Magnesium in PDB 8c0f: Tubulin-PTC596 Complex

The structure of Tubulin-PTC596 Complex, PDB code: 8c0f was solved by A.E.Prota, T.Muehlethaler, M.Weetall, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.68, 158.26, 180.54, 90, 90, 90
R / Rfree (%)	19.4 / 22.5

The structure of Tubulin-PTC596 Complex also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Fluorine	(F)	5 atoms

The binding sites of Magnesium atom in the Tubulin-PTC596 Complex (pdb code 8c0f). 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-PTC596 Complex, PDB code: 8c0f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.2 occ:1.00 O A:HOH625 2.0 44.6 1.0 O1B A:GTP501 2.1 41.3 1.0 O3G A:GTP501 2.1 37.0 1.0 O A:HOH676 2.2 45.9 1.0 O A:HOH616 2.2 76.8 1.0 O A:HOH644 2.3 73.2 1.0 PB A:GTP501 3.2 40.8 1.0 PG A:GTP501 3.2 46.4 1.0 O3B A:GTP501 3.6 53.1 1.0 O1G A:GTP501 3.6 43.5 1.0 O3A A:GTP501 3.6 53.8 1.0 NZ B:LYS254 3.9 54.6 1.0 OD1 A:ASP69 4.1 55.4 1.0 CB A:GLN11 4.1 43.0 1.0 OD2 A:ASP69 4.3 53.9 1.0 OE1 A:GLU71 4.3 78.9 1.0 N A:GLN11 4.3 49.9 1.0 CG A:GLU71 4.4 73.8 1.0 OD2 A:ASP98 4.4 54.9 1.0 O2B A:GTP501 4.5 48.3 1.0 O2G A:GTP501 4.5 52.8 1.0 O1A A:GTP501 4.6 45.2 1.0 CG A:ASP69 4.6 57.5 1.0 CB A:ASP98 4.6 53.2 1.0 PA A:GTP501 4.7 46.4 1.0 CA A:GLN11 4.8 47.5 1.0 CG A:ASP98 4.8 55.6 1.0 OE1 A:GLN11 4.8 56.1 1.0 CD A:GLU71 4.8 77.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.7 occ:1.00 O B:HOH655 2.1 37.8 1.0 OE1 B:GLN11 2.1 44.4 1.0 O C:HOH648 2.3 48.2 1.0 O1A B:GDP501 2.3 44.9 1.0 O B:HOH669 2.4 53.5 1.0 O B:HOH628 2.4 52.2 1.0 O B:HOH704 3.0 73.8 1.0 CD B:GLN11 3.3 49.8 1.0 PA B:GDP501 3.6 39.8 1.0 O3A B:GDP501 3.8 44.2 1.0 OD2 B:ASP179 4.0 49.3 1.0 CB B:GLN11 4.0 39.4 1.0 CG B:GLN11 4.2 40.6 1.0 OD1 B:ASN101 4.3 40.9 1.0 NE2 B:GLN11 4.3 47.3 1.0 C5' B:GDP501 4.4 43.4 1.0 O5' B:GDP501 4.4 37.6 1.0 O C:HOH628 4.5 50.1 1.0 OE1 C:GLU254 4.5 44.1 1.0 O1B B:GDP501 4.6 34.7 1.0 O2A B:GDP501 4.7 38.0 1.0 PB B:GDP501 4.9 39.8 1.0 C8 B:GDP501 4.9 45.4 1.0 ND2 B:ASN101 5.0 37.9 1.0 CG B:ASP179 5.0 51.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:37.0 occ:1.00 O C:HOH668 2.0 37.4 1.0 O1G C:GTP501 2.0 32.6 1.0 O C:HOH687 2.0 38.4 1.0 O C:HOH615 2.0 34.9 1.0 O1B C:GTP501 2.0 34.4 1.0 O C:HOH627 2.1 35.1 1.0 PG C:GTP501 3.2 39.0 1.0 PB C:GTP501 3.2 37.9 1.0 O3B C:GTP501 3.6 42.0 1.0 O2G C:GTP501 3.6 38.9 1.0 O3A C:GTP501 3.7 43.1 1.0 NZ D:LYS254 3.9 41.9 1.0 OE1 C:GLU71 4.0 52.2 1.0 OD1 C:ASP69 4.0 45.7 1.0 OD2 C:ASP98 4.2 51.7 1.0 CB C:GLN11 4.2 35.2 1.0 OD2 C:ASP69 4.3 45.1 1.0 CG C:GLU71 4.3 49.7 1.0 N C:GLN11 4.4 32.0 1.0 CB C:ASP98 4.4 40.7 1.0 O2B C:GTP501 4.4 42.2 1.0 O3G C:GTP501 4.4 38.9 1.0 O1A C:GTP501 4.6 35.3 1.0 CG C:ASP69 4.6 44.5 1.0 CD C:GLU71 4.6 53.5 1.0 CG C:ASP98 4.7 45.3 1.0 PA C:GTP501 4.7 37.7 1.0 OE1 C:GLN11 4.9 50.7 1.0 CA C:GLN11 4.9 36.8 1.0 OG1 C:THR145 5.0 39.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:74.9 occ:1.00 O1A D:GDP501 2.4 78.9 1.0 OE1 D:GLN11 2.6 80.2 1.0 O D:HOH640 3.0 70.4 1.0 PA D:GDP501 3.6 69.2 1.0 O D:HOH653 3.7 68.6 1.0 CD D:GLN11 3.8 84.6 1.0 O3A D:GDP501 4.0 57.0 1.0 C5' D:GDP501 4.0 65.7 1.0 O5' D:GDP501 4.3 64.7 1.0 OD1 D:ASN101 4.4 88.5 1.0 CB D:GLN11 4.6 72.7 1.0 CG D:GLN11 4.7 75.1 1.0 NE2 D:GLN11 4.8 81.8 1.0 O2A D:GDP501 4.8 81.2 1.0 C8 D:GDP501 4.9 62.6 1.0 O1B D:GDP501 4.9 64.6 1.0

Magnesium binding site 5 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-PTC596 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:93.7 occ:1.00 OE2 F:GLU331 2.2 118.2 1.0 O3G F:ACP701 2.3 132.1 1.0 OE1 F:GLU331 2.4 116.8 1.0 O1B F:ACP701 2.4 133.9 1.0 CD F:GLU331 2.7 113.2 1.0 PG F:ACP701 3.5 133.0 1.0 PB F:ACP701 3.7 131.7 1.0 C3B F:ACP701 3.9 132.7 1.0 O1G F:ACP701 3.9 128.5 1.0 CE F:LYS74 4.1 86.6 1.0 CG F:GLU331 4.2 104.8 1.0 OD1 F:ASN333 4.3 138.1 1.0 CB F:ASN333 4.5 121.5 1.0 NZ F:LYS74 4.5 106.2 1.0 O2B F:ACP701 4.6 131.9 1.0 O3A F:ACP701 4.8 130.6 1.0 O2G F:ACP701 4.8 131.2 1.0 CG F:ASN333 4.9 135.8 1.0 CB F:GLU331 5.0 98.2 1.0

F.Jernigan, A.Branstrom, J.D.Baird, L.Cao, M.Dali, B.Furia, M.J.Kim, K.O'keefe, R.Kong, O.L.Laskin, J.M.Colacino, M.Pykett, A.Mollin, J.Sheedy, M.Dumble, Y.-C.Moon, R.Sheridan, T.Muehlethaler, R.J.Spiegel, A.E.Prota, M.O.Steinmetz, M.Weetall. Preclinical and Early Clinical Development of PTC596, A Novel Small-Molecule Tubulin-Binding Agent Mol Cancer Ther V. 20 1846 2021.
ISSN: ISSN 1535-7163
PubMed: 34315764
DOI: 10.1158/1535-7163.MCT-20-0774