Magnesium in PDB 5osk: Tubulin-7J Complex

The structure of Tubulin-7J Complex, PDB code: 5osk was solved by G.Menchon, A.E.Prota, M.O.Steinmetz, B.V.L.Potter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.79 / 2.11
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 (%)	19.5 / 23.2

The structure of Tubulin-7J Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Tubulin-7J Complex (pdb code 5osk). 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-7J Complex, PDB code: 5osk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-7J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-7J Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.8 occ:1.00 O A:HOH645 2.0 47.0 1.0 O A:HOH634 2.1 46.0 1.0 O A:HOH665 2.1 41.4 1.0 O2G A:GTP501 2.1 37.5 1.0 O A:HOH656 2.2 49.9 1.0 O1B A:GTP501 2.3 41.1 1.0 PG A:GTP501 3.3 44.4 1.0 PB A:GTP501 3.4 44.2 1.0 O1G A:GTP501 3.7 45.1 1.0 O3B A:GTP501 3.8 53.3 1.0 O3A A:GTP501 4.0 46.4 1.0 CB A:GLN11 4.1 45.2 1.0 OD1 A:ASP69 4.2 58.0 1.0 NZ B:LYS254 4.2 49.2 0.7 OD2 A:ASP69 4.2 55.6 1.0 OD2 A:ASP98 4.3 54.5 1.0 N A:GLN11 4.4 46.8 1.0 CB A:ASP98 4.5 51.9 1.0 OE2 A:GLU71 4.5 89.4 1.0 O1A A:GTP501 4.5 40.2 1.0 O3G A:GTP501 4.6 40.1 1.0 CG A:ASP69 4.6 58.1 1.0 O2B A:GTP501 4.7 51.8 1.0 OE1 A:GLN11 4.7 53.6 1.0 CG A:ASP98 4.8 52.7 1.0 CD A:GLU71 4.9 87.1 1.0 PA A:GTP501 4.9 43.4 1.0 CA A:GLN11 4.9 46.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-7J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-7J Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:37.8 occ:1.00 O B:HOH634 2.2 44.1 1.0 O C:HOH608 2.3 61.0 1.0 OE1 B:GLN11 2.3 52.4 1.0 O1A B:GDP502 2.3 37.4 1.0 O B:HOH690 2.4 52.6 1.0 O B:HOH639 2.6 47.7 1.0 CD B:GLN11 3.5 51.0 1.0 PA B:GDP502 3.6 40.1 1.0 O C:HOH833 3.6 65.9 1.0 O3A B:GDP502 3.9 38.9 1.0 OD2 B:ASP179 3.9 53.0 1.0 CB B:GLN11 4.2 38.6 1.0 C5' B:GDP502 4.3 42.3 1.0 O5' B:GDP502 4.3 43.0 1.0 OE2 C:GLU254 4.3 57.9 1.0 CG B:GLN11 4.3 44.7 1.0 OD1 B:ASN101 4.3 48.9 1.0 NE2 B:GLN11 4.5 48.4 1.0 O2A B:GDP502 4.7 39.3 1.0 O1B B:GDP502 4.7 37.6 1.0 O B:HOH732 4.7 74.8 1.0 O C:HOH738 4.8 75.0 1.0 C8 B:GDP502 4.8 48.5 1.0 CG B:ASP179 4.9 55.4 1.0 PB B:GDP502 4.9 40.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-7J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-7J Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.4 occ:1.00 O1G C:GTP501 2.0 38.7 1.0 O C:HOH654 2.1 37.5 1.0 O C:HOH653 2.1 41.5 1.0 O C:HOH732 2.1 41.4 1.0 O1B C:GTP501 2.1 37.5 1.0 O C:HOH646 2.2 40.2 1.0 PG C:GTP501 3.2 43.5 1.0 PB C:GTP501 3.2 40.5 1.0 O3B C:GTP501 3.6 41.8 1.0 O2G C:GTP501 3.6 43.5 1.0 O3A C:GTP501 3.8 42.1 1.0 OE2 C:GLU71 4.1 59.5 1.0 OD1 C:ASP69 4.1 48.6 1.0 NZ D:LYS254 4.2 46.9 1.0 CB C:GLN11 4.2 35.5 1.0 OD2 C:ASP98 4.3 54.0 1.0 CG C:GLU71 4.3 53.7 1.0 OD2 C:ASP69 4.3 44.4 1.0 N C:GLN11 4.4 32.8 1.0 O3G C:GTP501 4.5 39.6 1.0 O2B C:GTP501 4.5 41.5 1.0 CB C:ASP98 4.5 43.0 1.0 O1A C:GTP501 4.6 36.1 1.0 CD C:GLU71 4.7 56.9 1.0 CG C:ASP69 4.7 45.9 1.0 NE2 C:GLN11 4.8 43.8 1.0 PA C:GTP501 4.8 40.2 1.0 CG C:ASP98 4.8 48.3 1.0 O C:HOH736 4.8 79.9 1.0 CA C:GLN11 4.9 36.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-7J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-7J Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.9 occ:1.00 OE1 D:GLN11 2.1 0.1 1.0 O D:HOH613 2.4 61.0 1.0 O D:HOH649 2.4 65.3 1.0 O1A D:GDP501 2.5 75.4 1.0 O D:HOH671 2.5 71.2 1.0 O D:HOH655 2.7 66.8 1.0 CD D:GLN11 3.3 0.8 1.0 PA D:GDP501 3.8 73.0 1.0 NE2 D:GLN11 4.1 99.5 1.0 O3A D:GDP501 4.1 66.2 1.0 CG D:GLN11 4.2 90.3 1.0 CB D:GLN11 4.3 84.8 1.0 C5' D:GDP501 4.4 67.2 1.0 O5' D:GDP501 4.6 69.4 1.0 O2A D:GDP501 4.8 75.2 1.0 OD1 D:ASN101 4.8 92.3 1.0 C8 D:GDP501 4.9 60.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-7J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-7J Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.8 occ:1.00 O1B F:ACP402 2.4 0.4 1.0 OE2 F:GLU331 2.4 0.8 1.0 O1G F:ACP402 2.9 0.8 1.0 CD F:GLU331 3.2 0.3 1.0 ND2 F:ASN333 3.2 0.4 1.0 OE1 F:GLU331 3.3 0.4 1.0 PB F:ACP402 3.5 0.7 1.0 PG F:ACP402 3.6 0.8 1.0 O2G F:ACP402 3.7 0.2 1.0 C3B F:ACP402 3.7 0.4 1.0 CG F:ASN333 4.4 0.0 1.0 CE F:LYS74 4.6 0.1 1.0 O3A F:ACP402 4.6 0.8 1.0 OD1 F:ASN333 4.6 0.9 1.0 CG F:GLU331 4.6 0.7 1.0 O2B F:ACP402 4.6 0.6 1.0 NZ F:LYS74 4.6 0.3 1.0

W.Dohle, F.L.Jourdan, G.Menchon, A.E.Prota, P.A.Foster, P.Mannion, E.Hamel, M.P.Thomas, P.G.Kasprzyk, E.Ferrandis, M.O.Steinmetz, M.P.Leese, B.V.L.Potter. Quinazolinone-Based Anticancer Agents: Synthesis, Antiproliferative Sar, Antitubulin Activity, and Tubulin Co-Crystal Structure. J. Med. Chem. V. 61 1031 2018.
ISSN: ISSN 1520-4804
PubMed: 29227648
DOI: 10.1021/ACS.JMEDCHEM.7B01474