Magnesium in PDB 3ryi: Gdp-Tubulin: RB3 Stathmin-Like Domain Complex

The structure of Gdp-Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryi was solved by A.Nawrotek, M.Knossow, B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.720, 127.600, 250.200, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.1

The binding sites of Magnesium atom in the Gdp-Tubulin: RB3 Stathmin-Like Domain Complex (pdb code 3ryi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gdp-Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gdp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:54.6 occ:1.00 O1G A:GTP600 1.9 47.3 1.0 O A:HOH592 2.0 38.5 1.0 O A:HOH593 2.1 39.5 1.0 O A:HOH642 2.1 36.5 1.0 O A:HOH645 2.2 49.2 1.0 O1B A:GTP600 2.2 44.6 1.0 PG A:GTP600 3.1 45.1 1.0 PB A:GTP600 3.2 44.8 1.0 O3A A:GTP600 3.6 44.9 1.0 O3B A:GTP600 3.6 44.9 1.0 O2G A:GTP600 3.6 46.5 1.0 NZ B:LYS254 3.8 57.4 1.0 OD2 A:ASP98 4.1 50.7 1.0 OE1 A:GLU71 4.1 90.1 1.0 OD2 A:ASP69 4.2 52.7 1.0 CB A:GLN11 4.3 44.1 1.0 OD1 A:ASP69 4.4 49.8 1.0 O A:HOH595 4.4 81.5 1.0 O3G A:GTP600 4.4 47.4 1.0 CB A:ASP98 4.5 49.1 1.0 N A:GLN11 4.5 44.2 1.0 O1A A:GTP600 4.6 45.2 1.0 CG A:ASP98 4.6 50.4 1.0 O2B A:GTP600 4.6 44.4 1.0 CG A:ASP69 4.7 51.4 1.0 PA A:GTP600 4.7 45.1 1.0 CE B:LYS254 5.0 53.5 1.0

Magnesium binding site 2 out of 2 in the Gdp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gdp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:61.1 occ:1.00 O C:HOH621 1.9 57.5 1.0 O1G C:GTP600 1.9 53.6 1.0 O C:HOH596 2.0 57.0 1.0 O C:HOH598 2.0 47.3 1.0 O C:HOH597 2.1 51.5 1.0 O1B C:GTP600 2.2 52.8 1.0 PG C:GTP600 3.1 51.0 1.0 PB C:GTP600 3.2 52.7 1.0 O3B C:GTP600 3.5 52.1 1.0 O3A C:GTP600 3.6 53.8 1.0 O2G C:GTP600 3.6 52.2 1.0 NZ D:LYS254 4.0 57.3 1.0 OD2 C:ASP98 4.1 62.4 1.0 OD2 C:ASP69 4.2 64.6 1.0 CB C:GLN11 4.3 50.2 1.0 OD1 C:ASP69 4.4 61.7 1.0 OE1 C:GLU71 4.4 0.2 1.0 O3G C:GTP600 4.4 49.6 1.0 CB C:ASP98 4.5 56.4 1.0 N C:GLN11 4.5 49.1 1.0 O1A C:GTP600 4.6 55.1 1.0 O2B C:GTP600 4.6 52.3 1.0 CG C:ASP98 4.6 58.6 1.0 CD C:GLU71 4.7 99.4 1.0 CG C:ASP69 4.7 61.7 1.0 PA C:GTP600 4.7 54.5 1.0 OE2 C:GLU71 4.7 92.6 1.0 OE1 C:GLN11 5.0 62.8 1.0

A.Nawrotek, M.Knossow, B.Gigant. The Determinants That Govern Microtubule Assembly From the Atomic Structure of Gtp-Tubulin. J.Mol.Biol. V. 412 35 2011.
ISSN: ISSN 0022-2836
PubMed: 21787788
DOI: 10.1016/J.JMB.2011.07.029