Magnesium in PDB 6gwd: Tubulin:IIH5 Alpharep Complex

The structure of Tubulin:IIH5 Alpharep Complex, PDB code: 6gwd was solved by B.Gigant, V.Campanacci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.85 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	450.800, 53.840, 229.620, 90.00, 118.76, 90.00
R / Rfree (%)	23 / 27

The binding sites of Magnesium atom in the Tubulin:IIH5 Alpharep Complex (pdb code 6gwd). 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:IIH5 Alpharep Complex, PDB code: 6gwd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin:IIH5 Alpharep Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin:IIH5 Alpharep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:60.9 occ:1.00 O1G A:GTP600 2.1 95.0 1.0 O2B A:GTP600 2.2 98.7 1.0 OE1 A:GLU71 2.5 76.3 1.0 O2G A:GTP600 2.7 96.3 1.0 PG A:GTP600 2.9 95.4 1.0 CD A:GLU71 3.2 96.8 1.0 PB A:GTP600 3.2 97.9 1.0 O3B A:GTP600 3.3 96.4 1.0 OE2 A:GLU71 3.3 94.6 1.0 NZ B:LYS254 3.7 0.3 1.0 O3A A:GTP600 3.7 0.9 1.0 OD2 A:ASP69 4.0 0.7 1.0 O3G A:GTP600 4.2 95.7 1.0 CB A:GLN11 4.3 77.4 1.0 OD1 A:ASP69 4.4 93.9 1.0 O2A A:GTP600 4.5 0.2 1.0 O1B A:GTP600 4.5 95.3 1.0 CG A:GLU71 4.6 86.8 1.0 CB A:ASP98 4.6 82.3 1.0 N A:GLN11 4.6 75.3 1.0 CG A:ASP69 4.7 94.1 1.0 OD2 A:ASP98 4.7 0.8 1.0 PA A:GTP600 4.8 0.3 1.0 OE1 A:GLN11 4.8 0.2 1.0 CE B:LYS254 4.8 0.9 1.0 CG A:ASP98 4.9 96.8 1.0

Magnesium binding site 2 out of 3 in the Tubulin:IIH5 Alpharep Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin:IIH5 Alpharep Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:41.5 occ:1.00 O2B C:GTP600 2.2 88.6 1.0 O3G C:GTP600 2.4 82.2 1.0 PG C:GTP600 3.3 83.2 1.0 O2G C:GTP600 3.4 80.6 1.0 PB C:GTP600 3.5 84.7 1.0 O3B C:GTP600 3.7 83.9 1.0 OD2 C:ASP69 3.8 0.9 1.0 O3A C:GTP600 4.0 83.3 1.0 OD1 C:ASP69 4.1 97.9 1.0 CB C:GLN11 4.2 65.8 1.0 CG C:ASP69 4.4 96.9 1.0 OE1 C:GLN11 4.4 0.3 1.0 O2A C:GTP600 4.6 83.2 1.0 N C:GLN11 4.6 62.7 1.0 CB C:ASP98 4.6 83.9 1.0 O1G C:GTP600 4.6 83.6 1.0 O1B C:GTP600 4.7 84.6 1.0 OD2 C:ASP98 4.9 0.1 1.0 CG C:ASP98 4.9 97.7 1.0 CB C:GLU71 4.9 86.4 1.0 CG2 C:VAL74 5.0 83.8 1.0 CA C:GLN11 5.0 63.6 1.0 PA C:GTP600 5.0 79.1 1.0 NZ D:LYS254 5.0 0.3 1.0

Magnesium binding site 3 out of 3 in the Tubulin:IIH5 Alpharep Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin:IIH5 Alpharep Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:60.7 occ:1.00 OE2 E:GLU71 2.2 0.0 1.0 OE1 E:GLU71 2.4 0.3 1.0 CD E:GLU71 2.6 0.5 1.0 O2B E:GTP600 2.7 75.0 1.0 O3G E:GTP600 3.0 77.3 1.0 O2G E:GTP600 3.5 76.2 1.0 NZ F:LYS254 3.7 90.5 1.0 OE1 E:GLN11 3.7 85.4 1.0 PG E:GTP600 3.8 77.8 1.0 PB E:GTP600 3.9 76.0 1.0 CB E:GLN11 4.0 76.4 1.0 OD1 E:ASP69 4.0 91.0 1.0 CG E:GLU71 4.1 94.7 1.0 O3B E:GTP600 4.1 77.9 1.0 OD2 E:ASP69 4.2 98.4 1.0 O3A E:GTP600 4.4 78.4 1.0 CG E:ASP69 4.6 90.4 1.0 CD E:GLN11 4.6 89.6 1.0 CG2 E:VAL74 4.6 83.8 1.0 N E:GLN11 4.7 76.8 1.0 O1A E:GTP600 4.8 85.0 1.0 CG E:GLN11 4.8 80.2 1.0 CE F:LYS254 4.8 82.0 1.0 CB E:ASP98 4.9 75.5 1.0 CA E:GLN11 4.9 75.5 1.0

V.Campanacci, A.Urvoas, T.Consolati, S.Cantos-Fernandes, M.Aumont-Nicaise, M.Valerio-Lepiniec, T.Surrey, P.Minard, B.Gigant. Selection and Characterization of Artificial Proteins Targeting the Tubulin Alpha Subunit. Structure V. 27 497 2019.
ISSN: ISSN 1878-4186
PubMed: 30661854
DOI: 10.1016/J.STR.2018.12.001