0 C C:THR41 3.4 55.7 1.0 C C:GLY44 3.5 58.7 1.0 CA C:THR41 3.9 55.0 1.0 N C:THR41 4.2 50.9 1.0 CA C:GLY45 4.2 53.9 1.0 N C:GLY45 4.3 57.3 1.0 CG C:GLU55 4.4 40.1 1.0 CB C:ASP39 4.4 50.1 1.0 O C:HOH639 4.4 50.8 1.0 OD2 C:ASP47 4.4 53.9 1.0 N C:GLY44 4.4 53.3 1.0 CA C:GLY44 4.5 56.5 1.0 OD1 C:ASN50 4.6 46.6 1.0 CZ C:PHE49 4.6 39.5 1.0 NE2 C:HIS61 4.6 41.9 1.0 N C:ILE42 4.6 52.1 1.0 CG2 C:THR41 4.8 54.3 1.0 ND2 C:ASN50 4.8 38.6 1.0 CE1 C:PHE49 4.9 41.0 1.0 O C:HOH783 5.0 51.0 1.0

A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, F.Josa-Prado, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muhlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz. Structural Insight Into the Stabilization of Microtubules By Taxanes. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36876916
DOI: 10.7554/ELIFE.84791