Magnesium in PDB 5ov7: Tubulin - Rigosertib Complex

The structure of Tubulin - Rigosertib Complex, PDB code: 5ov7 was solved by G.Menchon, A.E.Prota, M.Steinmetz, M.Jost, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.732, 156.765, 182.629, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.5

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

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Tubulin - Rigosertib Complex (pdb code 5ov7). 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 - Rigosertib Complex, PDB code: 5ov7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin - Rigosertib Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.6 occ:1.00 O A:HOH615 1.9 48.9 1.0 O2G A:GTP501 2.0 34.1 1.0 O A:HOH617 2.0 60.6 1.0 O A:HOH611 2.0 48.9 1.0 O1B A:GTP501 2.2 44.5 1.0 O A:HOH621 2.3 51.3 1.0 PG A:GTP501 3.2 51.6 1.0 PB A:GTP501 3.3 48.5 1.0 O3B A:GTP501 3.6 65.5 1.0 OE2 A:GLU71 3.7 95.0 1.0 O3A A:GTP501 3.8 58.5 1.0 O1G A:GTP501 3.8 51.3 1.0 CB A:GLN11 4.1 50.5 1.0 OD1 A:ASP69 4.1 65.8 1.0 OD2 A:ASP69 4.2 69.5 1.0 N A:GLN11 4.4 56.0 1.0 O3G A:GTP501 4.5 35.2 1.0 OD2 A:ASP98 4.5 75.1 1.0 CB A:ASP98 4.6 56.9 1.0 CG A:ASP69 4.6 65.5 1.0 OE1 A:GLN11 4.6 48.6 1.0 O2B A:GTP501 4.6 65.2 1.0 O1A A:GTP501 4.6 52.0 1.0 PA A:GTP501 4.8 49.7 1.0 CA A:GLN11 4.8 55.2 1.0 CG A:ASP98 4.8 71.5 1.0 CD A:GLU71 4.9 96.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin - Rigosertib Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.5 occ:1.00 O1A B:GDP501 2.2 44.3 1.0 O C:HOH674 2.3 53.9 1.0 OE1 B:GLN11 2.3 57.8 1.0 O B:HOH613 2.3 95.6 1.0 O B:HOH620 2.4 65.1 1.0 O B:HOH645 2.4 49.7 1.0 O B:HOH662 3.4 59.8 1.0 O B:HOH668 3.5 66.2 1.0 CD B:GLN11 3.5 59.8 1.0 PA B:GDP501 3.5 41.1 1.0 OD2 B:ASP179 3.8 70.7 1.0 O3A B:GDP501 3.9 46.6 1.0 ND2 B:ASN101 4.1 43.6 1.0 CB B:GLN11 4.1 42.1 1.0 C5' B:GDP501 4.3 40.9 1.0 O5' B:GDP501 4.3 33.2 1.0 CG B:GLN11 4.3 46.2 1.0 O B:HOH628 4.4 83.7 1.0 NE2 B:GLN11 4.5 71.8 1.0 O1B B:GDP501 4.6 39.5 1.0 O2A B:GDP501 4.6 36.4 1.0 CG B:ASP179 4.8 66.8 1.0 OE1 C:GLU254 4.8 85.6 1.0 C8 B:GDP501 4.9 47.7 1.0 PB B:GDP501 4.9 45.7 1.0 OD1 B:ASN101 4.9 45.5 1.0 CG B:ASN101 5.0 41.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin - Rigosertib Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:42.5 occ:1.00 O C:HOH621 1.9 42.1 1.0 O C:HOH628 2.0 45.5 1.0 O C:HOH646 2.1 41.1 1.0 O1G C:GTP502 2.1 39.6 1.0 O C:HOH613 2.1 39.7 1.0 O1B C:GTP502 2.3 36.3 1.0 PG C:GTP502 3.3 46.0 1.0 OE1 C:GLU71 3.3 77.9 1.0 PB C:GTP502 3.5 42.0 1.0 O2G C:GTP502 3.6 43.2 1.0 O3B C:GTP502 3.8 47.7 1.0 O3A C:GTP502 4.0 59.0 1.0 OD1 C:ASP69 4.2 57.3 1.0 OD2 C:ASP69 4.2 54.9 1.0 CB C:GLN11 4.2 34.1 1.0 OD2 C:ASP98 4.3 70.0 1.0 CB C:ASP98 4.3 49.5 1.0 CD C:GLU71 4.5 75.8 1.0 N C:GLN11 4.5 46.6 1.0 O3G C:GTP502 4.5 36.9 1.0 NZ D:LYS254 4.6 69.8 1.0 CG C:ASP98 4.6 56.4 1.0 CG C:ASP69 4.6 49.2 1.0 O2B C:GTP502 4.7 44.1 1.0 O1A C:GTP502 4.7 48.7 1.0 OE1 C:GLN11 4.8 52.0 1.0 PA C:GTP502 4.9 41.1 1.0 CA C:GLN11 5.0 41.9 1.0 CB C:GLU71 5.0 58.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin - Rigosertib Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:66.2 occ:1.00 OE1 D:GLN11 1.8 0.8 1.0 O D:HOH607 2.3 66.3 1.0 O1A D:GDP501 2.4 0.9 1.0 O D:HOH623 2.4 92.6 1.0 O D:HOH627 3.0 71.0 1.0 CD D:GLN11 3.0 0.6 1.0 CB D:GLN11 3.9 98.3 1.0 PA D:GDP501 3.9 96.7 1.0 NE2 D:GLN11 3.9 0.1 1.0 CG D:GLN11 3.9 0.4 1.0 OD1 D:ASP179 4.0 0.9 1.0 O3A D:GDP501 4.6 93.0 1.0 O2A D:GDP501 4.6 90.6 1.0 CG D:ASP179 4.8 0.2 1.0 O1B D:GDP501 4.8 91.2 1.0 C5' D:GDP501 4.8 74.9 1.0 C8 D:GDP501 4.9 67.4 1.0 O5' D:GDP501 4.9 79.8 1.0 OD2 D:ASP179 4.9 0.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin - Rigosertib Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.1 occ:1.00 O3G F:ACP401 2.0 0.6 1.0 O1B F:ACP401 2.5 0.8 1.0 OD1 F:ASN333 2.7 0.5 1.0 OE1 F:GLU331 2.9 0.8 1.0 OE2 F:GLU331 3.3 0.2 1.0 PG F:ACP401 3.3 0.1 1.0 O F:HOH508 3.4 78.9 1.0 CD F:GLU331 3.5 0.9 1.0 PB F:ACP401 3.5 0.8 1.0 CG F:ASN333 3.8 0.0 1.0 C3B F:ACP401 3.9 0.6 1.0 O1G F:ACP401 3.9 0.3 1.0 O2B F:ACP401 4.0 0.9 1.0 ND2 F:ASN333 4.3 0.4 1.0 O2G F:ACP401 4.6 0.1 1.0 O3A F:ACP401 4.9 0.8 1.0 CG F:GLU331 5.0 0.3 1.0

M.Jost, Y.Chen, L.A.Gilbert, M.A.Horlbeck, L.Krenning, G.Menchon, A.Rai, M.Y.Cho, J.J.Stern, A.E.Prota, M.Kampmann, A.Akhmanova, M.O.Steinmetz, M.E.Tanenbaum, J.S.Weissman. Combined Crispri/A-Based Chemical Genetic Screens Reveal That Rigosertib Is A Microtubule-Destabilizing Agent. Mol. Cell V. 68 210 2017.
ISSN: ISSN 1097-4164
PubMed: 28985505
DOI: 10.1016/J.MOLCEL.2017.09.012