Magnesium in PDB 8bdg: Tubulin-Taxane-2B Complex

The structure of Tubulin-Taxane-2B Complex, PDB code: 8bdg was solved by A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muehlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.37 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.25, 158.64, 179.19, 90, 90, 90
R / Rfree (%)	18.3 / 21.4

The structure of Tubulin-Taxane-2B Complex also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Calcium	(Ca)	1 atom

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

Magnesium binding site 1 out of 5 in the Tubulin-Taxane-2B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Taxane-2B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.2 occ:1.00 O3G A:GTP501 2.0 43.9 1.0 O A:HOH619 2.0 48.1 1.0 O A:HOH605 2.1 46.5 1.0 O A:HOH609 2.2 46.4 1.0 O1B A:GTP501 2.2 46.6 1.0 O A:HOH618 2.2 46.6 1.0 PG A:GTP501 3.1 52.0 1.0 PB A:GTP501 3.3 45.3 1.0 O1G A:GTP501 3.3 44.4 1.0 O3B A:GTP501 3.5 66.2 1.0 O3A A:GTP501 3.8 57.8 1.0 NZ B:LYS254 3.8 54.6 1.0 OD1 A:ASP69 4.0 59.6 1.0 OE2 A:GLU71 4.0 80.7 1.0 CG A:GLU71 4.1 78.0 1.0 CB A:GLN11 4.3 50.3 1.0 CB A:ASP98 4.3 54.3 1.0 OD2 A:ASP69 4.3 58.6 1.0 OD2 A:ASP98 4.3 59.5 1.0 O2G A:GTP501 4.4 40.4 1.0 N A:GLN11 4.4 43.9 1.0 O2B A:GTP501 4.6 53.4 1.0 CG A:ASP98 4.6 55.3 1.0 CD A:GLU71 4.6 79.4 1.0 CG A:ASP69 4.6 64.0 1.0 O1A A:GTP501 4.7 57.3 1.0 OE1 A:GLN11 4.7 73.8 1.0 PA A:GTP501 4.8 52.2 1.0 OG1 A:THR145 4.9 49.0 1.0 CA A:GLN11 5.0 51.6 1.0 CE B:LYS254 5.0 52.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Taxane-2B Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:42.0 occ:1.00 O1A B:GDP501 2.2 58.7 1.0 O C:HOH652 2.3 49.0 1.0 OE1 B:GLN11 2.3 48.9 1.0 O B:HOH630 2.4 48.5 1.0 O B:HOH612 2.6 58.5 1.0 PA B:GDP501 3.5 45.7 1.0 CD B:GLN11 3.6 50.3 1.0 OD2 B:ASP179 3.7 60.8 1.0 O3A B:GDP501 4.0 49.3 1.0 OD1 B:ASN101 4.1 48.6 1.0 C5' B:GDP501 4.3 45.5 1.0 CB B:GLN11 4.3 42.4 1.0 O C:HOH648 4.3 62.8 1.0 CG B:GLN11 4.4 45.4 1.0 O5' B:GDP501 4.4 44.9 1.0 OE1 C:GLU254 4.4 68.4 1.0 NE2 B:GLN11 4.5 59.7 1.0 O2A B:GDP501 4.6 45.9 1.0 O1B B:GDP501 4.6 41.8 1.0 CG B:ASP179 4.7 47.4 1.0 ND2 B:ASN101 4.8 41.3 1.0 C8 B:GDP501 4.8 49.7 1.0 CG B:ASN101 4.9 47.4 1.0 PB B:GDP501 4.9 43.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Taxane-2B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Taxane-2B Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.9 occ:1.00 O1G C:GTP501 2.0 39.5 1.0 O C:HOH610 2.0 40.6 1.0 O C:HOH638 2.0 44.0 1.0 O C:HOH622 2.1 40.2 1.0 O C:HOH641 2.1 39.4 1.0 O1B C:GTP501 2.2 40.6 1.0 PG C:GTP501 3.1 49.8 1.0 PB C:GTP501 3.2 43.3 1.0 O3B C:GTP501 3.6 58.0 1.0 O2G C:GTP501 3.6 44.1 1.0 O3A C:GTP501 3.7 56.0 1.0 NZ D:LYS254 3.8 43.7 1.0 OD1 C:ASP69 4.1 47.8 1.0 OE1 C:GLU71 4.1 73.6 1.0 OD2 C:ASP69 4.2 45.5 1.0 CB C:GLN11 4.2 37.6 1.0 CG C:GLU71 4.2 62.1 1.0 OD2 C:ASP98 4.3 55.3 1.0 O3G C:GTP501 4.4 39.9 1.0 N C:GLN11 4.4 41.7 1.0 CB C:ASP98 4.5 45.1 1.0 O2B C:GTP501 4.5 54.9 1.0 CG C:ASP69 4.6 44.3 1.0 O1A C:GTP501 4.6 49.1 1.0 CD C:GLU71 4.7 68.6 1.0 PA C:GTP501 4.7 46.2 1.0 CG C:ASP98 4.8 50.4 1.0 OE1 C:GLN11 4.8 58.2 1.0 CA C:GLN11 4.9 40.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Taxane-2B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Taxane-2B Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:93.8 occ:1.00 O1A D:GDP501 2.2 103.3 1.0 OE1 D:GLN11 2.6 93.4 1.0 O D:HOH603 2.8 68.6 1.0 PA D:GDP501 3.7 74.1 1.0 CD D:GLN11 3.7 93.5 1.0 C5' D:GDP501 4.1 73.9 1.0 OD1 D:ASN101 4.2 92.2 1.0 O5' D:GDP501 4.4 76.2 1.0 O2A D:GDP501 4.5 70.1 1.0 NE2 D:GLN11 4.5 97.5 1.0 O3A D:GDP501 4.6 70.4 1.0 CB D:GLN11 4.7 78.4 1.0 CG D:GLN11 4.7 87.8 1.0 ND2 D:ASN101 4.9 101.5 1.0 O1B D:GDP501 4.9 74.2 1.0 CG D:ASN101 5.0 97.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Taxane-2B Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:86.2 occ:1.00 OE2 F:GLU331 2.3 139.8 1.0 ND2 F:ASN333 2.6 107.9 1.0 OE1 F:GLU331 2.7 139.7 1.0 CD F:GLU331 2.8 135.5 1.0 CG F:ASN333 3.8 105.3 1.0 NZ F:LYS74 4.0 114.0 1.0 OD1 F:ASN333 4.1 112.7 1.0 CG F:GLU331 4.2 122.4 1.0 CB A:GLU450 4.5 122.5 1.0 CG A:GLU450 4.6 121.5 1.0 CD A:GLU450 4.7 121.4 1.0 OE2 A:GLU450 4.9 121.5 1.0 CE F:LYS74 5.0 111.0 1.0

A.E.Prota, D.Lucena-Agell, Y.Ma, J.Estevez-Gallego, S.Li, K.Bargsten, F.Josa-Prado, K.H.Altmann, N.Gaillard, S.Kamimura, T.Muhlethaler, F.Gago, M.A.Oliva, M.O.Steinmetz, W.S.Fang, J.F.Diaz. Structural Insight Into the Stabilization of Microtubules By Taxanes. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36876916
DOI: 10.7554/ELIFE.84791