Magnesium in PDB 5s5q: Tubulin-Z396380540-Complex

The structure of Tubulin-Z396380540-Complex, PDB code: 5s5q was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.42 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.85, 158.62, 178.62, 90, 90, 90
R / Rfree (%)	21.2 / 24.4

The structure of Tubulin-Z396380540-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z396380540-Complex (pdb code 5s5q). 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-Z396380540-Complex, PDB code: 5s5q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:40.3 occ:1.00 O1G A:GTP501 2.0 37.6 1.0 O A:HOH624 2.0 39.8 1.0 O A:HOH653 2.1 38.9 1.0 O A:HOH622 2.1 41.4 1.0 O1B A:GTP501 2.2 39.4 1.0 O A:HOH617 2.2 44.2 1.0 PG A:GTP501 3.2 41.8 1.0 PB A:GTP501 3.3 40.2 1.0 O3B A:GTP501 3.6 46.4 1.0 O2G A:GTP501 3.7 42.8 1.0 O3A A:GTP501 3.7 44.1 1.0 NZ B:LYS254 3.8 53.4 1.0 OE1 A:GLU71 3.9 54.1 1.0 OD1 A:ASP69 4.1 48.8 1.0 CB A:GLN11 4.1 39.9 1.0 OD2 A:ASP69 4.2 47.0 1.0 N A:GLN11 4.3 42.6 1.0 CB A:ASP98 4.4 48.0 1.0 O3G A:GTP501 4.4 42.0 1.0 OD2 A:ASP98 4.4 54.1 1.0 O1A A:GTP501 4.5 41.8 1.0 O2B A:GTP501 4.6 43.9 1.0 CG A:ASP69 4.6 48.4 1.0 NE2 A:GLN11 4.6 45.7 1.0 PA A:GTP501 4.7 43.1 1.0 CG A:ASP98 4.8 50.6 1.0 CA A:GLN11 4.8 43.1 1.0 CE B:LYS254 4.8 49.0 1.0 O B:HOH626 5.0 54.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:31.7 occ:1.00 O C:HOH692 2.2 46.0 1.0 O B:HOH652 2.2 43.8 1.0 O1A B:GDP501 2.2 37.9 1.0 OE1 B:GLN11 2.3 41.9 1.0 O B:HOH673 2.3 47.4 1.0 O B:HOH624 2.4 45.8 1.0 O B:HOH648 2.5 39.6 1.0 CD B:GLN11 3.5 42.1 1.0 PA B:GDP501 3.6 36.7 1.0 O3A B:GDP501 3.9 40.4 1.0 CB B:GLN11 4.0 38.8 1.0 OD2 B:ASP179 4.1 45.2 1.0 O B:HOH682 4.2 56.0 1.0 CG B:GLN11 4.3 41.1 1.0 O C:HOH654 4.4 46.5 1.0 O1B B:GDP501 4.4 37.5 1.0 OD1 B:ASN101 4.4 38.0 1.0 C5' B:GDP501 4.4 41.9 1.0 OE1 C:GLU254 4.4 48.6 1.0 NE2 B:GLN11 4.5 45.4 1.0 O5' B:GDP501 4.5 40.9 1.0 O2A B:GDP501 4.6 36.7 1.0 PB B:GDP501 4.8 37.1 1.0 C8 B:GDP501 4.9 41.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.0 occ:1.00 O1G C:GTP501 2.0 36.2 1.0 O C:HOH630 2.0 35.6 1.0 O1B C:GTP501 2.0 36.4 1.0 O C:HOH657 2.1 38.8 1.0 O C:HOH695 2.1 39.6 1.0 O C:HOH635 2.3 40.0 1.0 PG C:GTP501 3.0 39.5 1.0 PB C:GTP501 3.1 38.3 1.0 O3B C:GTP501 3.4 39.8 1.0 O2G C:GTP501 3.5 36.1 1.0 O3A C:GTP501 3.6 40.4 1.0 NZ D:LYS254 3.9 38.8 1.0 OD1 C:ASP69 4.0 38.8 1.0 OD2 C:ASP69 4.2 37.3 1.0 OD2 C:ASP98 4.2 45.9 1.0 OE2 C:GLU71 4.2 50.1 1.0 CB C:GLN11 4.2 35.5 1.0 CG C:GLU71 4.3 47.2 1.0 N C:GLN11 4.4 32.0 1.0 O3G C:GTP501 4.4 36.5 1.0 O2B C:GTP501 4.4 39.7 1.0 CB C:ASP98 4.5 38.0 1.0 CG C:ASP69 4.6 38.5 1.0 O1A C:GTP501 4.6 39.6 1.0 PA C:GTP501 4.7 38.5 1.0 CG C:ASP98 4.7 43.2 1.0 CD C:GLU71 4.8 45.7 1.0 CA C:GLN11 4.9 36.7 1.0 OE1 C:GLN11 5.0 43.1 1.0 CE D:LYS254 5.0 41.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:64.3 occ:1.00 O D:HOH604 1.9 61.3 1.0 OE1 D:GLN11 2.0 64.4 1.0 O1A D:GDP501 2.1 66.7 1.0 CD D:GLN11 3.1 67.3 1.0 PA D:GDP501 3.6 59.1 1.0 CB D:GLN11 3.6 59.4 1.0 CG D:GLN11 3.9 59.8 1.0 O1B D:GDP501 4.0 55.7 1.0 NE2 D:GLN11 4.2 66.7 1.0 O3A D:GDP501 4.2 59.7 1.0 O2A D:GDP501 4.4 59.9 1.0 PB D:GDP501 4.6 59.3 1.0 O5' D:GDP501 4.6 60.6 1.0 C5' D:GDP501 4.7 62.3 1.0 OD1 D:ASN101 4.8 68.4 1.0 O3B D:GDP501 4.9 69.0 1.0 OE2 D:GLU71 4.9 85.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z396380540-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z396380540-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:77.6 occ:1.00 O3G F:ACP401 2.2 89.6 1.0 OE2 F:GLU331 2.3 85.0 1.0 O1B F:ACP401 2.6 92.7 1.0 OD1 F:ASN333 2.6 79.3 1.0 CD F:GLU331 3.2 81.5 1.0 OE1 F:GLU331 3.4 85.7 1.0 PB F:ACP401 3.7 94.5 1.0 PG F:ACP401 3.7 104.1 1.0 CG F:ASN333 3.8 75.5 1.0 O2B F:ACP401 4.0 102.2 1.0 NZ F:LYS74 4.0 97.1 1.0 C3B F:ACP401 4.4 95.2 1.0 ND2 F:ASN333 4.5 73.4 1.0 O2G F:ACP401 4.6 83.8 1.0 CG F:GLU331 4.6 74.4 1.0 O1G F:ACP401 4.6 96.6 1.0 O F:HOH513 4.8 65.0 1.0 CB F:ASN333 4.9 67.1 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273