Magnesium in PDB 5sb3: Tubulin-Todalam-4-Complex

The structure of Tubulin-Todalam-4-Complex, PDB code: 5sb3 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)	49.46 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.65, 157.714, 180.188, 90, 90, 90
R / Rfree (%)	19.5 / 22.5

The structure of Tubulin-Todalam-4-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Todalam-4-Complex (pdb code 5sb3). 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-4-Complex, PDB code: 5sb3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.8 occ:1.00 O1G A:GTP501 2.0 34.1 1.0 O A:HOH656 2.1 36.0 1.0 O A:HOH601 2.1 42.8 1.0 O A:HOH683 2.1 38.0 1.0 O A:HOH636 2.1 39.4 1.0 O1B A:GTP501 2.3 37.7 1.0 PG A:GTP501 3.2 37.0 1.0 PB A:GTP501 3.4 36.7 1.0 OE1 A:GLU71 3.4 62.6 1.0 O3B A:GTP501 3.6 42.0 1.0 O2G A:GTP501 3.7 36.6 1.0 O3A A:GTP501 3.8 38.1 1.0 NZ B:LYS254 3.8 45.7 1.0 OD1 A:ASP69 4.1 42.7 1.0 CB A:GLN11 4.2 38.2 1.0 CB A:ASP98 4.3 43.8 1.0 OD2 A:ASP98 4.3 48.6 1.0 OD2 A:ASP69 4.4 47.4 1.0 N A:GLN11 4.5 36.4 1.0 O3G A:GTP501 4.5 37.5 1.0 CG A:ASP98 4.6 48.5 1.0 CD A:GLU71 4.6 64.8 1.0 O2B A:GTP501 4.7 39.5 1.0 CG A:ASP69 4.7 46.8 1.0 O1A A:GTP501 4.7 38.6 1.0 OE1 A:GLN11 4.7 50.2 1.0 PA A:GTP501 4.8 36.0 1.0 CE B:LYS254 4.9 43.8 1.0 CA A:GLN11 4.9 39.9 1.0 CB A:GLU71 5.0 60.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.3 occ:1.00 OE1 B:GLN11 2.1 40.2 1.0 O B:HOH646 2.1 37.2 1.0 O C:HOH663 2.2 47.3 1.0 O1A B:GDP501 2.2 34.1 1.0 O B:HOH641 2.4 44.0 1.0 O B:HOH688 2.6 40.8 1.0 O B:HOH727 3.1 50.7 1.0 CD B:GLN11 3.3 45.9 1.0 PA B:GDP501 3.6 33.6 1.0 OD2 B:ASP179 3.9 41.9 1.0 O3A B:GDP501 4.0 36.1 1.0 CB B:GLN11 4.1 37.0 1.0 CG B:GLN11 4.1 42.6 1.0 NE2 B:GLN11 4.3 49.6 1.0 C5' B:GDP501 4.4 35.3 1.0 OD1 B:ASN101 4.4 36.0 1.0 O5' B:GDP501 4.5 34.3 1.0 OE1 C:GLU254 4.5 44.8 1.0 O1B B:GDP501 4.6 34.5 1.0 O2A B:GDP501 4.6 35.8 1.0 C8 B:GDP501 4.8 40.2 1.0 CG B:ASP179 4.8 40.8 1.0 PB B:GDP501 4.9 33.9 1.0 ND2 B:ASN101 5.0 34.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.3 occ:1.00 O1G C:GTP501 2.0 31.1 1.0 O C:HOH674 2.0 34.5 1.0 O C:HOH651 2.1 32.4 1.0 O C:HOH680 2.1 36.3 1.0 O C:HOH758 2.1 31.7 1.0 O1B C:GTP501 2.1 32.0 1.0 PG C:GTP501 3.1 33.1 1.0 PB C:GTP501 3.2 29.8 1.0 O2G C:GTP501 3.5 34.5 1.0 O3B C:GTP501 3.6 37.7 1.0 O3A C:GTP501 3.6 35.9 1.0 NZ D:LYS254 3.9 39.1 1.0 OD1 C:ASP69 4.0 35.6 1.0 OE2 C:GLU71 4.0 48.1 1.0 CG C:GLU71 4.1 42.5 1.0 CB C:GLN11 4.2 31.9 1.0 OD2 C:ASP69 4.2 34.6 1.0 OD2 C:ASP98 4.4 41.9 1.0 CB C:ASP98 4.4 37.4 1.0 N C:GLN11 4.4 31.8 1.0 O3G C:GTP501 4.4 32.6 1.0 O2B C:GTP501 4.5 34.7 1.0 CG C:ASP69 4.6 35.7 1.0 CD C:GLU71 4.6 42.3 1.0 O1A C:GTP501 4.7 34.0 1.0 PA C:GTP501 4.7 32.4 1.0 CG C:ASP98 4.8 40.1 1.0 NE2 C:GLN11 4.8 42.7 1.0 CA C:GLN11 4.9 33.9 1.0 OG1 C:THR145 4.9 36.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:70.7 occ:1.00 OE1 D:GLN11 2.3 75.2 1.0 O D:HOH605 2.4 57.9 1.0 O1A D:GDP501 2.5 71.8 1.0 O D:HOH631 2.5 67.5 1.0 O D:HOH661 2.5 63.3 1.0 CD D:GLN11 3.5 74.2 1.0 CB D:GLN11 3.8 65.7 1.0 PA D:GDP501 3.8 58.1 1.0 O1B D:GDP501 3.8 60.2 1.0 CG D:GLN11 4.2 64.6 1.0 O3A D:GDP501 4.4 58.8 1.0 O2A D:GDP501 4.4 60.8 1.0 NE2 D:GLN11 4.5 73.4 1.0 PB D:GDP501 4.6 55.2 1.0 OE2 D:GLU71 4.7 102.2 1.0 O3B D:GDP501 4.9 65.4 1.0 OD1 D:ASN101 5.0 71.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-4-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-4-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:90.3 occ:1.00 O3G F:ACP401 2.2 96.6 1.0 O1B F:ACP401 2.6 105.3 1.0 OE2 F:GLU331 2.7 92.1 1.0 OE1 F:GLU331 2.7 89.6 1.0 OD1 F:ASN333 3.1 88.6 1.0 CD F:GLU331 3.1 88.2 1.0 NZ F:LYS74 3.6 101.5 1.0 PG F:ACP401 3.7 109.8 1.0 PB F:ACP401 3.8 108.6 1.0 CG F:ASN333 3.9 80.2 1.0 ND2 F:ASN333 4.0 81.2 1.0 O2B F:ACP401 4.2 114.8 1.0 O1G F:ACP401 4.3 108.9 1.0 C3B F:ACP401 4.5 109.7 1.0 CG F:GLU331 4.6 79.2 1.0 CE F:LYS74 4.7 98.9 1.0 O2G F:ACP401 4.8 90.2 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