Magnesium in PDB 4f61: Tubulin:Stathmin-Like Domain Complex

The structure of Tubulin:Stathmin-Like Domain Complex, PDB code: 4f61 was solved by B.Gigant, I.Mignot, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 4.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	639.740, 66.100, 128.130, 90.00, 92.02, 90.00
R / Rfree (%)	24.1 / 26.1

The binding sites of Magnesium atom in the Tubulin:Stathmin-Like Domain Complex (pdb code 4f61). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin:Stathmin-Like Domain Complex, PDB code: 4f61:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin: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:Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.6 occ:1.00 O1G A:GTP600 2.1 0.5 1.0 O1B A:GTP600 2.1 99.9 1.0 OE2 A:GLU71 2.3 0.6 1.0 OE1 A:GLU71 2.5 0.1 1.0 CD A:GLU71 2.7 0.2 1.0 PB A:GTP600 3.1 0.5 1.0 PG A:GTP600 3.2 0.1 1.0 O3B A:GTP600 3.4 0.2 1.0 O3A A:GTP600 3.4 0.3 1.0 O2G A:GTP600 3.8 0.8 1.0 NZ B:LYS254 3.9 0.2 1.0 CB A:GLN11 4.1 0.6 1.0 CG A:GLU71 4.2 0.8 1.0 O1A A:GTP600 4.3 0.9 1.0 OD2 A:ASP69 4.3 99.1 1.0 OD1 A:ASP69 4.4 99.8 1.0 N A:GLN11 4.4 97.4 1.0 O2B A:GTP600 4.4 99.2 1.0 O3G A:GTP600 4.4 0.7 1.0 PA A:GTP600 4.5 0.4 1.0 NE2 A:GLN11 4.6 0.7 1.0 CG A:ASP69 4.8 99.3 1.0 CA A:GLN11 4.8 98.4 1.0 CB A:ASP98 5.0 1.0 1.0 CE B:LYS254 5.0 0.9 1.0

Magnesium binding site 2 out of 4 in the Tubulin: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:Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:0.5 occ:1.00 O1G C:GTP600 2.0 0.1 1.0 O1B C:GTP600 2.1 0.2 1.0 OE2 C:GLU71 2.3 0.1 1.0 OE1 C:GLU71 2.5 0.7 1.0 CD C:GLU71 2.7 0.8 1.0 PB C:GTP600 3.1 0.0 1.0 PG C:GTP600 3.2 0.2 1.0 O3B C:GTP600 3.4 0.5 1.0 O3A C:GTP600 3.5 0.5 1.0 O2G C:GTP600 3.8 0.1 1.0 NZ D:LYS254 3.8 0.5 1.0 CB C:GLN11 4.1 0.2 1.0 CG C:GLU71 4.2 0.6 1.0 O1A C:GTP600 4.3 0.9 1.0 OD2 C:ASP69 4.3 0.3 1.0 OD1 C:ASP69 4.4 0.9 1.0 O3G C:GTP600 4.4 0.5 1.0 O2B C:GTP600 4.4 0.4 1.0 N C:GLN11 4.5 0.2 1.0 PA C:GTP600 4.5 0.2 1.0 NE2 C:GLN11 4.6 0.8 1.0 CG C:ASP69 4.8 0.5 1.0 CA C:GLN11 4.9 0.9 1.0 CB C:ASP98 4.9 0.8 1.0

Magnesium binding site 3 out of 4 in the Tubulin: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:Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:0.3 occ:1.00 O1G E:GTP600 2.1 0.3 1.0 O1B E:GTP600 2.1 0.3 1.0 OE2 E:GLU71 2.3 0.4 1.0 OE1 E:GLU71 2.5 0.7 1.0 CD E:GLU71 2.7 0.6 1.0 PB E:GTP600 3.1 0.9 1.0 PG E:GTP600 3.2 0.0 1.0 O3B E:GTP600 3.4 0.7 1.0 O3A E:GTP600 3.5 0.6 1.0 NZ F:LYS254 3.8 0.4 1.0 O2G E:GTP600 3.8 0.4 1.0 CB E:GLN11 4.1 0.2 1.0 CG E:GLU71 4.2 0.3 1.0 O1A E:GTP600 4.3 0.7 1.0 OD2 E:ASP69 4.3 0.9 1.0 OD1 E:ASP69 4.4 0.4 1.0 O2B E:GTP600 4.4 0.6 1.0 N E:GLN11 4.4 0.8 1.0 O3G E:GTP600 4.5 0.1 1.0 PA E:GTP600 4.5 0.6 1.0 NE2 E:GLN11 4.6 0.7 1.0 CG E:ASP69 4.8 0.8 1.0 CA E:GLN11 4.9 0.6 1.0 CE F:LYS254 5.0 0.5 1.0 CB E:ASP98 5.0 0.7 1.0

Magnesium binding site 4 out of 4 in the Tubulin:Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin:Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:0.6 occ:1.00 O1G G:GTP600 2.0 0.9 1.0 O1B G:GTP600 2.1 0.2 1.0 OE2 G:GLU71 2.3 0.8 1.0 OE1 G:GLU71 2.5 0.3 1.0 CD G:GLU71 2.7 0.4 1.0 PB G:GTP600 3.1 0.2 1.0 PG G:GTP600 3.2 0.7 1.0 O3A G:GTP600 3.4 0.8 1.0 O3B G:GTP600 3.4 0.2 1.0 NZ H:LYS254 3.6 0.7 1.0 O2G G:GTP600 3.9 0.8 1.0 CB G:GLN11 4.1 0.0 1.0 CG G:GLU71 4.2 0.2 1.0 O1A G:GTP600 4.3 0.3 1.0 O3G G:GTP600 4.4 0.6 1.0 OD2 G:ASP69 4.4 0.9 1.0 PA G:GTP600 4.4 0.6 1.0 OD1 G:ASP69 4.5 0.0 1.0 O2B G:GTP600 4.5 0.1 1.0 N G:GLN11 4.5 0.8 1.0 NE2 G:GLN11 4.6 0.8 1.0 CE H:LYS254 4.8 0.2 1.0 CG G:ASP69 4.9 0.4 1.0 CA G:GLN11 4.9 0.6 1.0

I.Mignot, L.Pecqueur, A.Dorleans, M.Karuppasamy, R.B.Ravelli, B.Dreier, A.Pluckthun, M.Knossow, B.Gigant. Design and Characterization of Modular Scaffolds For Tubulin Assembly. J.Biol.Chem. V. 287 31085 2012.
ISSN: ISSN 0021-9258
PubMed: 22791712
DOI: 10.1074/JBC.M112.383869