Magnesium in PDB 6hx8: Tubulin-STX3451 Complex

The structure of Tubulin-STX3451 Complex, PDB code: 6hx8 was solved by W.Dohle, A.E.Prota, G.Menchon, E.Hamel, 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)	48.35 / 2.40
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 / 24

The structure of Tubulin-STX3451 Complex also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Tubulin-STX3451 Complex (pdb code 6hx8). 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-STX3451 Complex, PDB code: 6hx8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-STX3451 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-STX3451 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:55.9 occ:1.00 O A:HOH634 1.9 59.2 1.0 O A:HOH621 2.0 66.4 1.0 O A:HOH610 2.0 59.5 1.0 O A:HOH638 2.1 62.1 1.0 O2G A:GTP501 2.2 45.5 1.0 O1B A:GTP501 2.4 48.2 1.0 O A:HOH601 3.4 78.5 1.0 PG A:GTP501 3.5 63.7 1.0 PB A:GTP501 3.5 57.6 1.0 OE2 A:GLU71 3.7 97.7 1.0 O3B A:GTP501 3.9 74.6 1.0 O1G A:GTP501 4.0 52.9 1.0 O3A A:GTP501 4.0 70.8 1.0 CB A:GLN11 4.0 60.8 1.0 CG A:GLU71 4.1 0.9 1.0 OD1 A:ASP69 4.3 76.7 1.0 OE1 A:GLN11 4.4 85.2 1.0 CD A:GLU71 4.4 0.5 1.0 OD2 A:ASP69 4.5 77.0 1.0 N A:GLN11 4.5 63.8 1.0 CB A:ASP98 4.6 69.9 1.0 O A:HOH648 4.7 85.0 1.0 O1A A:GTP501 4.7 54.0 1.0 OD2 A:ASP98 4.7 81.9 1.0 O3G A:GTP501 4.7 45.6 1.0 O2B A:GTP501 4.8 66.8 1.0 CA A:GLN11 4.9 67.0 1.0 CG A:ASP69 4.9 72.4 1.0 CG A:ASP98 4.9 72.0 1.0 PA A:GTP501 4.9 53.8 1.0 CD A:GLN11 5.0 67.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-STX3451 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-STX3451 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:50.5 occ:1.00 O B:HOH628 2.0 61.5 1.0 OE1 B:GLN11 2.0 85.1 1.0 O1A B:GDP501 2.1 52.4 1.0 O B:HOH620 2.2 60.7 1.0 O C:HOH606 2.4 56.3 1.0 O B:HOH647 2.5 57.0 1.0 CD B:GLN11 3.3 72.7 1.0 PA B:GDP501 3.5 51.0 1.0 O3A B:GDP501 4.1 64.6 1.0 OD2 B:ASP179 4.1 72.6 1.0 NE2 B:GLN11 4.1 74.0 1.0 CB B:GLN11 4.2 52.5 1.0 CG B:GLN11 4.2 58.8 1.0 OE2 C:GLU254 4.3 88.1 1.0 O2A B:GDP501 4.5 51.1 1.0 O1B B:GDP501 4.5 54.5 1.0 OD1 B:ASN101 4.5 64.0 1.0 C5' B:GDP501 4.5 49.2 1.0 O5' B:GDP501 4.5 43.1 1.0 C8 B:GDP501 4.8 50.0 1.0 PB B:GDP501 4.9 66.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-STX3451 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-STX3451 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:58.6 occ:1.00 O C:HOH679 2.0 51.1 1.0 O C:HOH677 2.0 48.6 1.0 O1B C:GTP501 2.0 49.5 1.0 O C:HOH656 2.1 51.2 1.0 O1G C:GTP501 2.1 48.0 1.0 O C:HOH625 2.2 47.4 1.0 PB C:GTP501 3.2 56.8 1.0 PG C:GTP501 3.3 59.4 1.0 O3A C:GTP501 3.6 62.8 1.0 O3B C:GTP501 3.7 64.6 1.0 O2G C:GTP501 3.9 51.1 1.0 OE2 C:GLU71 4.1 75.1 1.0 CB C:GLN11 4.1 50.6 1.0 OD2 C:ASP98 4.3 54.9 1.0 OE1 C:GLN11 4.4 76.5 1.0 CG C:GLU71 4.4 59.2 1.0 O2B C:GTP501 4.5 65.3 1.0 OD1 C:ASP69 4.5 61.9 1.0 NZ D:LYS254 4.5 82.1 1.0 OD2 C:ASP69 4.5 53.9 1.0 O1A C:GTP501 4.5 59.9 1.0 O3G C:GTP501 4.6 46.5 1.0 N C:GLN11 4.6 53.3 1.0 PA C:GTP501 4.6 46.0 1.0 O C:HOH676 4.7 96.2 1.0 CD C:GLU71 4.7 71.3 1.0 CB C:ASP98 4.7 48.2 1.0 CA C:GLN11 5.0 59.3 1.0 CG C:ASP69 5.0 57.8 1.0 CG C:ASP98 5.0 50.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-STX3451 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-STX3451 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:78.0 occ:1.00 O D:HOH607 2.2 69.9 1.0 OE1 D:GLN11 2.5 1.0 1.0 O1A D:GDP501 2.8 0.9 1.0 O D:HOH628 2.9 83.2 1.0 CD D:GLN11 3.7 0.8 1.0 PA D:GDP501 3.7 1.0 1.0 O3A D:GDP501 3.7 0.1 1.0 C5' D:GDP501 3.8 99.7 1.0 OD1 D:ASN101 4.0 0.1 1.0 O5' D:GDP501 4.1 0.3 1.0 NE2 D:GLN11 4.3 0.3 1.0 CB D:GLN11 4.7 0.5 1.0 CG D:GLN11 4.8 0.8 1.0 CG D:ASN101 4.8 0.4 1.0 ND2 D:ASN101 4.9 0.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-STX3451 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-STX3451 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.4 occ:1.00 O1G F:ACP401 1.9 0.3 1.0 PG F:ACP401 3.2 0.3 1.0 O2B F:ACP401 3.4 0.4 1.0 ND2 F:ASN333 3.5 0.5 1.0 C3B F:ACP401 3.5 0.0 1.0 OE2 F:GLU331 3.7 0.9 1.0 PB F:ACP401 3.8 0.7 1.0 O1B F:ACP401 3.8 0.5 1.0 O3G F:ACP401 4.1 0.0 1.0 CG F:ASN333 4.3 0.5 1.0 O2G F:ACP401 4.3 0.7 1.0 OD1 F:ASN333 4.5 0.4 1.0 O F:HOH501 4.7 0.4 1.0 CD F:GLU331 4.9 0.5 1.0

W.Dohle, A.E.Prota, G.Menchon, E.Hamel, M.O.Steinmetz, B.V.L.Potter. Tetrahydroisoquinoline Sulfamates As Potent Microtubule Disruptors: Synthesis, Antiproliferative and Antitubulin Activity of Dichlorobenzyl-Based Derivatives, and A Tubulin Cocrystal Structure. Acs Omega V. 4 755 2019.
ISSN: ESSN 2470-1343
PubMed: 30775645
DOI: 10.1021/ACSOMEGA.8B02879