Magnesium in PDB 3hke: Tubulin-T138067: RB3 Stathmin-Like Domain Complex

The structure of Tubulin-T138067: RB3 Stathmin-Like Domain Complex, PDB code: 3hke 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 / 3.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	326.710, 326.710, 54.120, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.3

The structure of Tubulin-T138067: RB3 Stathmin-Like Domain Complex also contains other interesting chemical elements:

Fluorine

(F)

22 atoms

The binding sites of Magnesium atom in the Tubulin-T138067: RB3 Stathmin-Like Domain Complex (pdb code 3hke). 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-T138067: RB3 Stathmin-Like Domain Complex, PDB code: 3hke:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-T138067: 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-T138067: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:30.2 occ:1.00 O2B A:GTP600 1.8 64.6 1.0 O3G A:GTP600 2.1 65.8 1.0 N A:GLY144 3.0 65.8 1.0 PB A:GTP600 3.1 66.0 1.0 PG A:GTP600 3.2 66.5 1.0 N A:THR145 3.2 65.7 1.0 CG2 A:THR145 3.3 65.1 1.0 CA A:GLY144 3.3 65.7 1.0 CB A:ALA99 3.3 65.6 1.0 O2G A:GTP600 3.4 66.5 1.0 N A:ASN101 3.6 65.1 1.0 O3B A:GTP600 3.6 65.5 1.0 O3A A:GTP600 3.7 66.0 1.0 C A:GLY144 3.7 65.6 1.0 OD1 A:ASP98 3.9 68.8 1.0 N A:ALA100 4.0 65.3 1.0 CA A:ALA99 4.1 65.4 1.0 C A:ALA99 4.1 65.3 1.0 CA A:ASN101 4.2 64.8 1.0 C A:GLY143 4.2 65.9 1.0 N A:ALA99 4.2 65.6 1.0 O1B A:GTP600 4.3 65.8 1.0 CA A:THR145 4.3 65.8 1.0 CB A:THR145 4.3 65.8 1.0 OD1 A:ASN101 4.5 65.2 1.0 O1G A:GTP600 4.5 66.6 1.0 C A:ALA100 4.6 65.3 1.0 CA A:ALA100 4.7 65.5 1.0 CA A:GLY143 4.8 66.0 1.0 O A:ALA99 4.8 65.0 1.0 OG1 A:THR145 4.9 66.9 1.0 O A:GLY144 5.0 65.4 1.0

Magnesium binding site 2 out of 3 in the Tubulin-T138067: 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-T138067: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:53.5 occ:1.00 O2A B:GDP600 3.5 66.4 1.0 ND2 B:ASN101 3.5 66.4 1.0 OE1 C:GLU254 3.9 68.5 1.0 OE1 B:GLN11 4.1 67.6 1.0 O2B B:GDP600 4.3 66.3 1.0 CG B:ASN101 4.5 66.0 1.0 O3B B:GDP600 4.6 65.7 1.0 CB B:GLN11 4.6 66.5 1.0 PA B:GDP600 4.7 67.3 1.0 O3A B:GDP600 4.7 67.2 1.0 CG B:GLN11 4.7 67.0 1.0 PB B:GDP600 4.8 67.0 1.0 CD B:GLN11 4.9 67.3 1.0 CD C:GLU254 4.9 68.2 1.0 OD1 B:ASN101 4.9 66.0 1.0 OD2 B:ASP179 5.0 67.5 1.0

Magnesium binding site 3 out of 3 in the Tubulin-T138067: 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-T138067: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:30.2 occ:1.00 O2B C:GTP600 1.9 64.7 1.0 O3G C:GTP600 2.0 65.9 1.0 PG C:GTP600 3.0 66.5 1.0 PB C:GTP600 3.1 65.1 1.0 N C:GLY144 3.2 65.8 1.0 CG2 C:THR145 3.2 65.4 1.0 CB C:ALA99 3.3 65.5 1.0 N C:THR145 3.3 65.8 1.0 O2G C:GTP600 3.3 66.2 1.0 CA C:GLY144 3.4 65.8 1.0 O3B C:GTP600 3.6 65.2 1.0 N C:ASN101 3.6 65.0 1.0 OD1 C:ASP98 3.7 68.6 1.0 O3A C:GTP600 3.8 65.8 1.0 C C:GLY144 3.9 65.8 1.0 N C:ALA100 4.0 65.3 1.0 CA C:ALA99 4.1 65.4 1.0 N C:ALA99 4.1 65.7 1.0 C C:ALA99 4.1 65.2 1.0 CA C:ASN101 4.2 64.7 1.0 C C:GLY143 4.3 65.8 1.0 O1G C:GTP600 4.3 66.7 1.0 O1B C:GTP600 4.3 65.3 1.0 CB C:THR145 4.4 65.9 1.0 OD1 C:ASN101 4.4 65.1 1.0 CA C:THR145 4.4 65.8 1.0 NZ D:LYS254 4.5 67.7 1.0 C C:ALA100 4.6 65.3 1.0 CA C:ALA100 4.7 65.4 1.0 O C:ALA99 4.8 64.9 1.0 CA C:GLY143 4.8 66.0 1.0 CG C:ASP98 4.9 67.4 1.0 OG1 C:THR145 4.9 66.7 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