Magnesium in PDB 6gvn: Tubulin:Tm-3 Darpin Complex

The structure of Tubulin:Tm-3 Darpin Complex, PDB code: 6gvn was solved by B.Gigant, S.Cantos Fernandes, V.Campanacci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.08 / 2.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.100, 84.260, 81.980, 90.00, 99.00, 90.00
R / Rfree (%)	19.3 / 21.6

The binding sites of Magnesium atom in the Tubulin:Tm-3 Darpin Complex (pdb code 6gvn). 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:Tm-3 Darpin Complex, PDB code: 6gvn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tubulin:Tm-3 Darpin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin:Tm-3 Darpin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.9 occ:1.00 O A:HOH627 1.9 40.9 1.0 O A:HOH602 2.5 33.7 1.0 O2G A:GTP501 2.6 37.3 1.0 O1B A:GTP501 2.9 38.6 1.0 O A:HOH603 3.0 23.5 1.0 CB A:GLN11 3.7 33.5 1.0 OD2 A:ASP69 3.9 53.5 1.0 PB A:GTP501 3.9 34.8 1.0 OE1 A:GLU71 3.9 80.1 1.0 O3A A:GTP501 4.0 37.0 1.0 PG A:GTP501 4.0 36.3 1.0 OD1 A:ASP69 4.1 48.0 1.0 CG A:GLU71 4.2 52.5 1.0 N A:GLN11 4.2 33.4 1.0 O3B A:GTP501 4.3 35.0 1.0 OE1 A:GLN11 4.4 48.3 1.0 CG A:ASP69 4.4 48.0 1.0 NZ B:LYS254 4.4 64.3 1.0 OD2 A:ASP98 4.5 64.2 1.0 CA A:GLN11 4.5 32.2 1.0 CD A:GLU71 4.5 74.9 1.0 O1A A:GTP501 4.7 41.7 1.0 O1G A:GTP501 4.7 32.5 1.0 CG A:GLN11 4.8 35.9 1.0 CD A:GLN11 4.8 47.0 1.0 CG2 A:VAL74 4.9 49.0 1.0 PA A:GTP501 4.9 38.8 1.0 O B:HOH627 5.0 63.6 1.0

Magnesium binding site 2 out of 2 in the Tubulin:Tm-3 Darpin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin:Tm-3 Darpin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:50.6 occ:1.00 O1B B:GTP501 2.3 47.5 1.0 O2G B:GTP501 3.0 66.0 1.0 PB B:GTP501 3.5 44.0 1.0 CB B:GLN11 3.6 38.0 1.0 PG B:GTP501 3.6 64.0 1.0 O1G B:GTP501 3.6 67.8 1.0 O3A B:GTP501 3.9 42.1 1.0 O3B B:GTP501 3.9 54.0 1.0 N B:GLN11 4.1 36.8 1.0 O1A B:GTP501 4.1 40.7 1.0 OE1 B:GLU71 4.2 0.6 1.0 CB B:GLU71 4.3 57.5 1.0 CA B:GLN11 4.4 36.8 1.0 OD2 B:ASP69 4.4 70.5 1.0 O B:HOH611 4.5 29.7 1.0 CG B:GLU71 4.6 70.4 1.0 PA B:GTP501 4.6 41.5 1.0 OD1 B:ASP69 4.7 65.1 1.0 O2B B:GTP501 4.7 41.2 1.0 CG B:GLN11 4.8 41.7 1.0 CD B:GLU71 4.9 0.8 1.0 CD B:GLN11 4.9 62.3 1.0 CG B:ASP69 5.0 64.2 1.0 OE1 B:GLN11 5.0 57.6 1.0

V.Campanacci, A.Urvoas, S.Cantos-Fernandes, M.Aumont-Nicaise, A.A.Arteni, C.Velours, M.Valerio-Lepiniec, B.Dreier, A.Pluckthun, A.Pilon, C.Pous, P.Minard, B.Gigant. Insight Into Microtubule Nucleation From Tubulin-Capping Proteins. Proc.Natl.Acad.Sci.Usa V. 116 9859 2019.
ISSN: ESSN 1091-6490
PubMed: 31036638
DOI: 10.1073/PNAS.1813559116