Magnesium in PDB 5sb5: Tubulin-Todalam-9-Complex

The structure of Tubulin-Todalam-9-Complex, PDB code: 5sb5 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)	49.55 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.81, 157.711, 180.536, 90, 90, 90
R / Rfree (%)	18.8 / 22

The structure of Tubulin-Todalam-9-Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-Todalam-9-Complex (pdb code 5sb5). 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-9-Complex, PDB code: 5sb5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Todalam-9-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-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.0 occ:1.00 O A:HOH609 2.1 31.1 1.0 O1G A:GTP501 2.1 28.6 1.0 O A:HOH674 2.1 32.3 1.0 O A:HOH659 2.2 30.9 1.0 O A:HOH626 2.2 35.2 1.0 O1B A:GTP501 2.2 27.1 1.0 PG A:GTP501 3.3 35.4 1.0 PB A:GTP501 3.4 31.4 1.0 OE1 A:GLU71 3.4 52.1 1.0 O3B A:GTP501 3.6 37.0 1.0 O2G A:GTP501 3.8 32.6 1.0 OD1 A:ASP69 3.9 36.0 1.0 O3A A:GTP501 4.0 34.6 1.0 NZ B:LYS254 4.0 45.2 1.0 CB A:GLN11 4.2 33.2 1.0 OD2 A:ASP69 4.2 41.3 1.0 CB A:ASP98 4.4 38.5 1.0 OD2 A:ASP98 4.4 43.1 1.0 N A:GLN11 4.4 32.7 1.0 CG A:ASP69 4.5 42.0 1.0 O3G A:GTP501 4.5 29.7 1.0 CD A:GLU71 4.6 53.5 1.0 O2B A:GTP501 4.6 32.5 1.0 CG A:ASP98 4.7 41.1 1.0 O1A A:GTP501 4.7 34.0 1.0 OE1 A:GLN11 4.8 45.4 1.0 CA A:GLN11 4.9 33.8 1.0 PA A:GTP501 4.9 31.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Todalam-9-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-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.8 occ:1.00 OE1 B:GLN11 2.0 35.4 1.0 O C:HOH603 2.1 38.8 1.0 O B:HOH677 2.2 30.0 1.0 O1A B:GDP501 2.3 30.4 1.0 O B:HOH718 2.5 37.7 1.0 O B:HOH687 2.7 43.7 1.0 CD B:GLN11 3.2 39.0 1.0 O C:HOH811 3.3 50.0 1.0 PA B:GDP501 3.6 26.6 1.0 O3A B:GDP501 3.9 31.7 1.0 OD2 B:ASP179 4.0 34.3 1.0 CB B:GLN11 4.0 32.2 1.0 OE2 C:GLU254 4.0 41.0 1.0 CG B:GLN11 4.1 36.1 1.0 NE2 B:GLN11 4.2 38.6 1.0 C5' B:GDP501 4.3 30.3 1.0 O5' B:GDP501 4.4 27.2 1.0 OD1 B:ASN101 4.4 28.8 1.0 O C:HOH808 4.7 48.2 1.0 O1B B:GDP501 4.7 27.9 1.0 O2A B:GDP501 4.7 31.3 1.0 C8 B:GDP501 4.9 32.7 1.0 CG B:ASP179 4.9 35.9 1.0 PB B:GDP501 5.0 28.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Todalam-9-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-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:30.5 occ:1.00 O1G C:GTP501 2.0 24.7 1.0 O C:HOH684 2.0 26.6 1.0 O C:HOH711 2.0 28.5 1.0 O C:HOH678 2.1 28.3 1.0 O1B C:GTP501 2.1 24.6 1.0 O C:HOH650 2.1 32.9 1.0 PG C:GTP501 3.2 29.6 1.0 PB C:GTP501 3.2 25.2 1.0 O3B C:GTP501 3.6 33.2 1.0 O2G C:GTP501 3.7 28.6 1.0 O3A C:GTP501 3.7 30.8 1.0 NZ D:LYS254 3.9 34.1 1.0 OE2 C:GLU71 4.1 37.7 1.0 OD1 C:ASP69 4.1 31.5 1.0 CG C:GLU71 4.1 34.5 1.0 CB C:GLN11 4.2 26.2 1.0 OD2 C:ASP98 4.2 39.0 1.0 OD2 C:ASP69 4.3 28.0 1.0 N C:GLN11 4.4 25.1 1.0 O C:HOH662 4.4 39.0 1.0 CB C:ASP98 4.4 30.3 1.0 O3G C:GTP501 4.4 28.5 1.0 O2B C:GTP501 4.5 27.0 1.0 CD C:GLU71 4.6 39.0 1.0 O1A C:GTP501 4.6 26.3 1.0 CG C:ASP69 4.6 32.3 1.0 PA C:GTP501 4.7 26.8 1.0 CG C:ASP98 4.7 33.6 1.0 NE2 C:GLN11 4.8 35.9 1.0 CA C:GLN11 4.9 26.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Todalam-9-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-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:62.7 occ:1.00 O1B D:GDP501 3.0 53.5 1.0 OE2 D:GLU71 3.2 98.8 1.0 OE1 D:GLN11 3.2 63.3 1.0 O1A D:GDP501 3.2 65.8 1.0 O D:HOH602 3.2 46.6 1.0 CB D:GLN11 3.6 58.9 1.0 O3B D:GDP501 3.7 63.9 1.0 PB D:GDP501 3.7 51.7 1.0 O D:HOH603 3.9 51.2 1.0 CD D:GLN11 4.0 64.4 1.0 O3A D:GDP501 4.1 53.9 1.0 PA D:GDP501 4.1 52.7 1.0 O D:HOH604 4.1 57.7 1.0 CD D:GLU71 4.2 96.4 1.0 CG D:GLN11 4.4 59.9 1.0 O2A D:GDP501 4.7 54.2 1.0 N D:GLN11 4.7 54.3 1.0 OE1 D:GLU71 4.8 98.3 1.0 CA D:GLN11 4.8 56.4 1.0 NE2 D:GLN11 5.0 63.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-9-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-9-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:83.2 occ:1.00 O3G F:ACP401 2.1 91.5 1.0 O1B F:ACP401 2.5 96.5 1.0 OE2 F:GLU331 2.6 86.9 1.0 OE1 F:GLU331 3.0 86.1 1.0 CD F:GLU331 3.2 81.6 1.0 OD1 F:ASN333 3.2 81.5 1.0 PB F:ACP401 3.6 96.8 1.0 NZ F:LYS74 3.6 89.2 1.0 PG F:ACP401 3.7 103.0 1.0 O2B F:ACP401 3.8 101.5 1.0 CG F:ASN333 4.0 77.0 1.0 ND2 F:ASN333 4.2 78.5 1.0 C3B F:ACP401 4.3 97.7 1.0 O1G F:ACP401 4.4 99.4 1.0 CG F:GLU331 4.7 71.2 1.0 O2G F:ACP401 4.7 82.8 1.0 CE F:LYS74 4.8 88.5 1.0 O3A F:ACP401 5.0 98.5 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