Magnesium in PDB 6tiu: Drosophila Gtp-Tubulin Y222F Mutant

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

Resolution Low / High (Å)	48.00 / 3.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.97, 126.35, 249.79, 90, 90, 90
R / Rfree (%)	22.1 / 24.4

The binding sites of Magnesium atom in the Drosophila Gtp-Tubulin Y222F Mutant (pdb code 6tiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Drosophila Gtp-Tubulin Y222F Mutant, PDB code: 6tiu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Drosophila Gtp-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 Gtp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:95.4 occ:1.00 O1G A:GTP501 2.1 89.1 1.0 O1B A:GTP501 2.3 83.0 1.0 PG A:GTP501 3.2 87.7 1.0 OE1 A:GLU71 3.4 98.0 1.0 PB A:GTP501 3.4 81.9 1.0 O3B A:GTP501 3.7 87.7 1.0 OD2 A:ASP69 3.7 86.5 1.0 O2G A:GTP501 3.8 90.7 1.0 OD1 A:ASP69 3.9 88.3 1.0 O3A A:GTP501 4.0 82.4 1.0 NZ B:LYS252 4.1 106.8 1.0 CB A:GLN11 4.1 80.2 1.0 OD2 A:ASP98 4.1 90.8 1.0 CG A:ASP69 4.2 88.9 1.0 N A:GLN11 4.4 79.3 1.0 NE2 A:GLN11 4.5 98.1 1.0 CB A:ASP98 4.5 91.7 1.0 O3G A:GTP501 4.6 83.9 1.0 CD A:GLU71 4.6 112.9 1.0 O1A A:GTP501 4.8 84.5 1.0 CG A:ASP98 4.8 92.1 1.0 O2B A:GTP501 4.8 80.2 1.0 CB A:GLU71 4.8 99.3 1.0 CA A:GLN11 4.9 79.4 1.0

Magnesium binding site 2 out of 4 in the Drosophila Gtp-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 Gtp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:80.9 occ:0.50 O1B B:GTP501 2.8 81.9 0.5 CB B:GLN11 3.0 94.3 1.0 O1G B:GTP501 3.4 87.7 0.5 OG1 B:THR72 3.5 128.2 1.0 O2G B:GTP501 3.8 89.0 0.5 CG B:GLN11 3.9 117.2 1.0 CA B:GLN11 3.9 91.8 1.0 N B:GLN11 4.0 90.6 1.0 O2A B:GDP503 4.0 70.1 0.5 OE1 B:GLN11 4.1 131.8 1.0 PG B:GTP501 4.1 86.1 0.5 OD2 B:ASP67 4.1 109.3 1.0 PB B:GTP501 4.2 80.7 0.5 OE1 B:GLU69 4.2 118.1 1.0 CD B:GLN11 4.5 137.2 1.0 O3B B:GTP501 4.5 86.2 0.5 CB B:THR72 4.9 127.6 1.0 O1A B:GDP503 4.9 72.0 0.5 OD1 B:ASP67 4.9 103.2 1.0 PA B:GDP503 4.9 70.5 0.5 O3A B:GTP501 4.9 81.3 0.5 O1A B:GTP501 4.9 83.8 0.5 CG B:ASP67 5.0 105.0 1.0

Magnesium binding site 3 out of 4 in the Drosophila Gtp-Tubulin Y222F Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Drosophila Gtp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:94.2 occ:1.00 O1G C:GTP600 2.1 90.4 1.0 O1B C:GTP600 2.3 89.3 1.0 PG C:GTP600 3.2 88.1 1.0 OE2 C:GLU71 3.4 141.8 1.0 PB C:GTP600 3.5 86.8 1.0 OD2 C:ASP69 3.6 93.7 1.0 O3B C:GTP600 3.6 89.2 1.0 O2G C:GTP600 3.6 86.0 1.0 OD1 C:ASP69 3.7 90.0 1.0 CD C:GLU71 3.7 132.2 1.0 OE1 C:GLU71 3.8 133.3 1.0 OD2 C:ASP98 4.1 91.3 1.0 O3A C:GTP600 4.1 92.5 1.0 CG C:ASP69 4.1 90.5 1.0 NZ D:LYS252 4.1 99.2 1.0 CB C:GLN11 4.3 90.0 1.0 CB C:ASP98 4.3 91.1 1.0 N C:GLN11 4.5 88.3 1.0 O3G C:GTP600 4.6 85.4 1.0 CB C:GLU71 4.6 99.7 1.0 CG C:ASP98 4.6 91.6 1.0 NE2 C:GLN11 4.7 94.8 1.0 CG C:GLU71 4.8 109.2 1.0 O2B C:GTP600 4.8 88.7 1.0 CA C:GLN11 4.9 88.5 1.0 OG1 C:THR145 5.0 85.8 1.0 O1A C:GTP600 5.0 100.0 1.0

Magnesium binding site 4 out of 4 in the Drosophila Gtp-Tubulin Y222F Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Drosophila Gtp-Tubulin Y222F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:80.9 occ:1.00 O1B D:GTP501 2.8 85.3 1.0 CB D:GLN11 2.8 95.8 1.0 O1G D:GTP501 3.2 91.2 1.0 N D:GLN11 3.5 92.8 1.0 CA D:GLN11 3.6 94.1 1.0 OE1 D:GLN11 3.7 137.2 1.0 O2G D:GTP501 3.7 92.2 1.0 PG D:GTP501 3.9 89.5 1.0 CG D:GLN11 3.9 119.1 1.0 PB D:GTP501 3.9 84.0 1.0 OG1 D:THR72 4.0 119.4 1.0 OD2 D:ASP67 4.2 102.4 1.0 O3A D:GTP501 4.2 84.7 1.0 O1A D:GTP501 4.2 87.5 1.0 CD D:GLN11 4.2 139.0 1.0 O3B D:GTP501 4.3 89.5 1.0 OD1 D:ASP67 4.4 98.5 1.0 C D:GLY10 4.6 94.0 1.0 OE1 D:GLU69 4.6 143.7 1.0 CG D:ASP67 4.7 100.1 1.0 PA D:GTP501 4.8 87.5 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