Magnesium in PDB 4eb6: Tubulin-Vinblastine: Stathmin-Like Complex

The structure of Tubulin-Vinblastine: Stathmin-Like Complex, PDB code: 4eb6 was solved by F.M.Ranaivoson, B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 3.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.690, 129.680, 252.750, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.3

The binding sites of Magnesium atom in the Tubulin-Vinblastine: Stathmin-Like Complex (pdb code 4eb6). 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-Vinblastine: Stathmin-Like Complex, PDB code: 4eb6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tubulin-Vinblastine: Stathmin-Like Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Vinblastine: Stathmin-Like Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:0.4 occ:1.00 O1B A:GTP501 1.9 0.8 1.0 O A:HOH604 2.1 0.4 1.0 O2G A:GTP501 2.5 0.6 1.0 O A:HOH603 2.6 0.6 1.0 O A:HOH601 2.7 0.0 1.0 CB A:GLN11 2.8 0.5 1.0 PB A:GTP501 3.0 0.2 1.0 O A:HOH602 3.1 0.2 1.0 O3A A:GTP501 3.3 0.4 1.0 OE1 A:GLN11 3.5 0.5 1.0 O2A A:GTP501 3.6 0.2 1.0 CG A:GLN11 3.6 0.3 1.0 PG A:GTP501 3.7 0.2 1.0 CD A:GLN11 3.8 0.2 1.0 CA A:GLN11 3.8 0.8 1.0 N A:GLN11 3.8 0.6 1.0 O3B A:GTP501 3.9 0.6 1.0 PA A:GTP501 3.9 0.9 1.0 OD1 A:ASP69 4.1 0.7 1.0 O2B A:GTP501 4.2 0.3 1.0 O1A A:GTP501 4.2 0.5 1.0 NZ B:LYS254 4.3 0.2 1.0 O1G A:GTP501 4.4 0.8 1.0 OD2 A:ASP69 4.9 0.1 1.0 NE2 A:GLN11 4.9 0.3 1.0 CG A:ASP69 4.9 0.4 1.0 C A:GLY10 4.9 0.5 1.0 O3G A:GTP501 5.0 0.9 1.0

Magnesium binding site 2 out of 2 in the Tubulin-Vinblastine: Stathmin-Like Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Vinblastine: Stathmin-Like Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:0.7 occ:1.00 O1B C:GTP501 2.0 0.6 1.0 O2G C:GTP501 2.3 0.9 1.0 O C:HOH605 2.4 0.3 1.0 O C:HOH603 2.4 87.0 1.0 O C:HOH602 2.8 75.9 1.0 PB C:GTP501 3.0 0.3 1.0 CB C:GLN11 3.1 0.8 1.0 O D:HOH602 3.2 87.7 1.0 O3A C:GTP501 3.2 0.2 1.0 PG C:GTP501 3.6 0.8 1.0 O2A C:GTP501 3.7 0.9 1.0 OE1 C:GLN11 3.8 0.0 1.0 O3B C:GTP501 3.8 0.9 1.0 CD C:GLN11 3.9 0.9 1.0 PA C:GTP501 4.0 1.0 1.0 CG C:GLN11 4.0 0.7 1.0 N C:GLN11 4.1 0.1 1.0 CA C:GLN11 4.2 0.4 1.0 OD1 C:ASP69 4.3 0.6 1.0 O1G C:GTP501 4.3 0.6 1.0 NZ D:LYS254 4.3 0.5 1.0 O2B C:GTP501 4.3 0.5 1.0 O1A C:GTP501 4.4 0.5 1.0 NE2 C:GLN11 4.7 0.8 1.0 O3G C:GTP501 4.8 0.6 1.0 O C:HOH606 4.8 0.6 1.0 OD2 C:ASP69 5.0 0.7 1.0

F.M.Ranaivoson, B.Gigant, S.Berritt, M.Joullie, M.Knossow. Structural Plasticity of Tubulin Assembly Probed By Vinca-Domain Ligands. Acta Crystallogr.,Sect.D V. 68 927 2012.
ISSN: ISSN 0907-4449
PubMed: 22868758
DOI: 10.1107/S0907444912017143