Magnesium in PDB 6tiy: Drosophila Gmpcpp-Tubulin

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

Resolution Low / High (Å)	33.00 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.669, 126.564, 251.012, 90, 90, 90
R / Rfree (%)	18.7 / 21.7

The binding sites of Magnesium atom in the Drosophila Gmpcpp-Tubulin (pdb code 6tiy). 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 Gmpcpp-Tubulin, PDB code: 6tiy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Drosophila Gmpcpp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila Gmpcpp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:52.1 occ:1.00 O A:HOH698 1.9 44.2 1.0 O A:HOH616 1.9 51.8 1.0 O A:HOH656 2.0 44.0 1.0 O1G A:GTP501 2.2 46.8 1.0 O A:HOH662 2.2 46.1 1.0 O1B A:GTP501 2.2 47.6 1.0 PB A:GTP501 3.3 47.1 1.0 PG A:GTP501 3.3 46.3 1.0 O3B A:GTP501 3.6 47.1 1.0 O3A A:GTP501 3.8 46.9 1.0 O2G A:GTP501 3.8 45.7 1.0 OE1 A:GLU71 4.0 69.2 1.0 NZ B:LYS252 4.0 61.4 1.0 CB A:GLN11 4.1 46.2 1.0 OD2 A:ASP98 4.2 56.9 1.0 OD1 A:ASP69 4.2 50.4 1.0 OD2 A:ASP69 4.2 51.4 1.0 N A:GLN11 4.4 43.8 1.0 O1A A:GTP501 4.5 47.8 1.0 O A:HOH658 4.6 69.5 1.0 O2B A:GTP501 4.6 47.1 1.0 CB A:ASP98 4.6 53.0 1.0 O3G A:GTP501 4.6 46.0 1.0 CG A:ASP69 4.6 51.2 1.0 PA A:GTP501 4.7 47.4 1.0 CG A:ASP98 4.7 54.9 1.0 CA A:GLN11 4.9 44.8 1.0 NE2 A:GLN11 4.9 57.4 1.0

Magnesium binding site 2 out of 4 in the Drosophila Gmpcpp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila Gmpcpp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:68.7 occ:1.00 O B:HOH614 1.9 59.5 1.0 O B:HOH631 2.1 49.5 1.0 O B:HOH668 2.2 56.7 1.0 O B:HOH679 2.2 58.5 1.0 O1G B:G2P501 2.3 56.1 1.0 O2B B:G2P501 2.3 55.5 1.0 PB B:G2P501 3.4 55.5 1.0 PG B:G2P501 3.4 56.1 1.0 O3B B:G2P501 3.6 56.0 1.0 O B:HOH675 4.0 56.1 1.0 O2G B:G2P501 4.0 55.9 1.0 CB B:GLN11 4.1 56.4 1.0 N B:GLN11 4.2 51.4 1.0 O2A B:G2P501 4.2 57.3 1.0 OD1 B:ASP67 4.2 61.2 1.0 OD2 B:ASP67 4.2 61.8 1.0 C3A B:G2P501 4.3 56.1 1.0 OE1 B:GLU69 4.6 85.1 1.0 O3G B:G2P501 4.6 56.3 1.0 CG B:ASP67 4.7 60.1 1.0 O1B B:G2P501 4.7 56.0 1.0 CA B:GLN11 4.7 52.5 1.0 PA B:G2P501 4.8 56.7 1.0 OG1 B:THR72 4.9 78.4 1.0 OG1 B:THR143 5.0 47.9 1.0

Magnesium binding site 3 out of 4 in the Drosophila Gmpcpp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Drosophila Gmpcpp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.2 occ:1.00 O C:HOH624 2.0 49.3 1.0 O1G C:GTP501 2.1 53.1 1.0 O C:HOH627 2.1 51.7 1.0 O1B C:GTP501 2.1 56.3 1.0 O C:HOH634 2.1 44.3 1.0 O C:HOH668 2.2 46.6 1.0 PG C:GTP501 3.1 53.1 1.0 PB C:GTP501 3.2 56.5 1.0 O3B C:GTP501 3.4 54.9 1.0 O2G C:GTP501 3.6 52.8 1.0 O3A C:GTP501 3.7 59.9 1.0 NZ D:LYS252 3.9 61.8 1.0 OD1 C:ASP69 4.1 55.3 1.0 OD2 C:ASP98 4.2 58.5 1.0 OD2 C:ASP69 4.2 56.3 1.0 CB C:GLN11 4.3 55.7 1.0 OE2 C:GLU71 4.3 84.5 1.0 CB C:ASP98 4.4 55.8 1.0 O3G C:GTP501 4.4 52.1 1.0 N C:GLN11 4.5 53.6 1.0 O2B C:GTP501 4.5 56.9 1.0 O1A C:GTP501 4.6 62.8 1.0 OE1 C:GLU71 4.6 82.6 1.0 CG C:ASP69 4.6 55.2 1.0 CD C:GLU71 4.6 79.9 1.0 CG C:ASP98 4.7 57.8 1.0 PA C:GTP501 4.8 62.8 1.0 OG1 C:THR145 4.9 49.8 1.0 CA C:GLN11 5.0 54.2 1.0

Magnesium binding site 4 out of 4 in the Drosophila Gmpcpp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Drosophila Gmpcpp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:58.7 occ:1.00 O D:HOH665 2.0 49.5 1.0 O1G D:G2P501 2.1 55.1 1.0 O D:HOH655 2.1 72.5 1.0 O D:HOH677 2.2 62.8 1.0 O D:HOH603 2.2 48.1 1.0 O2B D:G2P501 2.3 51.0 1.0 PG D:G2P501 3.0 54.9 1.0 PB D:G2P501 3.2 51.0 1.0 O2G D:G2P501 3.3 55.7 1.0 O3B D:G2P501 3.4 53.2 1.0 O D:HOH604 3.8 69.4 1.0 C3A D:G2P501 3.9 50.2 1.0 CB D:GLN11 4.3 49.1 1.0 OD1 D:ASP67 4.3 56.9 1.0 N D:GLN11 4.4 47.0 1.0 O3G D:G2P501 4.4 55.0 1.0 O2A D:G2P501 4.5 49.8 1.0 O1B D:G2P501 4.6 51.5 1.0 PA D:G2P501 4.7 50.1 1.0 OD2 D:ASP67 4.7 61.1 1.0 CB D:GLU69 4.7 71.0 1.0 OE1 D:GLU69 4.7 91.9 1.0 OG1 D:THR143 4.9 49.7 1.0 CA D:GLN11 4.9 47.8 1.0 CG D:ASP67 5.0 57.3 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