Magnesium in PDB 8bde: Tubulin-Baccatin III Complex

The structure of Tubulin-Baccatin III Complex, PDB code: 8bde 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)	49.20 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.1, 157.15, 179.15, 90, 90, 90
R / Rfree (%)	19.2 / 21.8

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

Calcium

(Ca)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.0 occ:1.00 O A:HOH664 2.0 34.8 1.0 O2G A:GTP501 2.0 30.6 1.0 O A:HOH708 2.1 37.2 1.0 O A:HOH656 2.1 36.7 1.0 O1B A:GTP501 2.1 30.0 1.0 O A:HOH685 2.2 34.8 1.0 PG A:GTP501 3.1 33.5 1.0 PB A:GTP501 3.2 34.1 1.0 O3G A:GTP501 3.6 36.1 1.0 O3B A:GTP501 3.6 40.5 1.0 O3A A:GTP501 3.7 35.2 1.0 NZ B:LYS254 3.7 36.2 1.0 OE2 A:GLU71 4.0 65.5 1.0 OD1 A:ASP69 4.1 41.6 1.0 CB A:GLN11 4.2 34.5 1.0 OD2 A:ASP69 4.3 40.1 1.0 CG A:GLU71 4.3 55.0 1.0 OD2 A:ASP98 4.4 40.1 1.0 CB A:ASP98 4.4 35.5 1.0 N A:GLN11 4.4 39.9 1.0 O1G A:GTP501 4.4 36.7 1.0 O1A A:GTP501 4.5 34.5 1.0 O2B A:GTP501 4.5 35.1 1.0 NE2 A:GLN11 4.5 43.9 1.0 CG A:ASP69 4.6 43.0 1.0 PA A:GTP501 4.7 35.1 1.0 CD A:GLU71 4.7 61.1 1.0 CG A:ASP98 4.7 42.3 1.0 CE B:LYS254 4.8 35.1 1.0 CA A:GLN11 4.9 34.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.8 occ:1.00 O1A B:GDP501 2.3 33.5 1.0 OE1 B:GLN11 2.3 40.9 1.0 O B:HOH625 2.3 43.0 1.0 O C:HOH674 2.4 47.6 1.0 O B:HOH693 2.5 42.3 1.0 O B:HOH613 2.5 43.3 1.0 O B:HOH728 2.7 67.6 1.0 CD B:GLN11 3.5 45.0 1.0 PA B:GDP501 3.6 33.5 1.0 OD2 B:ASP179 3.8 41.7 1.0 O3A B:GDP501 3.9 34.8 1.0 CB B:GLN11 4.1 32.8 1.0 CG B:GLN11 4.2 38.9 1.0 OD1 B:ASN101 4.3 38.8 1.0 C5' B:GDP501 4.4 33.8 1.0 O5' B:GDP501 4.4 33.5 1.0 NE2 B:GLN11 4.5 46.5 1.0 OE1 C:GLU254 4.5 46.1 1.0 O1B B:GDP501 4.6 29.4 1.0 O C:HOH656 4.6 49.6 1.0 O2A B:GDP501 4.7 33.3 1.0 C8 B:GDP501 4.8 36.1 1.0 CG B:ASP179 4.9 40.1 1.0 PB B:GDP501 4.9 30.4 1.0 O B:HOH710 4.9 56.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.3 occ:1.00 O C:HOH694 2.0 32.3 1.0 O1B C:GTP501 2.0 33.7 1.0 O1G C:GTP501 2.0 32.3 1.0 O C:HOH769 2.1 33.8 1.0 O C:HOH692 2.1 31.3 1.0 O C:HOH684 2.1 31.0 1.0 PB C:GTP501 3.2 31.7 1.0 PG C:GTP501 3.2 33.0 1.0 O3B C:GTP501 3.5 36.6 1.0 O2G C:GTP501 3.6 33.5 1.0 O3A C:GTP501 3.7 33.2 1.0 OE1 C:GLU71 3.9 52.3 1.0 NZ D:LYS254 3.9 33.6 1.0 OD1 C:ASP69 4.0 35.4 1.0 CB C:GLN11 4.2 29.9 1.0 CG C:GLU71 4.2 40.9 1.0 OD2 C:ASP69 4.2 35.2 1.0 OD2 C:ASP98 4.3 39.7 1.0 N C:GLN11 4.4 30.7 1.0 CB C:ASP98 4.4 39.7 1.0 O2B C:GTP501 4.4 32.9 1.0 O3G C:GTP501 4.5 29.8 1.0 CD C:GLU71 4.6 46.5 1.0 CG C:ASP69 4.6 35.4 1.0 O1A C:GTP501 4.6 30.4 1.0 CG C:ASP98 4.7 38.5 1.0 PA C:GTP501 4.8 31.1 1.0 OE1 C:GLN11 4.8 42.0 1.0 CA C:GLN11 4.9 29.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:82.6 occ:1.00 O D:HOH670 2.0 75.6 1.0 OE1 D:GLN11 2.1 85.6 1.0 O1A D:GDP501 2.4 58.4 1.0 O D:HOH688 2.7 64.4 1.0 O D:HOH606 2.8 71.4 1.0 CD D:GLN11 3.4 67.5 1.0 PA D:GDP501 3.7 55.6 1.0 O D:HOH707 3.9 63.1 1.0 O3A D:GDP501 4.0 52.4 1.0 NE2 D:GLN11 4.2 62.2 1.0 OD1 D:ASN101 4.3 75.6 1.0 C5' D:GDP501 4.3 59.3 1.0 CB D:GLN11 4.3 51.7 1.0 CG D:GLN11 4.3 61.2 1.0 O5' D:GDP501 4.5 58.5 1.0 O2A D:GDP501 4.8 54.6 1.0 O1B D:GDP501 4.8 45.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Baccatin III Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Baccatin III Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:82.3 occ:1.00 O F:HOH514 2.1 85.5 1.0 OE1 F:GLU331 2.3 105.5 1.0 O2B F:ACP402 2.4 125.7 1.0 OD1 F:ASN333 2.5 97.4 1.0 O1G F:ACP402 2.6 134.7 1.0 CD F:GLU331 3.0 98.4 1.0 OE2 F:GLU331 3.0 104.0 1.0 O3G F:ACP402 3.3 135.0 1.0 PG F:ACP402 3.4 134.8 1.0 PB F:ACP402 3.7 123.9 1.0 CG F:ASN333 3.7 86.9 1.0 NZ F:LYS74 4.1 95.8 1.0 O1B F:ACP402 4.1 123.7 1.0 C3B F:ACP402 4.2 129.8 1.0 ND2 F:ASN333 4.2 83.2 1.0 CG F:GLU331 4.4 82.0 1.0 O2G F:ACP402 4.8 133.2 1.0 CE F:LYS74 4.9 90.9 1.0 CB F:ASN333 4.9 73.3 1.0 O3A F:ACP402 5.0 118.1 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