Magnesium in PDB 8a0l: Tubulin-CW1-Complex

The structure of Tubulin-CW1-Complex, PDB code: 8a0l was solved by A.E.Prota, J.F.Diaz, M.O.Steinmetz, M.A.Oliva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.51 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.63, 156.559, 179.318, 90, 90, 90
R / Rfree (%)	18.8 / 22.6

The structure of Tubulin-CW1-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-CW1-Complex (pdb code 8a0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-CW1-Complex, PDB code: 8a0l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-CW1-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-CW1-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.1 occ:1.00 O A:HOH617 2.0 33.9 1.0 O A:HOH633 2.0 35.9 1.0 O A:HOH721 2.1 37.6 1.0 O1G A:GTP501 2.1 32.1 1.0 O A:HOH610 2.1 37.1 1.0 O1B A:GTP501 2.2 33.4 1.0 PG A:GTP501 3.2 37.8 1.0 PB A:GTP501 3.3 36.9 1.0 O3B A:GTP501 3.6 46.3 1.0 O2G A:GTP501 3.7 39.6 1.0 NZ B:LYS254 3.8 42.0 1.0 O3A A:GTP501 3.8 37.0 1.0 OD1 A:ASP69 4.1 47.2 1.0 CB A:GLN11 4.1 36.1 1.0 OE2 A:GLU71 4.1 60.0 1.0 OD2 A:ASP98 4.2 50.6 1.0 OD2 A:ASP69 4.2 41.2 1.0 N A:GLN11 4.3 34.0 1.0 CB A:ASP98 4.4 37.7 1.0 CG A:GLU71 4.4 53.4 1.0 O1A A:GTP501 4.4 37.1 1.0 O3G A:GTP501 4.6 35.4 1.0 O2B A:GTP501 4.6 42.8 1.0 OE1 A:GLN11 4.6 47.4 1.0 CG A:ASP69 4.6 48.4 1.0 CG A:ASP98 4.7 46.8 1.0 PA A:GTP501 4.7 38.2 1.0 CD A:GLU71 4.8 59.5 1.0 CA A:GLN11 4.8 36.6 1.0 CE B:LYS254 4.9 36.5 1.0

Magnesium binding site 2 out of 4 in the Tubulin-CW1-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-CW1-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:32.3 occ:1.00 O B:HOH642 2.2 47.7 1.0 O1A B:GDP501 2.3 36.1 1.0 OE1 B:GLN11 2.3 43.5 1.0 O C:HOH694 2.4 50.1 1.0 O B:HOH602 2.5 44.3 1.0 O B:HOH691 2.5 51.4 1.0 O B:HOH724 3.0 81.9 1.0 CD B:GLN11 3.5 50.2 1.0 PA B:GDP501 3.6 34.4 1.0 O3A B:GDP501 3.8 34.7 1.0 OD2 B:ASP179 3.9 47.9 1.0 CB B:GLN11 4.2 31.3 1.0 CG B:GLN11 4.3 39.9 1.0 OD1 B:ASN101 4.4 42.0 1.0 O5' B:GDP501 4.4 33.8 1.0 C5' B:GDP501 4.4 33.1 1.0 OE1 C:GLU254 4.5 55.1 1.0 O C:HOH676 4.5 60.0 1.0 NE2 B:GLN11 4.5 49.7 1.0 O1B B:GDP501 4.7 29.9 1.0 O2A B:GDP501 4.7 28.7 1.0 C8 B:GDP501 4.8 39.6 1.0 CG B:ASP179 4.9 50.2 1.0 PB B:GDP501 4.9 34.1 1.0

Magnesium binding site 3 out of 4 in the Tubulin-CW1-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-CW1-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.1 occ:1.00 O1G C:GTP501 2.0 30.2 1.0 O C:HOH670 2.0 36.4 1.0 O C:HOH730 2.0 34.7 1.0 O C:HOH664 2.1 34.4 1.0 O C:HOH625 2.1 35.3 1.0 O1B C:GTP501 2.2 33.0 1.0 PG C:GTP501 3.1 37.5 1.0 PB C:GTP501 3.3 34.6 1.0 O2G C:GTP501 3.5 36.8 1.0 O3B C:GTP501 3.6 40.3 1.0 NZ D:LYS254 3.8 39.2 1.0 O3A C:GTP501 3.9 36.0 1.0 OD1 C:ASP69 4.1 45.4 1.0 OD2 C:ASP98 4.1 48.5 1.0 OE2 C:GLU71 4.2 57.1 1.0 CG C:GLU71 4.2 43.8 1.0 CB C:GLN11 4.2 28.7 1.0 OD2 C:ASP69 4.2 37.1 1.0 O3G C:GTP501 4.4 32.2 1.0 CB C:ASP98 4.4 42.2 1.0 N C:GLN11 4.4 30.8 1.0 O2B C:GTP501 4.6 36.6 1.0 O1A C:GTP501 4.6 33.7 1.0 CG C:ASP69 4.6 40.7 1.0 CG C:ASP98 4.6 42.2 1.0 CD C:GLU71 4.7 52.7 1.0 NE2 C:GLN11 4.8 40.0 1.0 PA C:GTP501 4.8 36.0 1.0 CE D:LYS254 4.9 39.5 1.0 CA C:GLN11 4.9 30.0 1.0

Magnesium binding site 4 out of 4 in the Tubulin-CW1-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-CW1-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.5 occ:1.00 O D:HOH627 2.0 57.2 1.0 OE1 D:GLN11 2.0 84.4 1.0 O D:HOH651 2.3 59.4 1.0 O1A D:GDP501 2.4 67.8 1.0 OD2 D:ASP179 3.2 108.0 1.0 CD D:GLN11 3.2 74.9 1.0 PA D:GDP501 3.7 60.5 1.0 O3A D:GDP501 4.1 57.4 1.0 CG D:GLN11 4.1 67.9 1.0 CB D:GLN11 4.1 61.5 1.0 NE2 D:GLN11 4.2 75.3 1.0 C5' D:GDP501 4.3 65.2 1.0 CG D:ASP179 4.4 114.4 1.0 O5' D:GDP501 4.5 63.2 1.0 OD1 D:ASN101 4.5 81.2 1.0 O1B D:GDP501 4.7 54.5 1.0 O2A D:GDP501 4.7 57.8 1.0 C8 D:GDP501 4.9 49.0 1.0

J.Estevez-Gallego, B.Alvarez-Bernad, B.Pera, C.Wullschleger, O.Raes, D.Menche, J.C.Martinez, D.Lucena-Agell, A.E.Prota, F.Bonato, K.Bargsten, J.Cornelus, J.F.Gimenez-Abian, P.Northcote, M.O.Steinmetz, S.Kamimura, K.H.Altmann, I.Paterson, F.Gago, J.Van Der Eycken, J.F.Diaz, M.A.Oliva. Chemical Modulation of Microtubule Structure Through the Laulimalide/Peloruside Site. Structure 2022.
ISSN: ISSN 0969-2126
PubMed: 36462501
DOI: 10.1016/J.STR.2022.11.006