Magnesium in PDB 5s4u: Tubulin-Z30620520-Complex

The structure of Tubulin-Z30620520-Complex, PDB code: 5s4u 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)	62.56 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.88, 158.88, 178.91, 90, 90, 90
R / Rfree (%)	21.1 / 25.2

The structure of Tubulin-Z30620520-Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-Z30620520-Complex (pdb code 5s4u). 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-Z30620520-Complex, PDB code: 5s4u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z30620520-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z30620520-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.4 occ:1.00 O A:HOH608 2.0 55.3 1.0 O1G A:GTP501 2.1 48.5 1.0 O A:HOH615 2.1 54.3 1.0 O A:HOH639 2.2 52.9 1.0 O A:HOH625 2.2 50.7 1.0 O1B A:GTP501 2.4 50.4 1.0 PG A:GTP501 3.3 54.3 1.0 PB A:GTP501 3.4 54.5 1.0 O3B A:GTP501 3.7 56.2 1.0 OE1 A:GLU71 3.8 62.4 1.0 O3A A:GTP501 3.8 56.7 1.0 O2G A:GTP501 3.9 50.7 1.0 NZ B:LYS254 4.0 63.9 1.0 CB A:GLN11 4.1 56.0 1.0 OD1 A:ASP69 4.1 56.8 1.0 OD2 A:ASP69 4.2 64.1 1.0 CB A:ASP98 4.2 56.9 1.0 OD2 A:ASP98 4.3 61.3 1.0 N A:GLN11 4.4 53.9 1.0 NE2 A:GLN11 4.4 60.5 1.0 O3G A:GTP501 4.5 50.9 1.0 CG A:ASP69 4.6 58.7 1.0 O1A A:GTP501 4.6 57.1 1.0 CG A:ASP98 4.6 57.3 1.0 O2B A:GTP501 4.7 55.6 1.0 CA A:GLN11 4.8 54.5 1.0 PA A:GTP501 4.8 56.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z30620520-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z30620520-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:50.4 occ:1.00 O B:HOH623 1.9 52.6 1.0 O B:HOH643 2.1 58.0 1.0 O1A B:GDP501 2.1 51.0 1.0 OE1 B:GLN11 2.2 59.8 1.0 O C:HOH661 2.3 51.9 1.0 O B:HOH638 2.6 52.0 1.0 CD B:GLN11 3.4 58.5 1.0 PA B:GDP501 3.6 53.1 1.0 OD2 B:ASP179 4.0 54.3 1.0 CB B:GLN11 4.0 51.3 1.0 O3A B:GDP501 4.1 51.3 1.0 CG B:GLN11 4.2 56.3 1.0 OD1 B:ASN101 4.3 59.0 1.0 O1B B:GDP501 4.3 48.0 1.0 NE2 B:GLN11 4.4 66.1 1.0 C5' B:GDP501 4.4 50.0 1.0 O5' B:GDP501 4.5 46.7 1.0 OE1 C:GLU254 4.5 67.0 1.0 O2A B:GDP501 4.5 48.1 1.0 PB B:GDP501 4.8 51.2 1.0 C8 B:GDP501 4.9 53.3 1.0 ND2 B:ASN101 5.0 61.7 1.0 CG B:ASP179 5.0 58.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z30620520-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z30620520-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:56.5 occ:1.00 O1G C:GTP501 1.9 52.2 1.0 O C:HOH657 2.0 52.4 1.0 O C:HOH613 2.0 51.9 1.0 O C:HOH679 2.1 50.1 1.0 O1B C:GTP501 2.2 48.0 1.0 O C:HOH626 2.2 53.9 1.0 PG C:GTP501 3.0 47.7 1.0 PB C:GTP501 3.2 51.6 1.0 O3B C:GTP501 3.4 59.0 1.0 O2G C:GTP501 3.4 51.1 1.0 NZ D:LYS254 3.8 56.4 1.0 O3A C:GTP501 3.8 56.4 1.0 OD2 C:ASP98 3.9 58.1 1.0 OD1 C:ASP69 4.0 53.0 1.0 CG C:GLU71 4.1 60.5 1.0 OE2 C:GLU71 4.1 61.5 1.0 OD2 C:ASP69 4.2 52.6 1.0 O3G C:GTP501 4.3 47.9 1.0 CB C:ASP98 4.3 51.5 1.0 CB C:GLN11 4.4 50.7 1.0 O2B C:GTP501 4.5 52.5 1.0 N C:GLN11 4.5 45.7 1.0 CG C:ASP69 4.5 53.7 1.0 CG C:ASP98 4.6 55.6 1.0 CD C:GLU71 4.6 58.9 1.0 O1A C:GTP501 4.7 55.6 1.0 PA C:GTP501 4.8 48.6 1.0 NE2 C:GLN11 4.9 57.5 1.0 CE D:LYS254 4.9 55.1 1.0 OG1 C:THR145 4.9 53.8 1.0 O C:HOH671 4.9 68.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z30620520-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z30620520-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:82.8 occ:1.00 OE1 D:GLN11 1.8 79.4 1.0 O D:HOH601 1.9 75.1 1.0 O1A D:GDP501 2.8 91.3 1.0 CD D:GLN11 3.0 77.7 1.0 NE2 D:GLN11 3.7 78.9 1.0 PA D:GDP501 4.0 76.1 1.0 CB D:GLN11 4.1 75.7 1.0 O D:HOH618 4.1 79.9 1.0 CG D:GLN11 4.1 76.6 1.0 O2A D:GDP501 4.2 72.6 1.0 O1B D:GDP501 4.5 74.6 1.0 C5' D:GDP501 4.8 80.4 1.0 OD1 D:ASN101 4.9 79.2 1.0 O5' D:GDP501 5.0 78.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z30620520-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z30620520-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:99.5 occ:1.00 OE2 F:GLU331 2.1 106.8 1.0 O3G F:ACP401 2.2 109.8 1.0 O1B F:ACP401 2.4 119.8 1.0 OD1 F:ASN333 2.9 104.4 1.0 CD F:GLU331 2.9 106.8 1.0 OE1 F:GLU331 3.1 112.2 1.0 PB F:ACP401 3.6 120.8 1.0 PG F:ACP401 3.8 126.7 1.0 O2B F:ACP401 3.9 123.6 1.0 NZ F:LYS74 3.9 119.0 1.0 CG F:ASN333 4.0 96.7 1.0 CG F:GLU331 4.4 97.5 1.0 C3B F:ACP401 4.4 117.2 1.0 ND2 F:ASN333 4.5 96.1 1.0 O1G F:ACP401 4.6 118.0 1.0 O2G F:ACP401 4.6 108.1 1.0 O3A F:ACP401 4.9 120.3 1.0 O1A F:ACP401 4.9 114.9 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