Magnesium in PDB 5sb7: Tubulin-Todalam-18-Complex

The structure of Tubulin-Todalam-18-Complex, PDB code: 5sb7 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)	48.08 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.148, 158.288, 179.988, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Todalam-18-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Todalam-18-Complex (pdb code 5sb7). 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-18-Complex, PDB code: 5sb7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.5 occ:1.00 O1G A:GTP501 2.1 29.3 1.0 O A:HOH617 2.1 37.8 1.0 O A:HOH671 2.1 34.0 1.0 O A:HOH667 2.1 34.2 1.0 O A:HOH611 2.1 34.5 1.0 O1B A:GTP501 2.3 25.8 1.0 PG A:GTP501 3.3 31.2 1.0 PB A:GTP501 3.4 28.9 1.0 OE1 A:GLU71 3.4 60.1 1.0 O3B A:GTP501 3.7 39.2 1.0 O2G A:GTP501 3.8 31.9 1.0 O3A A:GTP501 3.8 38.1 1.0 NZ B:LYS254 3.9 39.4 1.0 OD1 A:ASP69 4.0 35.9 1.0 CB A:GLN11 4.1 30.2 1.0 OD2 A:ASP69 4.2 32.6 1.0 CB A:ASP98 4.3 35.8 1.0 N A:GLN11 4.4 31.8 1.0 OD2 A:ASP98 4.5 42.1 1.0 O3G A:GTP501 4.5 32.6 1.0 CG A:ASP69 4.5 36.9 1.0 CD A:GLU71 4.6 57.3 1.0 O1A A:GTP501 4.7 32.5 1.0 O2B A:GTP501 4.7 35.2 1.0 CG A:ASP98 4.7 38.9 1.0 OE1 A:GLN11 4.7 48.4 1.0 PA A:GTP501 4.8 31.7 1.0 CA A:GLN11 4.8 36.1 1.0 CB A:GLU71 5.0 52.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.3 occ:1.00 OE1 B:GLN11 2.1 36.8 1.0 O B:HOH667 2.1 34.4 1.0 O1A B:GDP501 2.2 30.3 1.0 O C:HOH718 2.4 47.5 1.0 O B:HOH625 2.4 43.9 1.0 O B:HOH686 2.5 36.8 1.0 CD B:GLN11 3.3 43.2 1.0 O B:HOH744 3.4 54.4 1.0 PA B:GDP501 3.6 28.9 1.0 OD2 B:ASP179 3.9 38.1 1.0 O3A B:GDP501 3.9 32.0 1.0 CB B:GLN11 4.0 34.1 1.0 CG B:GLN11 4.1 38.1 1.0 NE2 B:GLN11 4.2 42.0 1.0 C5' B:GDP501 4.3 32.5 1.0 O C:HOH679 4.4 54.3 1.0 O5' B:GDP501 4.4 32.0 1.0 OD1 B:ASN101 4.4 37.5 1.0 O1B B:GDP501 4.6 27.9 1.0 O2A B:GDP501 4.6 30.8 1.0 OE1 C:GLU254 4.7 46.6 1.0 C8 B:GDP501 4.8 33.7 1.0 CG B:ASP179 4.9 41.5 1.0 PB B:GDP501 4.9 30.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.1 occ:1.00 O1G C:GTP501 2.0 27.9 1.0 O C:HOH722 2.0 32.1 1.0 O C:HOH713 2.0 29.3 1.0 O C:HOH662 2.0 30.2 1.0 O1B C:GTP501 2.1 25.9 1.0 O C:HOH767 2.2 31.6 1.0 PG C:GTP501 3.2 30.2 1.0 PB C:GTP501 3.2 27.8 1.0 O3B C:GTP501 3.6 33.1 1.0 O2G C:GTP501 3.6 28.5 1.0 O3A C:GTP501 3.7 32.1 1.0 NZ D:LYS254 4.0 32.5 1.0 OD1 C:ASP69 4.1 31.7 1.0 CG C:GLU71 4.2 38.0 1.0 OE2 C:GLU71 4.2 45.5 1.0 CB C:GLN11 4.2 23.4 1.0 OD2 C:ASP69 4.2 27.2 1.0 N C:GLN11 4.4 23.8 1.0 O3G C:GTP501 4.4 25.9 1.0 OD2 C:ASP98 4.4 38.9 1.0 CB C:ASP98 4.5 30.8 1.0 O2B C:GTP501 4.5 35.0 1.0 O1A C:GTP501 4.6 30.6 1.0 CG C:ASP69 4.6 29.5 1.0 O C:HOH669 4.6 41.5 1.0 CD C:GLU71 4.7 41.5 1.0 NE2 C:GLN11 4.7 38.0 1.0 PA C:GTP501 4.7 29.3 1.0 CG C:ASP98 4.8 36.4 1.0 CA C:GLN11 4.9 27.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:60.9 occ:1.00 OE1 D:GLN11 2.2 60.9 1.0 O1A D:GDP501 2.2 71.0 1.0 O D:HOH605 2.3 59.6 1.0 O D:HOH696 2.4 57.8 1.0 O D:HOH639 2.6 50.6 1.0 CD D:GLN11 3.3 60.2 1.0 PA D:GDP501 3.7 56.0 1.0 CB D:GLN11 4.0 50.7 1.0 CG D:GLN11 4.2 52.2 1.0 NE2 D:GLN11 4.3 63.7 1.0 O1B D:GDP501 4.3 46.5 1.0 O2A D:GDP501 4.4 54.2 1.0 O3A D:GDP501 4.5 53.4 1.0 O D:HOH698 4.6 64.4 1.0 C5' D:GDP501 4.7 56.8 1.0 O5' D:GDP501 4.8 54.2 1.0 PB D:GDP501 5.0 50.3 1.0 OD1 D:ASN101 5.0 63.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:72.7 occ:1.00 O3G F:ACP401 2.4 77.1 1.0 OE1 F:GLU331 2.6 79.4 1.0 OE2 F:GLU331 2.6 78.2 1.0 O1B F:ACP401 2.6 82.1 1.0 CD F:GLU331 2.9 73.7 1.0 ND2 F:ASN333 3.3 74.6 1.0 NZ F:LYS74 3.3 81.2 1.0 PB F:ACP401 3.8 81.5 1.0 PG F:ACP401 4.0 93.2 1.0 O2B F:ACP401 4.1 91.8 1.0 CG F:ASN333 4.4 72.0 1.0 CG F:GLU331 4.4 62.1 1.0 CE F:LYS74 4.6 81.4 1.0 C3B F:ACP401 4.6 81.4 1.0 O1G F:ACP401 4.6 91.2 1.0 O F:HOH548 5.0 58.0 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