Calcium in PDB 5la6: Tubulin-Pironetin Complex

The structure of Tubulin-Pironetin Complex, PDB code: 5la6 was solved by A.E.Prota, J.Setter, A.B.Waight, K.Bargsten, J.Murga, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.680, 157.200, 180.990, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.1

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

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Tubulin-Pironetin Complex (pdb code 5la6). 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-Pironetin Complex, PDB code: 5la6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:88.6 occ:1.00 O A:GLY44 2.3 0.8 1.0 OE2 A:GLU55 2.5 84.3 1.0 OD1 A:ASP39 2.5 95.6 1.0 O A:THR41 2.5 0.9 1.0 OD2 A:ASP39 2.7 98.1 1.0 OG1 A:THR41 2.7 92.5 1.0 OE1 A:GLU55 2.8 86.2 1.0 CG A:ASP39 2.9 93.3 1.0 CD A:GLU55 3.0 89.5 1.0 CB A:THR41 3.3 0.1 1.0 C A:GLY44 3.5 0.4 1.0 C A:THR41 3.5 0.9 1.0 CA A:THR41 3.9 0.6 1.0 CA A:GLY45 4.1 0.6 1.0 N A:THR41 4.2 0.6 1.0 N A:GLY45 4.2 0.0 1.0 CZ A:PHE49 4.3 89.7 1.0 OD1 A:ASN50 4.4 93.2 1.0 CB A:ASP39 4.4 91.5 1.0 CA A:GLY44 4.5 0.9 1.0 CG A:GLU55 4.5 87.8 1.0 OD1 A:ASP47 4.5 0.7 1.0 N A:GLY44 4.6 0.6 1.0 ND2 A:ASN50 4.6 84.1 1.0 CG2 A:THR41 4.7 0.1 1.0 N A:ILE42 4.7 0.2 1.0 CE2 A:PHE49 4.9 84.4 1.0 C A:GLY45 4.9 0.3 1.0 NE2 A:HIS61 4.9 86.6 1.0 CG A:ASN50 4.9 83.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.2 occ:1.00 O A:HOH664 2.4 71.8 1.0 O A:HOH658 2.7 65.8 1.0 O A:HOH650 3.5 69.3 1.0 OD2 E:ASP44 3.6 0.8 1.0 O A:GLU196 3.8 69.4 1.0 OD1 E:ASP44 4.3 0.5 1.0 CG E:ASP44 4.4 0.9 1.0 OD1 A:ASP199 4.6 76.0 1.0 OG A:SER158 4.7 61.9 1.0 NZ A:LYS166 4.8 69.7 1.0 CA A:HIS197 4.9 63.8 1.0 O A:HIS197 4.9 68.9 1.0 C A:GLU196 5.0 66.0 1.0

Calcium binding site 3 out of 4 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.5 occ:1.00 O B:HOH604 2.4 65.3 1.0 OE2 B:GLU113 2.9 97.4 1.0 OE1 B:GLU113 3.7 88.4 1.0 CD B:GLU113 3.7 89.6 1.0 OE1 B:GLU110 4.5 71.7 1.0 OG B:SER97 4.8 0.6 1.0

Calcium binding site 4 out of 4 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:72.8 occ:1.00 O C:THR41 2.4 73.1 1.0 O C:GLY44 2.4 85.8 1.0 OD2 C:ASP39 2.5 64.6 1.0 OG1 C:THR41 2.5 71.5 1.0 O C:HOH606 2.5 61.8 1.0 OD1 C:ASP39 2.6 69.2 1.0 OE1 C:GLU55 2.6 60.2 1.0 OE2 C:GLU55 2.7 72.3 1.0 CG C:ASP39 2.9 69.3 1.0 CD C:GLU55 3.0 63.9 1.0 C C:GLY44 3.4 84.7 1.0 C C:THR41 3.4 75.9 1.0 CB C:THR41 3.4 72.6 1.0 CA C:THR41 3.8 76.6 1.0 CA C:GLY45 4.1 81.0 1.0 N C:GLY45 4.1 81.5 1.0 N C:THR41 4.1 75.5 1.0 OD2 C:ASP47 4.3 83.5 1.0 O C:HOH622 4.3 65.2 1.0 CA C:GLY44 4.4 86.1 1.0 N C:GLY44 4.4 91.8 1.0 CB C:ASP39 4.4 71.5 1.0 CG C:GLU55 4.5 59.2 1.0 N C:ILE42 4.6 81.9 1.0 CZ C:PHE49 4.6 60.8 1.0 NE2 C:HIS61 4.7 56.1 1.0 OD1 C:ASN50 4.7 61.5 1.0 CG2 C:THR41 4.8 64.3 1.0 O C:HOH735 4.9 66.6 1.0 ND2 C:ASN50 5.0 57.0 1.0 CE1 C:PHE49 5.0 62.7 1.0

A.E.Prota, J.Setter, A.B.Waight, K.Bargsten, J.Murga, J.F.Diaz, M.O.Steinmetz. Pironetin Binds Covalently to Alpha CYS316 and Perturbs A Major Loop and Helix of Alpha-Tubulin to Inhibit Microtubule Formation. J.Mol.Biol. V. 428 2981 2016.
ISSN: ESSN 1089-8638
PubMed: 27395016
DOI: 10.1016/J.JMB.2016.06.023