Magnesium in PDB 5s4s: Tubulin-Z240297434-Complex

The structure of Tubulin-Z240297434-Complex, PDB code: 5s4s 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)	86.68 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.55, 164.17, 173.36, 90, 90, 90
R / Rfree (%)	24.4 / 28.4

The structure of Tubulin-Z240297434-Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Z240297434-Complex (pdb code 5s4s). 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-Z240297434-Complex, PDB code: 5s4s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z240297434-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z240297434-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.5 occ:1.00 O A:HOH601 1.9 61.3 1.0 O A:HOH603 2.2 57.2 1.0 O A:HOH606 2.2 55.2 1.0 O A:HOH602 2.3 63.1 1.0 O1G A:GTP501 2.3 54.1 1.0 O1B A:GTP501 2.4 57.4 1.0 OE1 A:GLU71 2.9 82.2 1.0 CD A:GLU71 3.6 82.2 1.0 PG A:GTP501 3.6 56.3 1.0 PB A:GTP501 3.6 57.0 1.0 OE2 A:GLU71 3.7 85.7 1.0 OD2 A:ASP69 3.9 55.9 1.0 OD1 A:ASP69 3.9 56.0 1.0 O3B A:GTP501 3.9 61.7 1.0 CB A:GLN11 4.0 55.6 1.0 O2G A:GTP501 4.1 60.9 1.0 O3A A:GTP501 4.1 53.9 1.0 CB A:ASP98 4.3 61.8 1.0 CG A:ASP69 4.3 57.5 1.0 N A:GLN11 4.3 55.2 1.0 NE2 A:GLN11 4.4 59.5 1.0 NZ B:LYS254 4.4 53.3 1.0 OD2 A:ASP98 4.7 67.6 1.0 CA A:GLN11 4.7 57.5 1.0 O1A A:GTP501 4.8 55.9 1.0 O3G A:GTP501 4.8 53.7 1.0 CG A:ASP98 4.8 60.2 1.0 O2B A:GTP501 4.8 59.2 1.0 CG A:GLU71 4.9 75.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z240297434-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z240297434-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:51.8 occ:1.00 O B:HOH615 1.9 51.6 1.0 O B:HOH606 1.9 58.0 1.0 O B:HOH616 2.1 52.2 1.0 O1A B:GDP501 2.1 54.4 1.0 OE1 B:GLN11 2.2 52.1 1.0 O C:HOH641 2.4 52.1 1.0 CD B:GLN11 3.4 53.1 1.0 PA B:GDP501 3.5 53.8 1.0 OD2 B:ASP179 3.9 53.5 1.0 CB B:GLN11 4.1 53.6 1.0 O3A B:GDP501 4.2 54.6 1.0 OD1 B:ASN101 4.2 56.6 1.0 CG B:GLN11 4.3 56.9 1.0 OE1 C:GLU254 4.3 52.0 1.0 O1B B:GDP501 4.3 57.8 1.0 C5' B:GDP501 4.3 55.2 1.0 NE2 B:GLN11 4.4 61.1 1.0 O5' B:GDP501 4.4 51.3 1.0 O2A B:GDP501 4.4 51.6 1.0 PB B:GDP501 4.9 55.7 1.0 C8 B:GDP501 5.0 52.1 1.0 CG B:ASP179 5.0 51.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z240297434-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z240297434-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:69.8 occ:1.00 O C:HOH601 2.1 59.8 1.0 O1G C:GTP501 2.7 59.9 1.0 O C:HOH662 2.7 75.8 1.0 O C:HOH603 2.7 60.0 1.0 O C:HOH624 2.7 60.0 1.0 OD2 C:ASP98 2.9 61.1 1.0 OE2 C:GLU71 3.0 65.9 1.0 NZ D:LYS254 3.2 60.4 1.0 O D:HOH613 3.3 75.8 1.0 CG C:GLU71 3.4 63.0 1.0 CD C:GLU71 3.5 63.4 1.0 CG C:ASP98 3.8 61.3 1.0 O1B C:GTP501 3.9 59.3 1.0 CB C:ASP98 4.0 67.9 1.0 PG C:GTP501 4.1 62.1 1.0 O D:HOH603 4.3 71.7 1.0 O2G C:GTP501 4.4 60.2 1.0 CE D:LYS254 4.5 60.6 1.0 OE1 C:GLU71 4.6 64.8 1.0 CB C:GLU71 4.8 61.7 1.0 PB C:GTP501 5.0 59.0 1.0 OD1 C:ASP98 5.0 67.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z240297434-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z240297434-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:80.9 occ:1.00 O1A D:GDP501 2.1 90.4 1.0 OE1 D:GLN11 2.2 92.4 1.0 CD D:GLN11 3.4 93.4 1.0 PA D:GDP501 3.6 84.2 1.0 CB D:GLN11 4.1 85.7 1.0 NE2 D:GLN11 4.2 93.4 1.0 CG D:GLN11 4.3 89.7 1.0 O2A D:GDP501 4.4 75.6 1.0 O3A D:GDP501 4.4 85.5 1.0 C5' D:GDP501 4.5 83.6 1.0 OD1 D:ASN101 4.5 89.7 1.0 O5' D:GDP501 4.5 82.8 1.0 O3B D:GDP501 4.6 83.1 1.0 O1B D:GDP501 4.7 87.4 1.0 PB D:GDP501 4.8 78.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z240297434-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z240297434-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:114.9 occ:1.00 O2B F:ACP401 2.8 118.1 1.0 C F:GLY154 3.3 144.5 1.0 O F:GLY154 3.4 144.4 1.0 PB F:ACP401 4.4 115.0 1.0 CA F:GLY154 4.4 147.1 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