Magnesium in PDB 5sb6: Tubulin-Todalam-10-Complex

The structure of Tubulin-Todalam-10-Complex, PDB code: 5sb6 was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.27, 156.726, 180.456, 90, 90, 90
R / Rfree (%)	20.1 / 23.7

The structure of Tubulin-Todalam-10-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Fluorine	(F)	1 atom

The binding sites of Magnesium atom in the Tubulin-Todalam-10-Complex (pdb code 5sb6). 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-Todalam-10-Complex, PDB code: 5sb6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.3 occ:1.00 O A:HOH615 2.0 41.4 1.0 O1G A:GTP501 2.0 37.2 1.0 O A:HOH655 2.0 42.7 1.0 O A:HOH631 2.1 41.4 1.0 O1B A:GTP501 2.2 37.2 1.0 O A:HOH602 2.2 42.8 1.0 PG A:GTP501 3.2 42.1 1.0 PB A:GTP501 3.2 40.5 1.0 OE1 A:GLU71 3.3 63.5 1.0 O3B A:GTP501 3.6 49.1 1.0 O3A A:GTP501 3.7 44.5 1.0 O2G A:GTP501 3.8 40.8 1.0 NZ B:LYS254 3.9 51.2 1.0 CB A:GLN11 4.1 45.0 1.0 OD1 A:ASP69 4.1 46.9 1.0 N A:GLN11 4.3 40.4 1.0 OD2 A:ASP69 4.4 54.6 1.0 O3G A:GTP501 4.4 37.2 1.0 CB A:ASP98 4.5 48.3 1.0 O1A A:GTP501 4.5 43.6 1.0 OD2 A:ASP98 4.5 50.5 1.0 O2B A:GTP501 4.5 44.9 1.0 CD A:GLU71 4.6 65.5 1.0 CG A:ASP69 4.7 51.7 1.0 PA A:GTP501 4.7 40.7 1.0 OE1 A:GLN11 4.7 52.9 1.0 CG A:ASP98 4.8 48.4 1.0 CA A:GLN11 4.8 43.5 1.0 CB A:GLU71 5.0 60.3 1.0 CE B:LYS254 5.0 46.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.4 occ:1.00 O B:HOH643 2.0 37.4 1.0 OE1 B:GLN11 2.0 44.5 1.0 O C:HOH612 2.1 43.6 1.0 O1A B:GDP501 2.2 38.9 1.0 O B:HOH624 2.6 50.0 1.0 O B:HOH669 2.6 45.4 1.0 O C:HOH759 2.8 50.1 1.0 CD B:GLN11 3.2 49.5 1.0 PA B:GDP501 3.6 34.7 1.0 CB B:GLN11 3.9 43.2 1.0 O3A B:GDP501 4.0 37.7 1.0 O C:HOH752 4.0 49.8 1.0 OE2 C:GLU254 4.0 45.8 1.0 OD2 B:ASP179 4.1 44.5 1.0 CG B:GLN11 4.1 46.5 1.0 NE2 B:GLN11 4.2 54.1 1.0 O1B B:GDP501 4.4 36.0 1.0 OD1 B:ASN101 4.5 37.0 1.0 C5' B:GDP501 4.5 38.5 1.0 O5' B:GDP501 4.6 37.2 1.0 O2A B:GDP501 4.6 39.9 1.0 PB B:GDP501 4.8 36.5 1.0 C8 B:GDP501 4.9 43.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:37.4 occ:1.00 O1G C:GTP501 1.9 36.7 1.0 O C:HOH671 2.0 38.5 1.0 O C:HOH717 2.0 36.2 1.0 O C:HOH627 2.1 38.1 1.0 O C:HOH672 2.2 43.8 1.0 O1B C:GTP501 2.2 34.8 1.0 PG C:GTP501 3.1 38.9 1.0 PB C:GTP501 3.2 37.5 1.0 O3B C:GTP501 3.5 43.5 1.0 O2G C:GTP501 3.5 35.5 1.0 O3A C:GTP501 3.7 41.7 1.0 NZ D:LYS254 3.8 42.1 1.0 OE2 C:GLU71 4.1 51.5 1.0 OD1 C:ASP69 4.2 40.3 1.0 CG C:GLU71 4.2 43.2 1.0 CB C:GLN11 4.2 34.9 1.0 OD2 C:ASP98 4.3 48.1 1.0 O3G C:GTP501 4.3 35.5 1.0 OD2 C:ASP69 4.4 39.5 1.0 CB C:ASP98 4.4 41.1 1.0 N C:GLN11 4.5 32.1 1.0 O2B C:GTP501 4.6 36.7 1.0 O1A C:GTP501 4.6 38.1 1.0 CD C:GLU71 4.6 47.2 1.0 CG C:ASP69 4.7 41.2 1.0 PA C:GTP501 4.7 38.1 1.0 NE2 C:GLN11 4.7 50.3 1.0 CG C:ASP98 4.8 44.1 1.0 CE D:LYS254 5.0 40.4 1.0 OG1 C:THR145 5.0 39.0 1.0 CA C:GLN11 5.0 34.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.0 occ:1.00 O D:HOH642 2.4 66.8 1.0 O1B D:GDP501 3.0 68.7 1.0 OE1 D:GLN11 3.0 72.9 1.0 OE2 D:GLU71 3.0 107.3 1.0 CB D:GLN11 3.2 67.6 1.0 O1A D:GDP501 3.3 74.2 1.0 O D:HOH603 3.4 64.6 1.0 CD D:GLN11 3.6 76.0 1.0 O3B D:GDP501 3.9 72.3 1.0 PB D:GDP501 3.9 62.5 1.0 CG D:GLN11 4.0 73.4 1.0 CD D:GLU71 4.1 109.0 1.0 O D:HOH604 4.2 69.5 1.0 PA D:GDP501 4.2 65.4 1.0 O3A D:GDP501 4.3 61.9 1.0 CA D:GLN11 4.4 70.5 1.0 N D:GLN11 4.4 68.6 1.0 NE2 D:GLN11 4.6 77.3 1.0 O2A D:GDP501 4.7 65.6 1.0 O D:HOH602 4.7 69.1 1.0 OE1 D:GLU71 4.8 110.5 1.0 OG1 D:THR74 4.8 83.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-10-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Todalam-10-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:93.5 occ:1.00 O3G F:ACP401 2.3 104.4 1.0 O1B F:ACP401 2.4 110.8 1.0 OE2 F:GLU331 2.7 96.8 1.0 OD1 F:ASN333 2.9 91.2 1.0 OE1 F:GLU331 3.0 94.7 1.0 CD F:GLU331 3.2 93.6 1.0 NZ F:LYS74 3.6 105.6 1.0 PB F:ACP401 3.7 115.1 1.0 CG F:ASN333 3.8 83.3 1.0 PG F:ACP401 3.9 117.3 1.0 O2B F:ACP401 4.1 114.5 1.0 ND2 F:ASN333 4.2 86.6 1.0 O1G F:ACP401 4.5 113.5 1.0 C3B F:ACP401 4.5 110.4 1.0 CE F:LYS74 4.7 104.2 1.0 CG F:GLU331 4.7 86.9 1.0 O1A F:ACP401 4.9 107.4 1.0 O2G F:ACP401 4.9 94.4 1.0 O3A F:ACP401 4.9 113.2 1.0

T.Muhlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz. Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052