Magnesium in PDB 6tde: Tubulin-Inhibitor Complex

The structure of Tubulin-Inhibitor Complex, PDB code: 6tde was solved by P.F.Varela, B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.477, 128.142, 251.117, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.2

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

Magnesium binding site 1 out of 2 in the Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:54.3 occ:1.00 O1G A:GTP502 1.9 51.4 1.0 O A:HOH614 1.9 51.0 1.0 O A:HOH603 1.9 60.7 1.0 O1B A:GTP502 1.9 51.9 1.0 O A:HOH608 2.2 43.6 1.0 O A:HOH605 2.2 45.0 1.0 PB A:GTP502 3.0 51.5 1.0 PG A:GTP502 3.1 51.4 1.0 O3B A:GTP502 3.2 51.7 1.0 O3A A:GTP502 3.4 51.3 1.0 CB A:GLN11 3.9 53.6 1.0 O2G A:GTP502 3.9 51.2 1.0 NZ B:LYS254 4.0 68.8 1.0 OD1 A:ASP69 4.2 67.5 1.0 N A:GLN11 4.2 53.2 1.0 O1A A:GTP502 4.2 50.8 1.0 OD2 A:ASP98 4.2 67.2 1.0 O3G A:GTP502 4.3 51.1 1.0 O2B A:GTP502 4.3 51.3 1.0 OD2 A:ASP69 4.3 68.7 1.0 NE2 A:GLN11 4.4 60.3 1.0 OE2 A:GLU71 4.4 76.8 1.0 PA A:GTP502 4.4 50.9 1.0 CG A:GLU71 4.5 69.6 1.0 CG A:ASP69 4.7 67.3 1.0 CA A:GLN11 4.7 53.2 1.0 CB A:ASP98 4.7 62.3 1.0 CG A:ASP98 4.8 65.6 1.0 O2A A:GTP502 4.9 50.9 1.0

Magnesium binding site 2 out of 2 in the Tubulin-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:55.7 occ:1.00 O C:HOH603 1.9 52.4 1.0 O C:HOH601 1.9 34.4 1.0 O1G C:GTP504 2.2 53.8 1.0 O1B C:GTP504 2.4 54.4 1.0 PB C:GTP504 3.3 54.0 1.0 O3A C:GTP504 3.4 53.9 1.0 PG C:GTP504 3.5 53.7 1.0 O C:HOH620 3.6 66.7 1.0 O C:HOH608 3.6 59.1 1.0 CB C:GLN11 3.6 54.9 1.0 NE2 C:GLN11 3.7 58.4 1.0 O3B C:GTP504 3.7 54.0 1.0 O1A C:GTP504 3.7 53.8 1.0 NZ D:LYS254 3.9 75.9 1.0 PA C:GTP504 4.1 54.1 1.0 OE2 C:GLU71 4.4 78.1 1.0 CD C:GLN11 4.4 58.5 1.0 N C:GLN11 4.4 54.4 1.0 O3G C:GTP504 4.5 53.6 1.0 O2G C:GTP504 4.5 53.7 1.0 ND2 D:ASN249 4.5 87.9 1.0 OD2 C:ASP98 4.6 72.2 1.0 CG C:GLN11 4.6 56.6 1.0 CA C:GLN11 4.6 54.4 1.0 OD1 D:ASN249 4.6 88.4 1.0 O2B C:GTP504 4.7 54.0 1.0 OD2 C:ASP69 4.8 64.9 1.0 O2A C:GTP504 4.8 54.0 1.0 CG D:ASN249 4.9 87.2 1.0 OD1 C:ASP69 4.9 62.2 1.0 CG C:GLU71 4.9 71.9 1.0

E.S.Shchegravina, E.V.Svirshchevskaya, S.Combes, D.Allegro, P.Barbier, B.Gigant, P.F.Varela, A.E.Gavryushin, D.A.Kobanova, A.E.Shchekotikhin, A.Y.Fedorov. Discovery of Dihydrofuranoallocolchicinoids - Highly Potent Antimitotic Agents with Low Acute Toxicity. Eur.J.Med.Chem. V. 207 12724 2020.
ISSN: ISSN 0223-5234
PubMed: 32827941
DOI: 10.1016/J.EJMECH.2020.112724