Magnesium in PDB 3hkd: Tubulin-TN16 : RB3 Stathmin-Like Domain Complex

The structure of Tubulin-TN16 : RB3 Stathmin-Like Domain Complex, PDB code: 3hkd was solved by A.Dorleans, B.Gigant, R.B.G.Ravelli, P.Mailliet, V.Mikol, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	328.530, 328.530, 54.410, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 26.4

The binding sites of Magnesium atom in the Tubulin-TN16 : RB3 Stathmin-Like Domain Complex (pdb code 3hkd). 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-TN16 : RB3 Stathmin-Like Domain Complex, PDB code: 3hkd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-TN16 : 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-TN16 : RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:5.1 occ:1.00 O2B A:GTP600 1.6 36.7 1.0 O3G A:GTP600 2.1 36.0 1.0 PB A:GTP600 2.9 37.2 1.0 N A:THR145 3.0 42.4 1.0 CA A:GLY144 3.1 42.4 1.0 N A:GLY144 3.1 42.3 1.0 CG2 A:THR145 3.2 42.5 1.0 PG A:GTP600 3.3 35.6 1.0 CB A:ALA99 3.4 42.2 1.0 O3A A:GTP600 3.5 37.0 1.0 O3B A:GTP600 3.5 36.5 1.0 C A:GLY144 3.5 42.4 1.0 OD1 A:ASP98 3.6 45.3 1.0 NZ B:LYS254 3.7 42.0 1.0 N A:ASN101 3.8 41.6 1.0 O2G A:GTP600 4.0 35.3 1.0 O1B A:GTP600 4.1 35.5 1.0 CA A:THR145 4.2 42.6 1.0 CB A:THR145 4.3 42.6 1.0 CA A:ALA99 4.3 42.1 1.0 N A:ALA100 4.4 41.9 1.0 C A:GLY143 4.4 42.1 1.0 CA A:ASN101 4.4 41.5 1.0 C A:ALA99 4.4 42.0 1.0 N A:ALA99 4.5 42.4 1.0 O1G A:GTP600 4.5 34.8 1.0 C A:ALA100 4.7 41.8 1.0 OG1 A:THR145 4.7 43.1 1.0 O A:GLY144 4.8 42.1 1.0 CG A:ASP98 4.8 44.5 1.0 CA A:ALA100 4.9 42.0 1.0 N A:GLY146 5.0 42.8 1.0

Magnesium binding site 2 out of 3 in the Tubulin-TN16 : 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-TN16 : RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:15.5 occ:1.00 OE1 B:GLN11 2.7 43.9 1.0 O2A B:GDP600 3.5 34.1 1.0 CD B:GLN11 3.9 43.6 1.0 OD1 B:ASN101 4.0 44.2 1.0 OE2 C:GLU254 4.0 50.0 1.0 O2B B:GDP600 4.3 36.4 1.0 CD C:GLU254 4.4 49.8 1.0 PA B:GDP600 4.5 36.1 1.0 CG B:ASN101 4.6 43.5 1.0 OD2 B:ASP179 4.6 46.1 1.0 OE1 C:GLU254 4.7 49.9 1.0 NE2 B:GLN11 4.7 43.7 1.0 O1A B:GDP600 4.7 35.6 1.0 O3A B:GDP600 4.8 37.8 1.0 ND2 B:ASN101 4.8 43.7 1.0 CB B:GLN11 4.9 43.8 1.0 CG B:GLN11 5.0 43.2 1.0 PB B:GDP600 5.0 37.9 1.0

Magnesium binding site 3 out of 3 in the Tubulin-TN16 : 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-TN16 : RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:5.1 occ:1.00 O2B C:GTP600 1.9 25.0 1.0 O3G C:GTP600 1.9 29.7 1.0 OD1 C:ASP98 2.8 44.7 1.0 CB C:ALA99 2.9 42.2 1.0 PG C:GTP600 3.1 29.9 1.0 CG2 C:THR145 3.2 42.7 1.0 PB C:GTP600 3.3 25.2 1.0 NZ D:LYS254 3.3 42.3 1.0 N C:THR145 3.4 42.4 1.0 N C:ALA100 3.5 42.1 1.0 O2G C:GTP600 3.5 30.1 1.0 CA C:GLY144 3.5 42.4 1.0 N C:ALA99 3.5 42.4 1.0 CA C:ALA99 3.5 42.2 1.0 O3B C:GTP600 3.6 27.3 1.0 N C:ASN101 3.7 41.5 1.0 C C:ALA99 3.7 42.1 1.0 N C:GLY144 3.9 42.4 1.0 C C:GLY144 4.0 42.3 1.0 CG C:ASP98 4.0 44.1 1.0 O3A C:GTP600 4.2 27.8 1.0 O1B C:GTP600 4.3 24.6 1.0 CA C:ALA100 4.3 42.0 1.0 C C:ALA100 4.4 41.7 1.0 O1G C:GTP600 4.4 29.6 1.0 CB C:THR145 4.4 42.5 1.0 CA C:THR145 4.5 42.6 1.0 O C:ALA99 4.5 42.0 1.0 CA C:ASN101 4.5 41.4 1.0 OD2 C:ASP98 4.6 44.4 1.0 CE D:LYS254 4.6 42.9 1.0 C C:ASP98 4.8 42.8 1.0 OG1 C:THR145 5.0 43.0 1.0

A.Dorleans, B.Gigant, R.B.G.Ravelli, P.Mailliet, V.Mikol, M.Knossow. Variations in the Colchicine-Binding Domain Provide Insight Into the Structural Switch of Tubulin Proc.Natl.Acad.Sci.Usa V. 106 13775 2009.
ISSN: ISSN 0027-8424
PubMed: 19666559
DOI: 10.1073/PNAS.0904223106