Calcium in PDB 5iyz: Tubulin-Mmae Complex

The structure of Tubulin-Mmae Complex, PDB code: 5iyz was solved by A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.96 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.510, 156.610, 182.420, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.2

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

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Mmae Complex (pdb code 5iyz). 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-Mmae Complex, PDB code: 5iyz:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:67.9 occ:1.00 OE1 A:GLU55 2.6 69.1 1.0 OE2 A:GLU55 2.6 65.5 1.0 OD2 A:ASP39 2.6 81.0 1.0 O A:THR41 2.7 84.1 1.0 OD1 A:ASP39 2.7 75.8 1.0 OG1 A:THR41 2.8 73.7 1.0 CD A:GLU55 2.9 80.5 1.0 O A:GLY44 2.9 94.5 1.0 CG A:ASP39 3.1 73.1 1.0 CB A:THR41 3.2 80.9 1.0 C A:GLY44 3.3 75.0 1.0 C A:THR41 3.5 84.7 1.0 CA A:GLY45 3.5 85.4 1.0 N A:GLY45 3.6 83.2 1.0 CA A:THR41 3.9 86.1 1.0 N A:GLY44 4.1 89.0 1.0 CA A:GLY44 4.2 87.3 1.0 CG A:GLU55 4.3 80.2 1.0 N A:THR41 4.5 80.5 1.0 N A:ILE42 4.5 84.0 1.0 CB A:ASP39 4.6 70.5 1.0 CG2 A:THR41 4.6 77.7 1.0 OD1 A:ASN50 4.6 62.8 1.0 O A:HOH807 4.7 70.9 1.0 OD2 A:ASP47 4.7 72.9 1.0 CZ A:PHE49 4.7 78.8 1.0 NE2 A:HIS61 4.9 72.3 1.0 ND2 A:ASN50 4.9 62.9 1.0 N A:GLY43 4.9 77.4 1.0 C A:GLY45 4.9 81.7 1.0 CA A:ILE42 5.0 86.7 1.0

Calcium binding site 2 out of 2 in the Tubulin-Mmae Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:86.0 occ:1.00 O C:THR41 2.4 44.0 1.0 OD2 C:ASP39 2.5 40.2 1.0 O C:HOH645 2.5 38.1 1.0 O C:GLY44 2.5 48.4 1.0 OG1 C:THR41 2.5 49.8 1.0 OD1 C:ASP39 2.6 49.7 1.0 OE1 C:GLU55 2.7 50.0 1.0 OE2 C:GLU55 2.7 44.6 1.0 CG C:ASP39 2.9 45.8 1.0 CD C:GLU55 3.0 49.4 1.0 C C:THR41 3.4 56.0 1.0 CB C:THR41 3.5 51.7 1.0 C C:GLY44 3.7 65.5 1.0 CA C:THR41 3.9 60.5 1.0 N C:THR41 4.1 58.8 1.0 CB C:ASP39 4.4 49.0 1.0 CA C:GLY45 4.4 63.8 1.0 O C:HOH629 4.4 65.4 1.0 N C:GLY45 4.4 65.3 1.0 N C:GLY44 4.5 62.5 1.0 O C:HOH738 4.5 44.5 1.0 CZ C:PHE49 4.5 40.3 1.0 CG C:GLU55 4.5 46.6 1.0 NE2 C:HIS61 4.6 39.3 1.0 N C:ILE42 4.6 54.8 1.0 CA C:GLY44 4.6 65.7 1.0 OD2 C:ASP47 4.7 56.0 1.0 OD1 C:ASN50 4.7 39.7 1.0 CG2 C:THR41 4.8 54.3 1.0 CE1 C:PHE49 4.8 43.4 1.0 O C:HOH792 4.9 55.8 1.0 O C:HOH831 5.0 62.7 1.0 ND2 C:ASN50 5.0 39.8 1.0

A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota. Structural Basis of Microtubule Destabilization By Potent Auristatin Anti-Mitotics. Plos One V. 11 60890 2016.
ISSN: ESSN 1932-6203
PubMed: 27518442
DOI: 10.1371/JOURNAL.PONE.0160890