Magnesium in PDB 8bdf: Tubulin-Taxane-2A Complex

The structure of Tubulin-Taxane-2A Complex, PDB code: 8bdf 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)	49.28 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.84, 157.89, 179.09, 90, 90, 90
R / Rfree (%)	18.9 / 21.6

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

Calcium

(Ca)

1 atom

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

Magnesium binding site 1 out of 5 in the Tubulin-Taxane-2A 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-2A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:40.3 occ:1.00 O A:HOH647 2.0 38.1 1.0 O3G A:GTP501 2.0 31.9 1.0 O A:HOH737 2.1 38.3 1.0 O1B A:GTP501 2.2 31.7 1.0 O A:HOH689 2.2 39.2 1.0 PG A:GTP501 3.1 35.5 1.0 PB A:GTP501 3.2 35.7 1.0 O3B A:GTP501 3.5 42.8 1.0 O1G A:GTP501 3.6 37.1 1.0 O3A A:GTP501 3.6 37.3 1.0 NZ B:LYS254 3.7 42.6 1.0 OD1 A:ASP69 4.1 50.5 1.0 CB A:GLN11 4.1 37.3 1.0 OD2 A:ASP69 4.2 42.1 1.0 OE2 A:GLU71 4.3 62.0 1.0 OD2 A:ASP98 4.3 46.6 1.0 CG A:GLU71 4.3 59.0 1.0 CB A:ASP98 4.4 40.4 1.0 N A:GLN11 4.4 35.4 1.0 O2G A:GTP501 4.4 33.6 1.0 O A:HOH676 4.4 60.9 1.0 O2B A:GTP501 4.5 37.2 1.0 O1A A:GTP501 4.5 37.7 1.0 CG A:ASP69 4.6 49.3 1.0 PA A:GTP501 4.7 38.3 1.0 CG A:ASP98 4.7 45.3 1.0 OE1 A:GLN11 4.8 50.1 1.0 CE B:LYS254 4.8 40.8 1.0 CD A:GLU71 4.8 61.8 1.0 CA A:GLN11 4.9 36.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Taxane-2A 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-2A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:28.1 occ:1.00 O B:HOH656 2.2 35.1 1.0 OE1 B:GLN11 2.2 44.6 1.0 O1A B:GDP501 2.3 30.7 1.0 O C:HOH674 2.4 46.2 1.0 O B:HOH689 2.4 37.0 1.0 O B:HOH608 2.5 43.4 1.0 CD B:GLN11 3.4 42.6 1.0 PA B:GDP501 3.6 34.5 1.0 O3A B:GDP501 3.9 36.6 1.0 OD2 B:ASP179 3.9 42.0 1.0 CB B:GLN11 4.0 33.3 1.0 CG B:GLN11 4.1 39.0 1.0 OD1 B:ASN101 4.3 41.9 1.0 NE2 B:GLN11 4.4 47.3 1.0 C5' B:GDP501 4.4 39.3 1.0 OE1 C:GLU254 4.5 47.4 1.0 O5' B:GDP501 4.5 33.6 1.0 O C:HOH634 4.6 48.6 1.0 O1B B:GDP501 4.6 30.6 1.0 O2A B:GDP501 4.7 31.6 1.0 C8 B:GDP501 4.8 39.8 1.0 PB B:GDP501 4.9 34.1 1.0 CG B:ASP179 5.0 44.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Taxane-2A 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-2A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.1 occ:1.00 O C:HOH658 2.0 33.7 1.0 O C:HOH788 2.0 32.4 1.0 O1G C:GTP501 2.1 30.4 1.0 O1B C:GTP501 2.1 30.5 1.0 O C:HOH655 2.2 34.3 1.0 O C:HOH712 2.2 32.3 1.0 PB C:GTP501 3.2 35.8 1.0 PG C:GTP501 3.2 35.5 1.0 O3B C:GTP501 3.6 37.4 1.0 O2G C:GTP501 3.7 34.3 1.0 O3A C:GTP501 3.8 37.4 1.0 NZ D:LYS254 4.0 36.9 1.0 OD1 C:ASP69 4.0 38.1 1.0 OE1 C:GLU71 4.1 53.5 1.0 OD2 C:ASP69 4.1 34.4 1.0 CB C:GLN11 4.2 32.7 1.0 CG C:GLU71 4.2 48.7 1.0 N C:GLN11 4.4 29.3 1.0 OD2 C:ASP98 4.4 46.7 1.0 O3G C:GTP501 4.5 29.7 1.0 CB C:ASP98 4.5 40.6 1.0 O2B C:GTP501 4.5 31.0 1.0 CG C:ASP69 4.5 37.1 1.0 O1A C:GTP501 4.6 33.5 1.0 O C:HOH650 4.6 53.0 1.0 CD C:GLU71 4.6 50.4 1.0 PA C:GTP501 4.8 33.3 1.0 CG C:ASP98 4.8 39.0 1.0 CA C:GLN11 4.9 35.3 1.0 OE1 C:GLN11 4.9 43.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Taxane-2A 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-2A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.5 occ:1.00 OE1 D:GLN11 2.0 77.2 1.0 O D:HOH611 2.1 64.0 1.0 O1A D:GDP501 2.2 87.3 1.0 O D:HOH702 2.4 70.8 1.0 O D:HOH661 3.0 54.6 1.0 CD D:GLN11 3.3 70.2 1.0 PA D:GDP501 3.7 63.4 1.0 CG D:GLN11 4.1 70.7 1.0 CB D:GLN11 4.1 63.0 1.0 NE2 D:GLN11 4.2 75.0 1.0 O D:HOH701 4.3 69.9 1.0 C5' D:GDP501 4.4 63.9 1.0 O2A D:GDP501 4.5 61.0 1.0 O3A D:GDP501 4.5 56.6 1.0 O5' D:GDP501 4.6 66.7 1.0 O1B D:GDP501 4.7 49.0 1.0 OD1 D:ASN101 4.7 77.0 1.0 C8 D:GDP501 4.8 51.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Taxane-2A 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-2A Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:81.8 occ:1.00 O1G F:ACP401 2.3 148.7 1.0 ND2 F:ASN333 2.4 113.7 1.0 OE2 F:GLU331 2.5 119.2 1.0 O1B F:ACP401 2.6 153.1 1.0 CD F:GLU331 3.3 109.8 1.0 OE1 F:GLU331 3.4 117.0 1.0 PG F:ACP401 3.4 151.9 1.0 O3G F:ACP401 3.6 152.7 1.0 PB F:ACP401 3.7 147.2 1.0 CG F:ASN333 3.7 103.9 1.0 O2B F:ACP401 4.0 142.9 1.0 OD1 F:ASN333 4.2 112.2 1.0 C3B F:ACP401 4.2 150.2 1.0 NZ F:LYS74 4.2 110.1 1.0 CG A:GLU450 4.3 106.1 1.0 CB A:GLU450 4.3 107.5 1.0 CD A:GLU450 4.6 113.7 1.0 OE2 A:GLU450 4.7 112.4 1.0 O2G F:ACP401 4.8 152.6 1.0 CG F:GLU331 4.8 91.1 1.0 CB F:ASN333 4.8 77.7 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