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

The structure of Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryc 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)	43.14 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.450, 127.240, 250.340, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.1

The binding sites of Magnesium atom in the Tubulin: RB3 Stathmin-Like Domain Complex (pdb code 3ryc). 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: RB3 Stathmin-Like Domain Complex, PDB code: 3ryc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the 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 Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:42.1 occ:1.00 O A:HOH612 2.1 36.8 1.0 O A:HOH613 2.1 36.4 1.0 O1G A:GTP600 2.2 36.2 1.0 O A:HOH611 2.2 39.2 1.0 O1B A:GTP600 2.2 32.7 1.0 O A:HOH610 2.2 35.1 1.0 PG A:GTP600 3.2 34.2 1.0 PB A:GTP600 3.3 32.8 1.0 O3B A:GTP600 3.6 32.9 1.0 O2G A:GTP600 3.7 35.4 1.0 O3A A:GTP600 3.8 32.6 1.0 OD2 A:ASP69 4.0 37.3 1.0 NZ B:LYS254 4.1 46.4 1.0 OD1 A:ASP69 4.2 36.5 1.0 OD2 A:ASP98 4.2 36.8 1.0 OE1 A:GLU71 4.2 44.3 1.0 CB A:GLN11 4.2 33.8 1.0 N A:GLN11 4.3 32.0 1.0 CB A:ASP98 4.5 35.2 1.0 O A:HOH705 4.5 63.6 1.0 CG A:ASP69 4.5 38.8 1.0 O2B A:GTP600 4.6 32.8 1.0 O3G A:GTP600 4.6 34.8 1.0 O1A A:GTP600 4.6 33.1 1.0 CG A:ASP98 4.7 35.3 1.0 PA A:GTP600 4.8 32.8 1.0 CA A:GLN11 4.9 32.6 1.0 NE2 A:GLN11 4.9 38.5 1.0

Magnesium binding site 2 out of 3 in the 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 Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:36.4 occ:1.00 O1G C:GTP600 2.0 37.5 1.0 O C:HOH611 2.1 35.5 1.0 O C:HOH614 2.1 38.2 1.0 O C:HOH610 2.1 38.3 1.0 O C:HOH612 2.1 38.3 1.0 O1B C:GTP600 2.2 37.3 1.0 PG C:GTP600 3.1 35.4 1.0 PB C:GTP600 3.2 37.6 1.0 O3B C:GTP600 3.6 37.1 1.0 O3A C:GTP600 3.6 39.3 1.0 O2G C:GTP600 3.6 36.0 1.0 NZ D:LYS254 4.0 44.1 1.0 OD2 C:ASP98 4.1 39.9 1.0 OD2 C:ASP69 4.2 40.0 1.0 CB C:GLN11 4.3 36.6 1.0 OD1 C:ASP69 4.3 42.0 1.0 OE1 C:GLU71 4.4 57.5 1.0 O3G C:GTP600 4.4 34.9 1.0 CB C:ASP98 4.4 38.5 1.0 N C:GLN11 4.5 36.2 1.0 O1A C:GTP600 4.5 40.5 1.0 O2B C:GTP600 4.5 37.6 1.0 CG C:ASP98 4.6 42.9 1.0 CG C:ASP69 4.7 42.1 1.0 PA C:GTP600 4.7 40.1 1.0 NE2 C:GLN11 4.9 51.2 1.0 CA C:GLN11 5.0 35.8 1.0

Magnesium binding site 3 out of 3 in the 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 3 of Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:38.1 occ:0.60 O D:HOH613 1.9 18.1 0.4 O D:HOH613 1.9 64.8 0.6 O1B D:GTP600 2.0 29.9 0.6 O1G D:GTP600 2.1 35.4 0.6 O D:HOH612 2.2 19.2 0.4 O2B D:GTP600 2.2 33.1 0.4 O D:HOH614 2.3 32.6 0.6 O D:HOH612 3.0 46.0 0.6 PG D:GTP600 3.1 33.6 0.6 PB D:GTP600 3.2 30.1 0.6 PB D:GTP600 3.3 32.1 0.4 O2G D:GTP600 3.5 35.3 0.6 O3B D:GTP600 3.6 30.5 0.6 O D:HOH614 3.7 20.8 0.4 O3B D:GTP600 3.7 32.4 0.4 O3A D:GTP600 3.8 32.2 0.4 O3A D:GTP600 3.9 29.8 0.6 CB D:GLN11 3.9 32.6 1.0 N D:GLN11 4.1 32.7 1.0 OE1 D:GLU71 4.1 74.0 1.0 O1A D:GTP600 4.2 30.2 0.6 O D:HOH365 4.2 44.2 1.0 OD1 D:ASP69 4.2 38.7 1.0 O2B D:GTP600 4.4 30.4 0.6 OD2 D:ASP69 4.5 45.3 1.0 O3G D:GTP600 4.5 36.0 0.6 O1B D:GTP600 4.6 30.8 0.4 CA D:GLN11 4.6 32.1 1.0 PA D:GTP600 4.6 29.9 0.6 CB D:GLU71 4.7 50.0 1.0 CD D:GLU71 4.8 96.1 1.0 CG D:ASP69 4.8 40.5 1.0 PA D:GTP600 4.8 32.2 0.4 O1A D:GTP600 4.8 32.4 0.4 OE1 D:GLN11 4.9 60.9 1.0 OG1 D:THR145 4.9 36.3 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