Magnesium in PDB 5sb4: Tubulin-Todalam-8-Complex

The structure of Tubulin-Todalam-8-Complex, PDB code: 5sb4 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)	49.62 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.575, 157.329, 180.728, 90, 90, 90
R / Rfree (%)	19.8 / 23

The structure of Tubulin-Todalam-8-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-8-Complex (pdb code 5sb4). 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-8-Complex, PDB code: 5sb4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.5 occ:1.00 O A:HOH623 2.0 45.9 1.0 O1G A:GTP501 2.0 43.9 1.0 O A:HOH633 2.1 45.6 1.0 O A:HOH602 2.2 49.2 1.0 O1B A:GTP501 2.2 41.5 1.0 O A:HOH605 2.2 48.5 1.0 PG A:GTP501 3.2 42.2 1.0 PB A:GTP501 3.3 43.0 1.0 OE1 A:GLU71 3.3 61.0 1.0 O3B A:GTP501 3.5 51.0 1.0 O3A A:GTP501 3.8 49.0 1.0 O2G A:GTP501 3.8 44.3 1.0 OD1 A:ASP69 4.1 50.8 1.0 NZ B:LYS254 4.1 57.3 1.0 CB A:GLN11 4.1 48.4 1.0 N A:GLN11 4.4 46.8 1.0 CB A:ASP98 4.4 52.6 1.0 O3G A:GTP501 4.4 46.1 1.0 OD2 A:ASP69 4.5 59.0 1.0 O1A A:GTP501 4.5 46.6 1.0 CD A:GLU71 4.5 62.6 1.0 O2B A:GTP501 4.6 46.8 1.0 OD2 A:ASP98 4.6 56.4 1.0 PA A:GTP501 4.7 42.0 1.0 CG A:ASP69 4.7 54.8 1.0 CG A:ASP98 4.8 52.3 1.0 CA A:GLN11 4.8 48.3 1.0 OE1 A:GLN11 4.9 54.0 1.0 OG1 A:THR145 5.0 51.3 1.0 CB A:GLU71 5.0 63.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.1 occ:1.00 O B:HOH601 1.9 46.6 1.0 OE1 B:GLN11 2.0 48.3 1.0 O B:HOH614 2.1 37.2 1.0 O1A B:GDP501 2.2 41.2 1.0 O B:HOH662 2.3 45.6 1.0 O C:HOH606 2.4 45.6 1.0 CD B:GLN11 3.2 47.5 1.0 PA B:GDP501 3.6 37.4 1.0 O C:HOH711 3.8 54.9 1.0 OD2 B:ASP179 3.9 46.3 1.0 CB B:GLN11 4.0 42.9 1.0 O3A B:GDP501 4.0 41.7 1.0 CG B:GLN11 4.1 44.4 1.0 NE2 B:GLN11 4.1 53.2 1.0 OD1 B:ASN101 4.3 40.7 1.0 O1B B:GDP501 4.4 39.9 1.0 OE1 C:GLU254 4.4 48.5 1.0 C5' B:GDP501 4.6 37.2 1.0 O5' B:GDP501 4.6 38.3 1.0 O2A B:GDP501 4.6 38.3 1.0 PB B:GDP501 4.8 39.0 1.0 CG B:ASP179 5.0 44.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.0 occ:1.00 O1B C:GTP501 2.0 38.9 1.0 O C:HOH689 2.0 39.4 1.0 O1G C:GTP501 2.0 38.5 1.0 O C:HOH624 2.0 41.0 1.0 O C:HOH633 2.1 42.0 1.0 O C:HOH631 2.2 38.0 1.0 PB C:GTP501 3.2 35.0 1.0 PG C:GTP501 3.2 39.0 1.0 O3B C:GTP501 3.6 41.9 1.0 O3A C:GTP501 3.7 40.6 1.0 O2G C:GTP501 3.8 38.4 1.0 NZ D:LYS254 3.9 44.6 1.0 OE2 C:GLU71 3.9 53.8 1.0 CB C:GLN11 4.2 37.7 1.0 CG C:GLU71 4.2 46.4 1.0 OD1 C:ASP69 4.3 43.1 1.0 OD2 C:ASP69 4.4 43.5 1.0 O2B C:GTP501 4.5 37.1 1.0 O3G C:GTP501 4.5 39.9 1.0 N C:GLN11 4.5 35.4 1.0 CB C:ASP98 4.5 41.9 1.0 CD C:GLU71 4.6 50.8 1.0 O1A C:GTP501 4.6 39.1 1.0 NE2 C:GLN11 4.7 47.2 1.0 PA C:GTP501 4.7 33.5 1.0 CG C:ASP69 4.8 44.9 1.0 OD2 C:ASP98 4.9 54.1 1.0 CG C:ASP98 4.9 46.3 1.0 CA C:GLN11 4.9 39.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:78.2 occ:1.00 O D:HOH603 2.6 78.1 1.0 O D:HOH602 2.7 65.7 1.0 O1B D:GDP501 3.1 76.6 1.0 O1A D:GDP501 3.1 79.5 1.0 OE1 D:GLN11 3.5 74.5 1.0 OE2 D:GLU71 3.5 104.6 1.0 O3B D:GDP501 3.5 69.7 1.0 PB D:GDP501 3.8 68.5 1.0 O D:HOH607 3.9 63.6 1.0 O D:HOH605 4.0 71.9 1.0 CB D:GLN11 4.1 72.8 1.0 PA D:GDP501 4.2 64.9 1.0 O3A D:GDP501 4.2 68.9 1.0 OD1 D:ASN101 4.3 79.8 1.0 CD D:GLN11 4.4 77.5 1.0 CD D:GLU71 4.5 102.8 1.0 O2A D:GDP501 4.7 64.8 1.0 CG D:GLN11 4.9 78.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-8-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-8-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:105.8 occ:1.00 O3G F:ACP401 2.2 109.0 1.0 O1B F:ACP401 2.7 116.0 1.0 OE2 F:GLU331 2.7 101.2 1.0 OE1 F:GLU331 2.9 99.0 1.0 OD1 F:ASN333 3.2 93.9 1.0 CD F:GLU331 3.2 97.0 1.0 NZ F:LYS74 3.8 108.2 1.0 PG F:ACP401 3.8 123.6 1.0 CG F:ASN333 3.8 90.0 1.0 ND2 F:ASN333 3.8 92.4 1.0 PB F:ACP401 3.9 121.6 1.0 O2B F:ACP401 4.3 117.9 1.0 O1G F:ACP401 4.5 121.0 1.0 C3B F:ACP401 4.6 121.3 1.0 CG F:GLU331 4.7 85.2 1.0 O2G F:ACP401 4.8 100.5 1.0 CE F:LYS74 5.0 103.8 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