Magnesium in PDB 5s5l: Tubulin-Z1492796719-Complex

The structure of Tubulin-Z1492796719-Complex, PDB code: 5s5l 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)	62.67 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.12, 159.02, 179.19, 90, 90, 90
R / Rfree (%)	20.4 / 23.5

The structure of Tubulin-Z1492796719-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1492796719-Complex (pdb code 5s5l). 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-Z1492796719-Complex, PDB code: 5s5l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.2 occ:1.00 O A:HOH609 2.0 44.1 1.0 O1G A:GTP501 2.0 38.7 1.0 O A:HOH621 2.1 45.3 1.0 O A:HOH622 2.1 45.1 1.0 O A:HOH647 2.1 46.3 1.0 O1B A:GTP501 2.2 41.5 1.0 PG A:GTP501 3.2 47.7 1.0 PB A:GTP501 3.3 40.7 1.0 O3B A:GTP501 3.6 48.1 1.0 OE1 A:GLU71 3.7 56.7 1.0 O2G A:GTP501 3.8 43.4 1.0 O3A A:GTP501 3.8 45.8 1.0 NZ B:LYS254 3.9 57.5 1.0 OD1 A:ASP69 4.0 49.8 1.0 CB A:GLN11 4.2 42.6 1.0 OD2 A:ASP69 4.2 52.4 1.0 CB A:ASP98 4.2 50.8 1.0 N A:GLN11 4.4 44.0 1.0 O3G A:GTP501 4.5 45.3 1.0 OD2 A:ASP98 4.5 61.5 1.0 NE2 A:GLN11 4.5 54.2 1.0 CG A:ASP69 4.6 52.3 1.0 O2B A:GTP501 4.6 49.0 1.0 O1A A:GTP501 4.6 47.2 1.0 CG A:ASP98 4.8 53.6 1.0 PA A:GTP501 4.8 43.8 1.0 CA A:GLN11 4.9 46.4 1.0 CD A:GLU71 4.9 61.5 1.0 CE B:LYS254 5.0 55.3 1.0 OG1 A:THR145 5.0 50.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.8 occ:1.00 O B:HOH647 1.9 37.6 1.0 O B:HOH651 2.0 44.8 1.0 OE1 B:GLN11 2.1 41.0 1.0 O1A B:GDP501 2.2 37.0 1.0 O B:HOH656 2.3 43.7 1.0 O B:HOH629 2.5 41.3 1.0 CD B:GLN11 3.3 46.0 1.0 PA B:GDP501 3.5 39.3 1.0 O3A B:GDP501 3.9 38.8 1.0 CB B:GLN11 4.0 41.3 1.0 OD2 B:ASP179 4.0 46.5 1.0 CG B:GLN11 4.1 41.4 1.0 O C:HOH681 4.3 46.3 1.0 NE2 B:GLN11 4.3 55.8 1.0 OD1 B:ASN101 4.4 37.2 1.0 C5' B:GDP501 4.4 40.2 1.0 O B:HOH681 4.4 61.3 1.0 O5' B:GDP501 4.5 40.2 1.0 O1B B:GDP501 4.5 38.4 1.0 OE1 C:GLU254 4.6 45.2 1.0 O2A B:GDP501 4.6 41.2 1.0 C8 B:GDP501 4.8 44.0 1.0 PB B:GDP501 4.9 36.6 1.0 CG B:ASP179 5.0 44.0 1.0 ND2 B:ASN101 5.0 41.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.5 occ:1.00 O1G C:GTP501 1.9 39.1 1.0 O C:HOH670 2.0 40.4 1.0 O C:HOH644 2.0 40.8 1.0 O1B C:GTP501 2.1 37.0 1.0 O C:HOH716 2.1 38.8 1.0 O C:HOH669 2.2 42.3 1.0 PG C:GTP501 3.0 40.0 1.0 PB C:GTP501 3.1 36.7 1.0 O3B C:GTP501 3.4 44.5 1.0 O2G C:GTP501 3.4 37.2 1.0 O3A C:GTP501 3.6 39.9 1.0 NZ D:LYS254 3.9 39.9 1.0 OD1 C:ASP69 4.0 43.9 1.0 OE2 C:GLU71 4.2 50.6 1.0 OD2 C:ASP69 4.3 37.9 1.0 CG C:GLU71 4.3 48.5 1.0 O3G C:GTP501 4.3 37.8 1.0 CB C:ASP98 4.4 43.4 1.0 CB C:GLN11 4.4 37.5 1.0 OD2 C:ASP98 4.4 47.1 1.0 N C:GLN11 4.4 36.1 1.0 O2B C:GTP501 4.4 40.8 1.0 CG C:ASP69 4.6 39.6 1.0 CG C:ASP98 4.6 44.0 1.0 O1A C:GTP501 4.7 40.9 1.0 PA C:GTP501 4.7 38.0 1.0 CD C:GLU71 4.8 47.7 1.0 CE D:LYS254 5.0 42.9 1.0 OG1 C:THR145 5.0 40.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:62.7 occ:1.00 O D:HOH605 1.9 65.1 1.0 OE1 D:GLN11 2.0 67.0 1.0 O1A D:GDP501 2.2 76.7 1.0 CD D:GLN11 3.2 69.3 1.0 PA D:GDP501 3.7 65.5 1.0 CB D:GLN11 4.0 64.2 1.0 CG D:GLN11 4.1 68.9 1.0 NE2 D:GLN11 4.1 69.0 1.0 O D:HOH623 4.2 76.5 1.0 O1B D:GDP501 4.4 62.1 1.0 C5' D:GDP501 4.4 66.5 1.0 O3A D:GDP501 4.4 63.3 1.0 O2A D:GDP501 4.5 64.2 1.0 O5' D:GDP501 4.5 65.9 1.0 OD1 D:ASN101 4.6 74.8 1.0 C8 D:GDP501 4.9 64.7 1.0 PB D:GDP501 5.0 66.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1492796719-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1492796719-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:93.8 occ:1.00 O1B F:ACP401 2.3 103.7 1.0 O3G F:ACP401 2.3 97.1 1.0 OE2 F:GLU331 2.5 94.3 1.0 OD1 F:ASN333 3.1 89.4 1.0 CD F:GLU331 3.3 93.6 1.0 OE1 F:GLU331 3.4 99.3 1.0 PB F:ACP401 3.4 105.0 1.0 O2B F:ACP401 3.7 108.4 1.0 NZ F:LYS74 3.7 103.1 1.0 PG F:ACP401 3.8 111.5 1.0 CG F:ASN333 4.3 84.2 1.0 C3B F:ACP401 4.3 105.4 1.0 O1G F:ACP401 4.6 104.2 1.0 O3A F:ACP401 4.7 107.1 1.0 CG F:GLU331 4.8 83.1 1.0 ND2 F:ASN333 4.8 82.2 1.0 O2G F:ACP401 4.9 94.0 1.0 CE F:LYS74 4.9 100.9 1.0 O1A F:ACP401 4.9 102.8 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