Magnesium 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:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Pironetin Complex (pdb code 5la6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tubulin-Pironetin Complex, PDB code: 5la6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.6 occ:1.00 O1G A:GTP501 2.0 39.3 1.0 O A:HOH617 2.0 48.5 1.0 O A:HOH631 2.1 46.7 1.0 O A:HOH625 2.2 48.9 1.0 O A:HOH657 2.2 51.7 1.0 O1B A:GTP501 2.2 43.9 1.0 PG A:GTP501 3.1 50.6 1.0 PB A:GTP501 3.3 51.2 1.0 O3B A:GTP501 3.6 66.1 1.0 O2G A:GTP501 3.6 45.5 1.0 NZ B:LYS254 3.8 50.5 1.0 O3A A:GTP501 3.9 54.3 1.0 OD1 A:ASP69 4.0 54.5 1.0 OE1 A:GLU71 4.0 70.4 1.0 CG A:GLU71 4.2 68.6 1.0 OD2 A:ASP98 4.2 60.2 1.0 OD2 A:ASP69 4.2 56.1 1.0 CB A:GLN11 4.2 46.9 1.0 CB A:ASP98 4.3 53.1 1.0 O3G A:GTP501 4.4 41.0 1.0 N A:GLN11 4.4 51.7 1.0 CG A:ASP69 4.6 60.4 1.0 CG A:ASP98 4.6 54.4 1.0 O2B A:GTP501 4.6 51.8 1.0 CD A:GLU71 4.6 70.6 1.0 O1A A:GTP501 4.7 48.8 1.0 PA A:GTP501 4.9 52.5 1.0 OE1 A:GLN11 4.9 66.2 1.0 CE B:LYS254 4.9 48.8 1.0 CA A:GLN11 4.9 49.8 1.0 OG1 A:THR145 5.0 53.5 1.0

Magnesium binding site 2 out of 3 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:67.5 occ:1.00 O B:HOH613 2.1 56.6 1.0 OE1 B:GLN11 2.1 81.2 1.0 O B:HOH637 2.2 57.9 1.0 O1A B:GDP501 2.5 56.2 1.0 O B:HOH631 2.8 55.7 1.0 CD B:GLN11 3.3 76.5 1.0 PA B:GDP501 3.7 50.4 1.0 OD2 B:ASP179 3.8 83.2 1.0 CB B:GLN11 3.8 53.0 1.0 O3A B:GDP501 3.9 58.3 1.0 CG B:GLN11 4.1 57.6 1.0 NE2 B:GLN11 4.3 89.4 1.0 O1B B:GDP501 4.5 43.7 1.0 OD1 B:ASN101 4.6 73.4 1.0 O5' B:GDP501 4.6 49.6 1.0 C5' B:GDP501 4.6 52.5 1.0 O2A B:GDP501 4.8 45.8 1.0 CG B:ASP179 4.8 81.3 1.0 PB B:GDP501 4.9 50.0 1.0 C8 B:GDP501 5.0 49.5 1.0

Magnesium binding site 3 out of 3 in the Tubulin-Pironetin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Pironetin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:59.0 occ:1.00 O1G C:GTP501 1.9 37.4 1.0 O C:HOH620 2.1 48.4 1.0 O1B C:GTP501 2.1 45.0 1.0 O C:HOH627 2.1 41.1 1.0 O C:HOH679 2.1 40.6 1.0 O C:HOH709 2.2 43.8 1.0 PG C:GTP501 3.1 49.9 1.0 PB C:GTP501 3.2 42.9 1.0 O2G C:GTP501 3.5 46.6 1.0 O3B C:GTP501 3.5 51.4 1.0 O3A C:GTP501 3.8 51.6 1.0 NZ D:LYS254 3.9 49.9 1.0 OD1 C:ASP69 4.0 51.8 1.0 OE1 C:GLU71 4.1 59.8 1.0 OD2 C:ASP69 4.2 48.4 1.0 OD2 C:ASP98 4.3 60.5 1.0 CB C:GLN11 4.3 42.7 1.0 CG C:GLU71 4.3 56.6 1.0 O3G C:GTP501 4.4 40.8 1.0 CB C:ASP98 4.4 45.3 1.0 O C:HOH676 4.4 56.6 1.0 N C:GLN11 4.4 40.6 1.0 O2B C:GTP501 4.4 45.6 1.0 CG C:ASP69 4.5 49.5 1.0 O1A C:GTP501 4.6 45.9 1.0 CG C:ASP98 4.7 48.4 1.0 CD C:GLU71 4.8 64.4 1.0 PA C:GTP501 4.8 47.3 1.0 OE1 C:GLN11 5.0 48.5 1.0 CA C:GLN11 5.0 42.1 1.0 OG1 C:THR145 5.0 44.0 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