Magnesium in PDB 5m8d: Tubulin MTD265-R1 Complex

The structure of Tubulin MTD265-R1 Complex, PDB code: 5m8d was solved by T.Bohnacker, A.E.Prota, M.O.Steinmetz, M.P.Wymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.10 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.180, 157.020, 179.980, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21

The structure of Tubulin MTD265-R1 Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	5 atoms

The binding sites of Magnesium atom in the Tubulin MTD265-R1 Complex (pdb code 5m8d). 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 MTD265-R1 Complex, PDB code: 5m8d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.6 occ:1.00 O A:HOH613 2.0 32.8 1.0 O A:HOH631 2.1 41.5 1.0 O2G A:GTP501 2.1 31.4 1.0 O A:HOH697 2.2 36.0 1.0 O1B A:GTP501 2.2 29.4 1.0 O A:HOH619 2.2 40.4 1.0 PG A:GTP501 3.3 41.6 1.0 PB A:GTP501 3.4 38.1 1.0 O3B A:GTP501 3.6 55.9 1.0 O1G A:GTP501 3.7 43.3 1.0 OE1 A:GLU71 3.8 60.0 1.0 NZ B:LYS254 3.9 50.7 1.0 O3A A:GTP501 3.9 41.0 1.0 OD1 A:ASP69 3.9 49.6 1.0 CB A:GLN11 4.0 37.0 1.0 OD2 A:ASP69 4.0 46.0 1.0 N A:GLN11 4.2 37.5 1.0 OD2 A:ASP98 4.3 48.7 1.0 CG A:GLU71 4.3 57.3 1.0 CG A:ASP69 4.4 47.0 1.0 CB A:ASP98 4.5 41.7 1.0 CD A:GLU71 4.5 60.8 1.0 O3G A:GTP501 4.6 35.3 1.0 ND2 B:ASN249 4.6 0.6 1.0 O1A A:GTP501 4.6 38.5 1.0 O2B A:GTP501 4.6 43.8 1.0 OE1 A:GLN11 4.7 48.8 1.0 CA A:GLN11 4.7 36.7 1.0 CG A:ASP98 4.8 48.4 1.0 PA A:GTP501 4.8 43.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:33.0 occ:1.00 O B:HOH625 2.0 47.0 1.0 OE1 B:GLN11 2.2 45.3 1.0 O C:HOH632 2.3 54.9 1.0 O1A B:GDP502 2.3 42.0 1.0 O B:HOH665 2.4 39.1 1.0 O B:HOH605 2.6 45.1 1.0 O B:HOH693 3.3 66.2 1.0 CD B:GLN11 3.4 47.4 1.0 PA B:GDP502 3.6 33.6 1.0 O3A B:GDP502 3.9 40.5 1.0 OD2 B:ASP179 3.9 57.5 1.0 CB B:GLN11 4.0 37.7 1.0 CG B:GLN11 4.1 40.1 1.0 ND2 B:ASN101 4.4 41.7 1.0 C5' B:GDP502 4.4 37.6 1.0 NE2 B:GLN11 4.4 50.9 1.0 O5' B:GDP502 4.4 36.3 1.0 OE1 C:GLU254 4.5 55.0 1.0 O C:HOH678 4.6 57.4 1.0 O1B B:GDP502 4.6 27.0 1.0 O2A B:GDP502 4.7 41.3 1.0 CG B:ASP179 4.9 55.0 1.0 C8 B:GDP502 4.9 44.0 1.0 PB B:GDP502 4.9 35.1 1.0 OD1 B:ASN101 5.0 51.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.7 occ:1.00 O1G C:GTP501 2.0 31.5 1.0 O C:HOH643 2.0 37.7 1.0 O1B C:GTP501 2.1 28.8 1.0 O C:HOH713 2.1 32.0 1.0 O C:HOH610 2.1 34.4 1.0 O C:HOH646 2.2 34.2 1.0 PG C:GTP501 3.1 35.9 1.0 PB C:GTP501 3.1 30.6 1.0 O3B C:GTP501 3.5 46.3 1.0 O2G C:GTP501 3.5 34.2 1.0 O3A C:GTP501 3.7 38.9 1.0 NZ D:LYS254 3.8 38.6 1.0 OD1 C:ASP69 4.0 39.3 1.0 CB C:GLN11 4.2 27.7 1.0 OE1 C:GLU71 4.2 51.2 1.0 OD2 C:ASP98 4.2 50.8 1.0 OD2 C:ASP69 4.3 35.0 1.0 N C:GLN11 4.3 31.5 1.0 CG C:GLU71 4.3 41.5 1.0 O3G C:GTP501 4.4 29.9 1.0 O2B C:GTP501 4.4 37.7 1.0 O1A C:GTP501 4.5 36.4 1.0 CB C:ASP98 4.5 38.7 1.0 CG C:ASP69 4.6 39.0 1.0 NE2 C:GLN11 4.7 39.8 1.0 PA C:GTP501 4.7 32.6 1.0 CG C:ASP98 4.8 43.5 1.0 CD C:GLU71 4.8 45.9 1.0 CA C:GLN11 4.8 31.4 1.0 CE D:LYS254 5.0 41.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.3 occ:1.00 O D:HOH635 2.0 47.5 1.0 OE1 D:GLN11 2.1 70.8 1.0 O D:HOH634 2.4 66.8 1.0 O1A D:GDP501 2.5 65.3 1.0 CD D:GLN11 3.3 69.6 1.0 O D:HOH665 3.4 74.4 1.0 PA D:GDP501 3.8 63.2 1.0 CG D:GLN11 4.0 67.8 1.0 CB D:GLN11 4.1 66.1 1.0 O3A D:GDP501 4.1 55.4 1.0 NE2 D:GLN11 4.3 74.9 1.0 C5' D:GDP501 4.4 56.7 1.0 O5' D:GDP501 4.6 58.7 1.0 C8 D:GDP501 4.6 55.9 1.0 ND2 D:ASN101 4.7 63.1 1.0 O1B D:GDP501 4.8 46.0 1.0 O2A D:GDP501 4.8 65.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:78.3 occ:1.00 O1B F:ACP402 2.1 0.6 1.0 OE2 F:GLU331 2.1 82.8 1.0 O1G F:ACP402 2.6 0.1 1.0 OD1 F:ASN333 2.8 94.9 1.0 CD F:GLU331 2.9 84.0 1.0 OE1 F:GLU331 3.0 92.7 1.0 PB F:ACP402 3.5 0.7 1.0 NZ F:LYS74 3.6 96.6 1.0 CG F:ASN333 3.6 84.1 1.0 PG F:ACP402 3.6 0.8 1.0 ND2 F:ASN333 3.6 85.6 1.0 O3G F:ACP402 3.9 0.9 1.0 C3B F:ACP402 4.1 0.8 1.0 O2B F:ACP402 4.2 0.6 1.0 CG F:GLU331 4.4 74.0 1.0 CE F:LYS74 4.6 86.2 1.0 O3A F:ACP402 4.7 0.2 1.0 O1A F:ACP402 4.9 0.4 1.0 CB F:ASN333 5.0 66.8 1.0

T.Bohnacker, A.E.Prota, F.Beaufils, J.E.Burke, A.Melone, A.J.Inglis, D.Rageot, A.M.Sele, V.Cmiljanovic, N.Cmiljanovic, K.Bargsten, A.Aher, A.Akhmanova, J.F.Diaz, D.Fabbro, M.Zvelebil, R.L.Williams, M.O.Steinmetz, M.P.Wymann. Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683