Magnesium in PDB 5s5o: Tubulin-Z27682767-Complex

The structure of Tubulin-Z27682767-Complex, PDB code: 5s5o 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)	62.74 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.25, 159.67, 179.23, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Z27682767-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z27682767-Complex (pdb code 5s5o). 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-Z27682767-Complex, PDB code: 5s5o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.5 occ:1.00 O1G A:GTP501 2.0 44.6 1.0 O A:HOH617 2.1 49.0 1.0 O A:HOH628 2.1 50.0 1.0 O A:HOH621 2.1 55.2 1.0 O1B A:GTP501 2.2 46.7 1.0 O A:HOH620 2.2 48.1 1.0 PG A:GTP501 3.2 51.2 1.0 PB A:GTP501 3.3 46.1 1.0 OE1 A:GLU71 3.5 67.0 1.0 O3B A:GTP501 3.6 56.7 1.0 O2G A:GTP501 3.6 49.9 1.0 NZ B:LYS254 3.9 59.2 1.0 O3A A:GTP501 3.9 52.0 1.0 OD1 A:ASP69 4.1 56.1 1.0 CB A:GLN11 4.2 51.7 1.0 CB A:ASP98 4.2 55.7 1.0 OD2 A:ASP69 4.3 59.6 1.0 OD2 A:ASP98 4.3 66.3 1.0 O3G A:GTP501 4.5 51.0 1.0 N A:GLN11 4.5 50.4 1.0 NE2 A:GLN11 4.5 58.6 1.0 CG A:ASP98 4.6 59.2 1.0 CG A:ASP69 4.6 59.5 1.0 O2B A:GTP501 4.6 48.0 1.0 CD A:GLU71 4.7 72.2 1.0 O1A A:GTP501 4.8 50.8 1.0 PA A:GTP501 4.9 50.6 1.0 CE B:LYS254 4.9 56.8 1.0 CA A:GLN11 5.0 51.5 1.0 CB A:GLU71 5.0 69.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:43.3 occ:1.00 O B:HOH643 2.0 48.7 1.0 O B:HOH609 2.1 58.7 1.0 OE1 B:GLN11 2.1 56.9 1.0 O C:HOH778 2.1 45.1 1.0 O1A B:GDP501 2.3 45.5 1.0 O B:HOH651 2.4 44.7 1.0 CD B:GLN11 3.3 55.2 1.0 PA B:GDP501 3.6 45.7 1.0 O3A B:GDP501 3.9 45.3 1.0 CB B:GLN11 4.1 50.5 1.0 OD2 B:ASP179 4.2 53.5 1.0 CG B:GLN11 4.2 50.6 1.0 NE2 B:GLN11 4.2 64.8 1.0 OD1 B:ASN101 4.3 47.6 1.0 C5' B:GDP501 4.5 49.6 1.0 OE1 C:GLU254 4.5 57.2 1.0 O5' B:GDP501 4.5 47.0 1.0 O C:HOH759 4.5 50.1 1.0 O1B B:GDP501 4.5 45.2 1.0 O2A B:GDP501 4.6 45.7 1.0 PB B:GDP501 4.9 48.0 1.0 ND2 B:ASN101 4.9 46.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:45.6 occ:1.00 O C:HOH733 2.0 45.8 1.0 O C:HOH776 2.0 44.5 1.0 O1B C:GTP602 2.1 42.3 1.0 O1G C:GTP602 2.1 43.5 1.0 O C:HOH722 2.1 44.0 1.0 O C:HOH772 2.3 45.3 1.0 PB C:GTP602 3.1 43.2 1.0 PG C:GTP602 3.1 45.1 1.0 O3B C:GTP602 3.4 47.2 1.0 O2G C:GTP602 3.6 44.5 1.0 O3A C:GTP602 3.6 50.3 1.0 OD1 C:ASP69 3.9 48.0 1.0 OD2 C:ASP69 4.1 46.7 1.0 OE2 C:GLU71 4.1 56.6 1.0 CB C:GLN11 4.1 45.4 1.0 NZ D:LYS254 4.2 46.0 1.0 N C:GLN11 4.3 43.6 1.0 CG C:GLU71 4.3 58.4 1.0 CG C:ASP69 4.4 45.6 1.0 O2B C:GTP602 4.4 47.4 1.0 O3G C:GTP602 4.4 42.5 1.0 OD2 C:ASP98 4.5 52.6 1.0 CB C:ASP98 4.5 47.4 1.0 O1A C:GTP602 4.6 51.1 1.0 PA C:GTP602 4.7 41.6 1.0 OE1 C:GLN11 4.7 57.6 1.0 CD C:GLU71 4.7 56.8 1.0 CA C:GLN11 4.8 47.5 1.0 CG C:ASP98 4.8 52.0 1.0 OG1 C:THR145 4.9 46.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.0 occ:1.00 O D:HOH604 1.9 70.5 1.0 OE1 D:GLN11 2.0 71.3 1.0 O1A D:GDP501 2.2 82.0 1.0 CD D:GLN11 3.1 75.1 1.0 PA D:GDP501 3.6 71.8 1.0 CB D:GLN11 3.7 71.9 1.0 O1B D:GDP501 4.0 66.0 1.0 CG D:GLN11 4.0 76.8 1.0 NE2 D:GLN11 4.1 72.2 1.0 O2A D:GDP501 4.2 69.2 1.0 O3A D:GDP501 4.4 71.9 1.0 OD1 D:ASN101 4.7 76.3 1.0 O5' D:GDP501 4.7 71.1 1.0 C5' D:GDP501 4.7 71.7 1.0 PB D:GDP501 4.7 68.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z27682767-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z27682767-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:98.8 occ:1.00 O3G F:ACP401 2.4 101.8 1.0 O1B F:ACP401 2.4 108.3 1.0 OE2 F:GLU331 2.7 103.2 1.0 OD1 F:ASN333 3.2 92.0 1.0 CD F:GLU331 3.5 101.0 1.0 OE1 F:GLU331 3.5 105.5 1.0 PB F:ACP401 3.5 109.4 1.0 NZ F:LYS74 3.7 104.6 1.0 O2B F:ACP401 3.7 111.7 1.0 PG F:ACP401 3.9 117.1 1.0 CG F:ASN333 4.3 86.9 1.0 C3B F:ACP401 4.4 109.4 1.0 O1G F:ACP401 4.6 110.2 1.0 O3A F:ACP401 4.9 110.5 1.0 CG F:GLU331 4.9 89.6 1.0 CE F:LYS74 4.9 104.9 1.0 O2G F:ACP401 4.9 99.2 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