Magnesium in PDB 3du7: Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain Complex

The structure of Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain Complex, PDB code: 3du7 was solved by A.Cormier, M.Marchand, R.B.Ravelli, M.Knossow, B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 4.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	327.126, 327.126, 53.672, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 26.5

The structure of Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain Complex (pdb code 3du7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tubulin-Colchicine-Phomopsin A: Stathmin-Like Domain Complex, PDB code: 3du7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tubulin-Colchicine-Phomopsin A: 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-Colchicine-Phomopsin A: Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:99.0 occ:1.00 O2B D:GTP600 1.2 99.0 1.0 O3G D:GTP600 1.8 99.0 1.0 PB D:GTP600 2.6 99.0 1.0 PG D:GTP600 2.9 99.0 1.0 CA A:GLY144 3.1 95.9 1.0 O3B D:GTP600 3.2 99.0 1.0 O2G D:GTP600 3.3 99.0 1.0 N A:GLY144 3.4 95.9 1.0 N A:THR145 3.4 95.9 1.0 OD1 A:ASP98 3.5 95.9 1.0 O3A D:GTP600 3.5 99.0 1.0 CB A:ALA99 3.5 95.9 1.0 O1B D:GTP600 3.6 99.0 1.0 N A:ASN101 3.7 95.9 1.0 C A:GLY144 3.7 95.9 1.0 CG2 A:THR145 3.8 95.9 1.0 C A:ALA99 4.1 95.9 1.0 N A:ALA100 4.2 95.9 1.0 O1G D:GTP600 4.2 99.0 1.0 CA A:ASN101 4.2 95.9 1.0 CA A:ALA99 4.2 95.9 1.0 O A:ALA99 4.4 95.9 1.0 CG A:ASP98 4.4 95.9 1.0 N A:ALA99 4.5 95.9 1.0 OD2 A:ASP98 4.5 95.9 1.0 C A:GLY143 4.5 95.9 1.0 CA A:THR145 4.6 95.9 1.0 C A:ALA100 4.7 95.9 1.0 CA A:ALA100 4.8 95.9 1.0 CB A:THR145 4.8 95.9 1.0 CG A:ASN101 5.0 95.9 1.0 O A:GLY144 5.0 95.9 1.0

Magnesium binding site 2 out of 2 in the Tubulin-Colchicine-Phomopsin A: 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-Colchicine-Phomopsin A: Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:99.0 occ:1.00 O2B D:GTP601 1.3 99.0 1.0 O3G D:GTP601 1.8 99.0 1.0 O2G D:GTP601 2.3 99.0 1.0 PG D:GTP601 2.4 99.0 1.0 PB D:GTP601 2.4 99.0 1.0 O3B D:GTP601 2.9 99.0 1.0 O3A D:GTP601 3.1 99.0 1.0 NZ D:LYS254 3.2 95.9 1.0 OD1 C:ASP98 3.3 95.9 1.0 CA C:GLY144 3.6 95.9 1.0 O1B D:GTP601 3.7 99.0 1.0 N C:GLY144 3.7 95.9 1.0 O1G D:GTP601 3.8 99.0 1.0 N C:THR145 3.9 95.9 1.0 N C:ASN101 3.9 95.9 1.0 CB C:ALA99 4.0 95.9 1.0 OD2 C:ASP98 4.2 95.9 1.0 CG C:ASP98 4.2 95.9 1.0 CG2 C:THR145 4.2 95.9 1.0 CE D:LYS254 4.3 95.9 1.0 C C:GLY144 4.3 95.9 1.0 N C:ALA100 4.3 95.9 1.0 C C:ALA99 4.4 95.9 1.0 CA C:ASN101 4.5 95.9 1.0 PA D:GTP601 4.6 99.0 1.0 CA C:ALA99 4.6 95.9 1.0 N C:ALA99 4.6 95.9 1.0 O C:ALA99 4.8 95.9 1.0 C C:GLY143 4.8 95.9 1.0 C C:ALA100 4.9 95.9 1.0 CA C:ALA100 4.9 95.9 1.0

A.Cormier, M.Marchand, R.B.Ravelli, M.Knossow, B.Gigant. Structural Insight Into the Inhibition of Tubulin By Vinca Domain Peptide Ligands Embo Rep. V. 9 1101 2008.
ISSN: ISSN 1469-221X
PubMed: 18787557
DOI: 10.1038/EMBOR.2008.171