Magnesium in PDB 6fii: Tubulin-Spongistatin Complex

The structure of Tubulin-Spongistatin Complex, PDB code: 6fii was solved by G.Menchon, A.E.Prota, D.Lucena Angell, P.Bucher, R.Mueller, I.Paterson, J.F.Diaz, K.-H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.17 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.670, 159.920, 181.010, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.6

The structure of Tubulin-Spongistatin Complex also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Tubulin-Spongistatin Complex (pdb code 6fii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Spongistatin Complex, PDB code: 6fii:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:45.6 occ:1.00 O A:HOH619 2.0 42.8 1.0 O2G A:GTP501 2.0 39.0 1.0 O A:HOH623 2.1 40.0 1.0 O A:HOH616 2.1 46.2 1.0 O A:HOH658 2.2 44.1 1.0 O1B A:GTP501 2.2 40.4 1.0 PG A:GTP501 3.2 49.8 1.0 PB A:GTP501 3.3 45.8 1.0 OE1 A:GLU71 3.5 86.5 1.0 O3B A:GTP501 3.6 56.7 1.0 O1G A:GTP501 3.6 45.7 1.0 NZ B:LYS254 3.9 58.0 1.0 O3A A:GTP501 3.9 49.9 1.0 OD2 A:ASP98 4.0 58.6 1.0 OD1 A:ASP69 4.3 54.2 1.0 CB A:GLN11 4.4 37.7 1.0 OD2 A:ASP69 4.4 56.6 1.0 CB A:ASP98 4.4 51.5 1.0 O3G A:GTP501 4.5 36.7 1.0 CG A:ASP98 4.5 57.9 1.0 N A:GLN11 4.6 47.3 1.0 O2B A:GTP501 4.6 55.2 1.0 CD A:GLU71 4.7 83.8 1.0 O1A A:GTP501 4.7 43.8 1.0 CG A:ASP69 4.8 55.8 1.0 PA A:GTP501 4.9 40.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:38.6 occ:1.00 O B:HOH623 1.9 43.0 1.0 O C:HOH676 2.2 56.0 1.0 OE1 B:GLN11 2.2 49.4 1.0 O1A B:GDP501 2.3 43.4 1.0 O B:HOH636 2.4 47.8 1.0 O B:HOH604 2.7 57.3 1.0 CD B:GLN11 3.4 52.9 1.0 PA B:GDP501 3.5 42.0 1.0 O5' B:GDP501 3.7 40.8 1.0 O3A B:GDP501 3.8 44.9 1.0 OD2 B:ASP179 3.8 56.4 1.0 CB B:GLN11 4.1 33.0 1.0 CG B:GLN11 4.2 41.7 1.0 NE2 B:GLN11 4.4 51.0 1.0 OD1 B:ASN101 4.5 48.8 1.0 O1B B:GDP501 4.6 34.5 1.0 O C:HOH659 4.6 61.1 1.0 C8 B:GDP501 4.7 48.8 1.0 O2A B:GDP501 4.8 43.9 1.0 OE1 C:GLU254 4.8 61.0 1.0 PB B:GDP501 4.9 40.7 1.0 O B:HOH679 5.0 93.7 1.0 CG B:ASP179 5.0 62.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.8 occ:1.00 O1G C:GTP501 2.0 27.9 1.0 O C:HOH642 2.1 36.8 1.0 O1B C:GTP501 2.1 38.1 1.0 O C:HOH637 2.1 35.1 1.0 O C:HOH641 2.1 44.7 1.0 O C:HOH713 2.1 39.5 1.0 PG C:GTP501 3.2 41.4 1.0 PB C:GTP501 3.2 40.9 1.0 O3B C:GTP501 3.6 45.4 1.0 O3G C:GTP501 3.7 38.2 1.0 O3A C:GTP501 3.8 48.5 1.0 OE1 C:GLU71 3.9 69.0 1.0 NZ D:LYS254 4.0 43.2 1.0 OD2 C:ASP98 4.2 48.1 1.0 OD1 C:ASP69 4.3 41.2 1.0 CB C:GLN11 4.4 30.5 1.0 OD2 C:ASP69 4.4 37.1 1.0 O2G C:GTP501 4.4 32.9 1.0 O2B C:GTP501 4.5 43.1 1.0 O1A C:GTP501 4.5 47.4 1.0 N C:GLN11 4.6 34.4 1.0 CB C:ASP98 4.7 39.1 1.0 PA C:GTP501 4.7 38.6 1.0 NE2 C:GLN11 4.8 50.2 1.0 CG C:ASP98 4.8 49.8 1.0 CG C:ASP69 4.8 42.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:80.4 occ:1.00 O D:HOH623 2.3 58.9 1.0 OE1 D:GLN11 2.5 82.2 1.0 O1A D:GDP501 2.5 90.6 1.0 O D:HOH603 3.3 86.3 1.0 CD D:GLN11 3.5 86.8 1.0 PA D:GDP501 4.0 75.1 1.0 NE2 D:GLN11 4.2 77.9 1.0 CG D:GLN11 4.4 84.2 1.0 CB D:GLN11 4.4 74.9 1.0 C5' D:GDP501 4.5 69.3 1.0 O3A D:GDP501 4.6 66.6 1.0 C8 D:GDP501 4.7 64.2 1.0 O5' D:GDP501 4.8 74.6 1.0 O2A D:GDP501 4.9 82.8 1.0 O1B D:GDP501 4.9 94.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Spongistatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Spongistatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.7 occ:1.00 O1B F:ACP401 2.3 0.7 1.0 O1G F:ACP401 2.5 0.8 1.0 OE2 F:GLU331 2.6 0.9 1.0 OD1 F:ASN333 3.2 0.1 1.0 NZ F:LYS74 3.4 0.4 1.0 CD F:GLU331 3.5 0.7 1.0 PG F:ACP401 3.6 0.5 1.0 PB F:ACP401 3.6 0.1 1.0 OE1 F:GLU331 3.7 0.4 1.0 O2G F:ACP401 3.9 0.3 1.0 H3B1 F:ACP401 3.9 0.7 1.0 C3B F:ACP401 4.0 0.4 1.0 CG F:ASN333 4.1 0.0 1.0 ND2 F:ASN333 4.2 0.1 1.0 O3A F:ACP401 4.5 0.8 1.0 O2B F:ACP401 4.7 0.7 1.0 CE F:LYS74 4.8 0.5 1.0 H3B2 F:ACP401 4.9 0.7 1.0 CG F:GLU331 4.9 98.0 1.0

G.Menchon, A.E.Prota, D.Lucena-Agell, P.Bucher, R.Jansen, H.Irschik, R.Muller, I.Paterson, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. A Fluorescence Anisotropy Assay to Discover and Characterize Ligands Targeting the Maytansine Site of Tubulin. Nat Commun V. 9 2106 2018.
ISSN: ESSN 2041-1723
PubMed: 29844393
DOI: 10.1038/S41467-018-04535-8