Magnesium in PDB 5s4m: Tubulin-Z2142244288-Complex

The structure of Tubulin-Z2142244288-Complex, PDB code: 5s4m 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)	63.02 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.67, 157.87, 179.17, 90, 90, 90
R / Rfree (%)	20.6 / 24.4

The structure of Tubulin-Z2142244288-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2142244288-Complex (pdb code 5s4m). 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-Z2142244288-Complex, PDB code: 5s4m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.5 occ:1.00 O1G A:GTP501 2.0 42.7 1.0 O A:HOH630 2.1 43.2 1.0 O A:HOH650 2.1 60.7 1.0 O A:HOH644 2.1 48.5 1.0 O A:HOH609 2.1 48.1 1.0 O1B A:GTP501 2.2 43.7 1.0 PG A:GTP501 3.2 51.0 1.0 PB A:GTP501 3.2 43.8 1.0 O3B A:GTP501 3.5 51.7 1.0 O3A A:GTP501 3.7 47.9 1.0 O2G A:GTP501 3.7 47.5 1.0 NZ B:LYS254 3.8 63.8 1.0 CB A:GLN11 4.0 45.0 1.0 OE1 A:GLU71 4.0 63.1 1.0 OD1 A:ASP69 4.1 55.0 1.0 OD2 A:ASP69 4.2 53.1 1.0 N A:GLN11 4.3 45.9 1.0 OD2 A:ASP98 4.3 63.5 1.0 NE2 A:GLN11 4.3 53.4 1.0 CB A:ASP98 4.4 53.5 1.0 O3G A:GTP501 4.4 44.9 1.0 O2B A:GTP501 4.5 47.9 1.0 O1A A:GTP501 4.5 48.0 1.0 CG A:ASP69 4.6 56.0 1.0 PA A:GTP501 4.7 46.4 1.0 CA A:GLN11 4.7 48.7 1.0 CG A:ASP98 4.8 56.5 1.0 CE B:LYS254 4.8 54.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.9 occ:1.00 O B:HOH646 2.1 49.1 1.0 OE1 B:GLN11 2.1 48.2 1.0 O C:HOH641 2.2 47.6 1.0 O1A B:GDP501 2.2 42.5 1.0 O B:HOH651 2.5 44.4 1.0 O B:HOH612 2.6 48.8 1.0 CD B:GLN11 3.3 46.7 1.0 PA B:GDP501 3.5 42.6 1.0 O3A B:GDP501 3.9 45.6 1.0 OD2 B:ASP179 3.9 50.4 1.0 CB B:GLN11 4.0 44.8 1.0 CG B:GLN11 4.2 46.6 1.0 NE2 B:GLN11 4.3 53.5 1.0 OD1 B:ASN101 4.3 49.2 1.0 O C:HOH651 4.4 52.1 1.0 OE1 C:GLU254 4.4 58.7 1.0 C5' B:GDP501 4.4 45.4 1.0 O5' B:GDP501 4.5 46.7 1.0 O1B B:GDP501 4.6 43.5 1.0 O2A B:GDP501 4.6 42.3 1.0 C8 B:GDP501 4.8 48.5 1.0 PB B:GDP501 4.9 44.0 1.0 CG B:ASP179 4.9 51.0 1.0 ND2 B:ASN101 4.9 48.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.4 occ:1.00 O1G C:GTP501 2.0 43.0 1.0 O C:HOH655 2.0 40.6 1.0 O C:HOH701 2.1 40.5 1.0 O1B C:GTP501 2.1 39.2 1.0 O C:HOH617 2.1 44.9 1.0 O C:HOH680 2.2 45.0 1.0 PG C:GTP501 3.1 43.9 1.0 PB C:GTP501 3.2 41.3 1.0 O3B C:GTP501 3.5 50.2 1.0 O2G C:GTP501 3.5 41.5 1.0 O3A C:GTP501 3.6 46.6 1.0 NZ D:LYS254 3.9 46.0 1.0 OD1 C:ASP69 4.1 45.8 1.0 OE2 C:GLU71 4.1 57.6 1.0 OD2 C:ASP69 4.2 41.8 1.0 CB C:GLN11 4.2 41.1 1.0 CG C:GLU71 4.3 52.9 1.0 OD2 C:ASP98 4.3 53.2 1.0 N C:GLN11 4.3 40.2 1.0 O3G C:GTP501 4.4 40.8 1.0 O2B C:GTP501 4.5 44.1 1.0 CB C:ASP98 4.5 46.1 1.0 CG C:ASP69 4.6 46.4 1.0 O C:HOH656 4.6 65.3 1.0 O1A C:GTP501 4.6 44.1 1.0 CD C:GLU71 4.7 54.0 1.0 PA C:GTP501 4.7 42.4 1.0 CG C:ASP98 4.7 48.6 1.0 OE1 C:GLN11 4.9 54.7 1.0 CA C:GLN11 4.9 44.7 1.0 OG1 C:THR145 5.0 44.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:72.7 occ:1.00 O D:HOH604 1.9 59.7 1.0 OE1 D:GLN11 2.0 68.7 1.0 O1A D:GDP501 2.2 80.0 1.0 CD D:GLN11 3.1 71.8 1.0 CB D:GLN11 3.6 64.8 1.0 PA D:GDP501 3.7 67.6 1.0 O1B D:GDP501 3.8 65.6 1.0 CG D:GLN11 3.9 69.6 1.0 NE2 D:GLN11 4.1 69.9 1.0 O2A D:GDP501 4.2 64.3 1.0 O3A D:GDP501 4.4 70.6 1.0 OD1 D:ASN101 4.5 72.0 1.0 PB D:GDP501 4.6 64.6 1.0 O5' D:GDP501 4.8 68.9 1.0 C5' D:GDP501 4.9 69.4 1.0 O3B D:GDP501 5.0 73.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:91.3 occ:1.00 O1B F:ACP401 2.4 103.0 1.0 OE2 F:GLU331 2.4 95.0 1.0 O3G F:ACP401 2.5 96.8 1.0 OD1 F:ASN333 2.6 87.7 1.0 OE1 F:GLU331 2.9 96.5 1.0 CD F:GLU331 3.0 92.4 1.0 NZ F:LYS74 3.6 108.9 1.0 PB F:ACP401 3.7 104.3 1.0 CG F:ASN333 3.8 84.0 1.0 PG F:ACP401 4.0 111.6 1.0 O2B F:ACP401 4.1 112.6 1.0 ND2 F:ASN333 4.4 83.0 1.0 CG F:GLU331 4.5 80.3 1.0 C3B F:ACP401 4.6 107.7 1.0 CE F:LYS74 4.7 101.8 1.0 O1G F:ACP401 4.8 106.9 1.0 O1A F:ACP401 4.9 101.9 1.0 CB F:ASN333 4.9 73.5 1.0 O3A F:ACP401 4.9 107.5 1.0 O2G F:ACP401 5.0 95.6 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