Magnesium in PDB 5s60: Tubulin-Z27695365-Complex

The structure of Tubulin-Z27695365-Complex, PDB code: 5s60 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)	63.73 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.35, 160.06, 178.51, 90, 90, 90
R / Rfree (%)	19.4 / 22.8

The structure of Tubulin-Z27695365-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z27695365-Complex (pdb code 5s60). 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-Z27695365-Complex, PDB code: 5s60:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.8 occ:1.00 O1G A:GTP501 2.0 42.4 1.0 O A:HOH612 2.1 46.7 1.0 O A:HOH645 2.1 44.3 1.0 O A:HOH629 2.1 44.4 1.0 O1B A:GTP501 2.1 43.0 1.0 O A:HOH616 2.2 48.0 1.0 PG A:GTP501 3.1 47.5 1.0 PB A:GTP501 3.2 44.6 1.0 O3B A:GTP501 3.4 55.0 1.0 O2G A:GTP501 3.6 42.8 1.0 O3A A:GTP501 3.7 49.1 1.0 OE1 A:GLU71 3.9 64.5 1.0 NZ B:LYS254 3.9 58.5 1.0 OD1 A:ASP69 4.0 56.0 1.0 CB A:GLN11 4.2 46.0 1.0 OD2 A:ASP98 4.2 58.6 1.0 OD2 A:ASP69 4.3 53.1 1.0 CB A:ASP98 4.3 51.7 1.0 O3G A:GTP501 4.4 47.3 1.0 N A:GLN11 4.4 46.1 1.0 O2B A:GTP501 4.5 47.9 1.0 O1A A:GTP501 4.6 49.6 1.0 CG A:ASP69 4.6 55.0 1.0 CG A:ASP98 4.6 54.4 1.0 O B:HOH645 4.6 57.2 1.0 NE2 A:GLN11 4.7 56.6 1.0 PA A:GTP501 4.7 51.1 1.0 CA A:GLN11 4.9 47.9 1.0 CE B:LYS254 4.9 56.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.9 occ:1.00 O B:HOH647 2.2 40.5 1.0 OE1 B:GLN11 2.2 45.6 1.0 O1A B:GDP501 2.2 43.6 1.0 O B:HOH640 2.2 48.8 1.0 O C:HOH811 2.2 43.0 1.0 O B:HOH696 2.3 46.5 1.0 O B:HOH672 2.3 39.3 1.0 CD B:GLN11 3.4 47.5 1.0 PA B:GDP501 3.5 43.8 1.0 O3A B:GDP501 3.9 47.0 1.0 CB B:GLN11 4.0 41.1 1.0 OD2 B:ASP179 4.0 44.3 1.0 CG B:GLN11 4.2 43.5 1.0 OD1 B:ASN101 4.3 42.7 1.0 NE2 B:GLN11 4.4 55.5 1.0 O C:HOH749 4.4 48.0 1.0 O1B B:GDP501 4.4 38.2 1.0 C5' B:GDP501 4.5 44.8 1.0 O5' B:GDP501 4.5 40.8 1.0 O2A B:GDP501 4.6 43.0 1.0 OE1 C:GLU254 4.6 52.0 1.0 PB B:GDP501 4.8 42.6 1.0 C8 B:GDP501 4.9 46.1 1.0 ND2 B:ASN101 5.0 41.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:44.4 occ:1.00 O1G C:GTP602 1.9 39.1 1.0 O C:HOH791 2.0 40.8 1.0 O C:HOH750 2.1 42.0 1.0 O C:HOH856 2.1 38.7 1.0 O1B C:GTP602 2.1 34.3 1.0 O C:HOH829 2.2 42.7 1.0 PG C:GTP602 3.0 43.1 1.0 PB C:GTP602 3.2 48.4 1.0 O3B C:GTP602 3.4 43.8 1.0 O2G C:GTP602 3.5 40.6 1.0 O3A C:GTP602 3.7 43.8 1.0 NZ D:LYS254 3.9 45.0 1.0 OD1 C:ASP69 3.9 42.4 1.0 OE1 C:GLU71 4.1 52.3 1.0 CG C:GLU71 4.1 51.0 1.0 OD2 C:ASP69 4.2 41.6 1.0 OD2 C:ASP98 4.2 50.8 1.0 O3G C:GTP602 4.3 39.2 1.0 CB C:GLN11 4.4 42.0 1.0 CB C:ASP98 4.4 42.2 1.0 N C:GLN11 4.5 36.4 1.0 O2B C:GTP602 4.5 43.8 1.0 CG C:ASP69 4.5 39.2 1.0 CD C:GLU71 4.6 52.4 1.0 O C:HOH771 4.6 51.5 1.0 O1A C:GTP602 4.6 44.0 1.0 CG C:ASP98 4.7 47.3 1.0 PA C:GTP602 4.8 42.1 1.0 OE1 C:GLN11 4.8 51.3 1.0 OG1 C:THR145 4.8 41.4 1.0 CE D:LYS254 5.0 45.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:69.6 occ:1.00 O D:HOH607 1.9 52.6 1.0 OE1 D:GLN11 2.1 68.5 1.0 O1A D:GDP501 2.1 75.5 1.0 CD D:GLN11 3.3 71.0 1.0 PA D:GDP501 3.6 66.4 1.0 CB D:GLN11 3.7 63.0 1.0 O1B D:GDP501 3.8 60.1 1.0 O D:HOH678 3.9 63.2 1.0 CG D:GLN11 4.1 64.5 1.0 O3A D:GDP501 4.1 64.7 1.0 O2A D:GDP501 4.3 63.7 1.0 NE2 D:GLN11 4.4 69.7 1.0 PB D:GDP501 4.4 62.6 1.0 OD1 D:ASN101 4.4 72.5 1.0 O3B D:GDP501 4.6 71.6 1.0 O5' D:GDP501 4.6 60.2 1.0 C5' D:GDP501 4.7 63.8 1.0 O D:HOH680 4.8 69.5 1.0 OE2 D:GLU71 4.8 98.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z27695365-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z27695365-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:97.8 occ:1.00 O3G F:ACP401 2.2 107.1 1.0 OD1 F:ASN333 2.5 92.6 1.0 OE2 F:GLU331 2.7 99.0 1.0 O1B F:ACP401 2.8 104.9 1.0 OE1 F:GLU331 3.4 97.8 1.0 CD F:GLU331 3.4 95.4 1.0 CG F:ASN333 3.6 87.4 1.0 PG F:ACP401 3.7 118.2 1.0 NZ F:LYS74 3.9 105.9 1.0 PB F:ACP401 4.0 109.6 1.0 O1G F:ACP401 4.1 116.6 1.0 ND2 F:ASN333 4.3 83.8 1.0 O2B F:ACP401 4.4 115.4 1.0 C3B F:ACP401 4.6 107.9 1.0 CB F:ASN333 4.8 74.9 1.0 O2G F:ACP401 4.8 101.0 1.0 CG F:GLU331 4.9 86.8 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