Magnesium in PDB 5s5s: Tubulin-Z166605480-Complex

The structure of Tubulin-Z166605480-Complex, PDB code: 5s5s 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)	72.32 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.55, 158.051, 179.339, 90, 90, 90
R / Rfree (%)	21.2 / 25.4

The structure of Tubulin-Z166605480-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z166605480-Complex (pdb code 5s5s). 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-Z166605480-Complex, PDB code: 5s5s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.0 occ:1.00 O A:HOH616 2.0 35.6 1.0 O1G A:GTP501 2.1 30.7 1.0 O1B A:GTP501 2.1 30.1 1.0 O A:HOH619 2.1 35.1 1.0 O A:HOH625 2.2 36.1 1.0 O A:HOH643 2.2 32.0 1.0 PG A:GTP501 3.1 36.7 1.0 PB A:GTP501 3.2 32.0 1.0 O3B A:GTP501 3.5 40.0 1.0 O2G A:GTP501 3.6 35.0 1.0 O3A A:GTP501 3.8 32.4 1.0 OE1 A:GLU71 3.8 46.7 1.0 NZ B:LYS254 3.9 47.0 1.0 OD1 A:ASP69 4.0 40.5 1.0 CB A:GLN11 4.1 34.2 1.0 OD2 A:ASP69 4.2 41.9 1.0 OD2 A:ASP98 4.3 45.1 1.0 N A:GLN11 4.3 33.9 1.0 CB A:ASP98 4.3 42.1 1.0 NE2 A:GLN11 4.4 47.0 1.0 O B:HOH627 4.4 44.1 1.0 O3G A:GTP501 4.5 29.2 1.0 O2B A:GTP501 4.5 35.4 1.0 CG A:ASP69 4.5 43.3 1.0 O1A A:GTP501 4.5 32.4 1.0 PA A:GTP501 4.7 33.3 1.0 CG A:ASP98 4.8 43.5 1.0 CA A:GLN11 4.8 36.5 1.0 CE B:LYS254 5.0 45.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:26.6 occ:1.00 O B:HOH641 1.8 36.7 1.0 OE1 B:GLN11 2.1 35.5 1.0 O1A B:GDP501 2.2 32.7 1.0 O C:HOH699 2.3 39.7 1.0 O B:HOH664 2.4 35.2 1.0 O B:HOH617 2.5 37.7 1.0 CD B:GLN11 3.3 37.0 1.0 PA B:GDP501 3.6 26.0 1.0 OD2 B:ASP179 3.9 39.5 1.0 CB B:GLN11 4.0 32.9 1.0 O3A B:GDP501 4.0 30.4 1.0 CG B:GLN11 4.2 35.0 1.0 NE2 B:GLN11 4.3 44.1 1.0 OD1 B:ASN101 4.3 38.8 1.0 C5' B:GDP501 4.4 32.7 1.0 O C:HOH627 4.5 44.9 1.0 O5' B:GDP501 4.5 30.2 1.0 O C:HOH713 4.6 53.3 1.0 O2A B:GDP501 4.6 31.0 1.0 O1B B:GDP501 4.6 28.4 1.0 OE1 C:GLU254 4.7 48.7 1.0 C8 B:GDP501 4.8 34.2 1.0 CG B:ASP179 4.9 38.0 1.0 PB B:GDP501 4.9 25.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.8 occ:1.00 O C:HOH619 1.7 34.4 1.0 O1G C:GTP501 1.8 28.1 1.0 O C:HOH632 1.9 28.9 1.0 O1B C:GTP501 2.1 27.3 1.0 O C:HOH675 2.2 30.2 1.0 O C:HOH621 2.7 29.4 1.0 PG C:GTP501 2.8 27.8 1.0 PB C:GTP501 3.1 26.2 1.0 O2G C:GTP501 3.2 26.8 1.0 O3B C:GTP501 3.3 32.3 1.0 O3A C:GTP501 3.6 28.3 1.0 NZ D:LYS254 3.8 32.6 1.0 OD1 C:ASP69 4.1 30.6 1.0 O3G C:GTP501 4.1 27.7 1.0 OD2 C:ASP98 4.1 35.6 1.0 CB C:ASP98 4.2 32.2 1.0 CG C:GLU71 4.3 36.3 1.0 OE2 C:GLU71 4.4 41.2 1.0 O2B C:GTP501 4.4 28.9 1.0 CG C:ASP98 4.4 34.7 1.0 CB C:GLN11 4.5 26.8 1.0 OD2 C:ASP69 4.5 25.7 1.0 N C:GLN11 4.6 24.9 1.0 PA C:GTP501 4.7 28.1 1.0 CG C:ASP69 4.8 30.2 1.0 O1A C:GTP501 4.8 31.6 1.0 CE D:LYS254 4.8 32.0 1.0 OG1 C:THR145 4.8 27.4 1.0 CD C:GLU71 4.9 38.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:57.2 occ:1.00 O D:HOH603 2.0 52.1 1.0 OE1 D:GLN11 2.0 64.3 1.0 O1A D:GDP501 2.3 65.2 1.0 CD D:GLN11 3.1 63.0 1.0 PA D:GDP501 3.7 56.9 1.0 O D:HOH631 3.8 61.8 1.0 CB D:GLN11 3.9 57.5 1.0 CG D:GLN11 4.0 59.1 1.0 NE2 D:GLN11 4.1 65.3 1.0 O2A D:GDP501 4.2 50.2 1.0 O1B D:GDP501 4.5 53.8 1.0 C5' D:GDP501 4.6 55.6 1.0 O5' D:GDP501 4.7 54.2 1.0 O3A D:GDP501 4.8 54.1 1.0 C8 D:GDP501 4.8 53.3 1.0 OD1 D:ASN101 4.9 59.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z166605480-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z166605480-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:73.2 occ:1.00 O1B F:ACP401 2.3 90.8 1.0 OE2 F:GLU331 2.3 78.1 1.0 O3G F:ACP401 2.4 83.2 1.0 OD1 F:ASN333 3.0 74.0 1.0 CD F:GLU331 3.0 79.0 1.0 OE1 F:GLU331 3.1 85.4 1.0 PB F:ACP401 3.5 91.2 1.0 NZ F:LYS74 3.7 92.6 1.0 PG F:ACP401 3.8 96.4 1.0 O2B F:ACP401 3.9 93.8 1.0 CG F:ASN333 4.1 66.7 1.0 C3B F:ACP401 4.3 92.0 1.0 CG F:GLU331 4.5 68.5 1.0 ND2 F:ASN333 4.6 66.0 1.0 O2G F:ACP401 4.7 81.4 1.0 O1G F:ACP401 4.8 89.7 1.0 O3A F:ACP401 4.8 92.8 1.0 CE F:LYS74 4.8 91.6 1.0 O1A F:ACP401 5.0 86.3 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