Magnesium in PDB 6tiz: Drosophila Gdp-Tubulin Y222F Mutant

The structure of Drosophila Gdp-Tubulin Y222F Mutant, PDB code: 6tiz was solved by B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.176, 126.732, 250.364, 90, 90, 90
R / Rfree (%)	17.5 / 20.9

The binding sites of Magnesium atom in the Drosophila Gdp-Tubulin Y222F Mutant (pdb code 6tiz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Drosophila Gdp-Tubulin Y222F Mutant, PDB code: 6tiz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drosophila Gdp-Tubulin Y222F Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila Gdp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.6 occ:1.00 O A:HOH738 1.9 37.0 1.0 O A:HOH604 2.0 35.2 1.0 O A:HOH669 2.1 30.8 1.0 O1G A:GTP501 2.1 37.3 1.0 O A:HOH659 2.1 37.0 1.0 O1B A:GTP501 2.2 36.5 1.0 PG A:GTP501 3.2 37.0 1.0 PB A:GTP501 3.3 36.2 1.0 O3B A:GTP501 3.5 37.3 1.0 O3A A:GTP501 3.8 36.6 1.0 O2G A:GTP501 3.8 37.4 1.0 NZ B:LYS252 3.9 45.9 1.0 OE1 A:GLU71 4.0 54.3 1.0 CB A:GLN11 4.1 36.5 1.0 OD2 A:ASP69 4.1 37.1 1.0 OD1 A:ASP69 4.2 39.5 1.0 OD2 A:ASP98 4.2 42.2 1.0 N A:GLN11 4.4 34.2 1.0 O1A A:GTP501 4.5 37.0 1.0 O3G A:GTP501 4.5 36.0 1.0 CB A:ASP98 4.6 40.4 1.0 O2B A:GTP501 4.6 35.3 1.0 CG A:ASP69 4.6 39.2 1.0 PA A:GTP501 4.7 37.4 1.0 CG A:ASP98 4.7 41.1 1.0 O A:HOH601 4.8 49.5 1.0 CA A:GLN11 4.8 35.1 1.0 O B:HOH733 5.0 55.8 1.0

Magnesium binding site 2 out of 2 in the Drosophila Gdp-Tubulin Y222F Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila Gdp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.2 occ:1.00 O C:HOH692 2.0 44.0 1.0 O1G C:GTP501 2.0 42.7 1.0 O C:HOH626 2.0 38.6 1.0 O C:HOH640 2.1 40.3 1.0 O1B C:GTP501 2.1 43.8 1.0 O C:HOH623 2.1 42.3 1.0 PG C:GTP501 3.1 42.4 1.0 PB C:GTP501 3.2 43.9 1.0 O3B C:GTP501 3.4 43.5 1.0 O2G C:GTP501 3.6 41.8 1.0 O3A C:GTP501 3.7 46.0 1.0 NZ D:LYS252 3.8 46.6 1.0 OD1 C:ASP69 4.2 46.2 1.0 OE2 C:GLU71 4.2 75.1 1.0 OD2 C:ASP69 4.2 48.1 1.0 CB C:GLN11 4.2 45.1 1.0 OD2 C:ASP98 4.2 46.5 1.0 O3G C:GTP501 4.4 41.5 1.0 N C:GLN11 4.4 43.6 1.0 CB C:ASP98 4.5 46.1 1.0 O1A C:GTP501 4.5 48.5 1.0 O2B C:GTP501 4.5 44.2 1.0 CD C:GLU71 4.6 73.0 1.0 CG C:ASP69 4.6 46.3 1.0 CG C:ASP98 4.7 46.9 1.0 PA C:GTP501 4.7 48.0 1.0 OE1 C:GLU71 4.8 78.2 1.0 CA C:GLN11 4.9 43.5 1.0 CE D:LYS252 5.0 45.1 1.0

R.Ayukawa, S.Iwata, H.Imai, S.Kamimura, M.Hayashi, K.X.Ngo, I.Minoura, S.Uchimura, T.Makino, M.Shirouzu, H.Shigematsu, K.Sekimoto, B.Gigant, E.Muto. Gtp-Dependent Formation of Straight Tubulin Oligomers Leads to Microtubule Nucleation J.Cell Biol. 2021.
ISSN: ESSN 1540-8140
DOI: 10.1083/JCB.202007033