Magnesium in PDB 5s4o: Tubulin-Z48847594-Complex

The structure of Tubulin-Z48847594-Complex, PDB code: 5s4o 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)	79.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.744, 158.001, 178.586, 90, 90, 90
R / Rfree (%)	21.6 / 26.2

The structure of Tubulin-Z48847594-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z48847594-Complex (pdb code 5s4o). 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-Z48847594-Complex, PDB code: 5s4o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.1 occ:1.00 O A:HOH625 2.0 28.0 1.0 O A:HOH643 2.0 26.6 1.0 O A:HOH641 2.0 25.5 1.0 O A:HOH615 2.1 24.8 1.0 O1G A:GTP501 2.1 25.4 1.0 O1B A:GTP501 2.2 20.1 1.0 PG A:GTP501 3.2 24.6 1.0 PB A:GTP501 3.3 23.4 1.0 O2G A:GTP501 3.6 23.4 1.0 O3B A:GTP501 3.6 33.8 1.0 OE1 A:GLU71 3.8 42.6 1.0 NZ B:LYS254 3.9 35.3 1.0 O3A A:GTP501 3.9 26.9 1.0 OD1 A:ASP69 4.1 29.3 1.0 CB A:GLN11 4.1 25.2 1.0 OD2 A:ASP69 4.3 34.0 1.0 CB A:ASP98 4.3 31.8 1.0 N A:GLN11 4.4 27.4 1.0 O3G A:GTP501 4.5 23.0 1.0 NE2 A:GLN11 4.5 35.7 1.0 O1A A:GTP501 4.6 27.8 1.0 O A:HOH636 4.6 35.5 1.0 O2B A:GTP501 4.6 24.6 1.0 OD2 A:ASP98 4.6 43.7 1.0 CG A:ASP69 4.7 30.8 1.0 CG A:ASP98 4.8 38.3 1.0 PA A:GTP501 4.8 27.2 1.0 CA A:GLN11 4.9 28.2 1.0 CE B:LYS254 5.0 30.8 1.0 CD A:GLU71 5.0 44.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.5 occ:1.00 O B:HOH628 1.8 32.0 1.0 O B:HOH621 2.1 34.4 1.0 OE1 B:GLN11 2.2 32.5 1.0 O1A B:GDP501 2.3 28.1 1.0 O C:HOH671 2.3 34.9 1.0 O B:HOH660 2.4 31.8 1.0 CD B:GLN11 3.4 37.8 1.0 PA B:GDP501 3.6 19.2 1.0 OD2 B:ASP179 3.7 36.4 1.0 O3A B:GDP501 3.9 19.9 1.0 CB B:GLN11 4.1 24.8 1.0 OD1 B:ASN101 4.3 30.3 1.0 CG B:GLN11 4.3 27.5 1.0 NE2 B:GLN11 4.3 49.3 1.0 C5' B:GDP501 4.4 31.7 1.0 O5' B:GDP501 4.4 22.8 1.0 OE1 C:GLU254 4.4 39.1 1.0 O1B B:GDP501 4.6 21.8 1.0 O C:HOH644 4.6 37.1 1.0 O2A B:GDP501 4.7 26.3 1.0 CG B:ASP179 4.7 37.9 1.0 C8 B:GDP501 4.8 28.7 1.0 PB B:GDP501 4.9 21.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.6 occ:1.00 O1G C:GTP501 1.9 18.9 1.0 O1B C:GTP501 2.0 21.9 1.0 O C:HOH669 2.0 20.5 1.0 O C:HOH665 2.1 22.9 1.0 O C:HOH679 2.1 23.2 1.0 O C:HOH704 2.1 22.6 1.0 PG C:GTP501 3.1 24.7 1.0 PB C:GTP501 3.1 20.3 1.0 O3B C:GTP501 3.4 28.4 1.0 O2G C:GTP501 3.6 18.4 1.0 O3A C:GTP501 3.7 24.8 1.0 NZ D:LYS254 3.9 27.8 1.0 OD1 C:ASP69 4.0 23.7 1.0 OE2 C:GLU71 4.1 37.0 1.0 CB C:GLN11 4.2 18.9 1.0 OD2 C:ASP69 4.2 23.7 1.0 CG C:GLU71 4.3 30.1 1.0 O3G C:GTP501 4.3 18.9 1.0 N C:GLN11 4.4 18.4 1.0 CB C:ASP98 4.4 26.2 1.0 O2B C:GTP501 4.4 22.4 1.0 CG C:ASP69 4.5 23.4 1.0 O1A C:GTP501 4.6 19.2 1.0 PA C:GTP501 4.7 21.5 1.0 OE1 C:GLN11 4.7 40.0 1.0 CD C:GLU71 4.7 35.0 1.0 O D:HOH606 4.8 36.9 1.0 OD2 C:ASP98 4.9 40.8 1.0 CA C:GLN11 4.9 22.3 1.0 CG C:ASP98 4.9 30.9 1.0 CE D:LYS254 5.0 28.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:40.9 occ:1.00 O D:HOH601 1.9 40.3 1.0 OE1 D:GLN11 2.0 40.0 1.0 O1A D:GDP501 2.1 60.4 1.0 O D:HOH650 3.2 47.1 1.0 CD D:GLN11 3.2 46.9 1.0 PA D:GDP501 3.6 41.2 1.0 CB D:GLN11 3.9 39.9 1.0 CG D:GLN11 4.0 43.6 1.0 O2A D:GDP501 4.1 43.3 1.0 NE2 D:GLN11 4.2 47.1 1.0 C5' D:GDP501 4.4 42.9 1.0 O1B D:GDP501 4.4 36.1 1.0 O5' D:GDP501 4.5 37.8 1.0 O3A D:GDP501 4.6 43.3 1.0 C8 D:GDP501 4.7 40.9 1.0 OD1 D:ASN101 4.9 47.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z48847594-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z48847594-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:57.7 occ:1.00 O3G F:ACP401 2.1 71.2 1.0 O1B F:ACP401 2.4 82.6 1.0 OE2 F:GLU331 2.6 68.8 1.0 OD1 F:ASN333 2.7 67.1 1.0 OE1 F:GLU331 2.8 70.3 1.0 CD F:GLU331 3.1 68.6 1.0 PB F:ACP401 3.6 86.1 1.0 NZ F:LYS74 3.6 75.5 1.0 PG F:ACP401 3.7 101.2 1.0 CG F:ASN333 3.8 58.7 1.0 O2B F:ACP401 4.0 90.3 1.0 ND2 F:ASN333 4.3 59.5 1.0 C3B F:ACP401 4.3 85.8 1.0 O1G F:ACP401 4.4 86.8 1.0 CG F:GLU331 4.5 53.2 1.0 O2G F:ACP401 4.7 76.8 1.0 O1A F:ACP401 4.8 77.8 1.0 CE F:LYS74 4.8 69.6 1.0 O3A F:ACP401 4.9 85.3 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