Magnesium in PDB 5s5t: Tubulin-Z198194394-Complex

The structure of Tubulin-Z198194394-Complex, PDB code: 5s5t 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 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.834, 158.225, 178.442, 90, 90, 90
R / Rfree (%)	21.1 / 25.6

The structure of Tubulin-Z198194394-Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-Z198194394-Complex (pdb code 5s5t). 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-Z198194394-Complex, PDB code: 5s5t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.7 occ:1.00 O A:HOH617 2.0 37.2 1.0 O A:HOH651 2.1 34.6 1.0 O A:HOH614 2.1 41.7 1.0 O A:HOH616 2.1 34.4 1.0 O1G A:GTP501 2.2 33.4 1.0 O1B A:GTP501 2.2 35.5 1.0 PB A:GTP501 3.4 36.2 1.0 PG A:GTP501 3.4 39.9 1.0 OE1 A:GLU71 3.6 49.1 1.0 O3B A:GTP501 3.7 45.7 1.0 NZ B:LYS254 3.8 50.8 1.0 O3A A:GTP501 3.9 41.9 1.0 O2G A:GTP501 4.0 35.7 1.0 CB A:GLN11 4.0 36.1 1.0 OD1 A:ASP69 4.2 44.0 1.0 CB A:ASP98 4.3 42.8 1.0 OD2 A:ASP69 4.4 41.6 1.0 N A:GLN11 4.4 38.5 1.0 NE2 A:GLN11 4.4 43.8 1.0 OD2 A:ASP98 4.5 51.8 1.0 O1A A:GTP501 4.5 36.5 1.0 O3G A:GTP501 4.6 36.4 1.0 O2B A:GTP501 4.7 42.9 1.0 O B:HOH625 4.7 47.0 1.0 CG A:ASP69 4.7 44.3 1.0 PA A:GTP501 4.8 37.4 1.0 CG A:ASP98 4.8 47.3 1.0 CA A:GLN11 4.8 39.8 1.0 CD A:GLU71 4.8 51.9 1.0 CE B:LYS254 5.0 48.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.6 occ:1.00 O B:HOH612 1.7 51.2 1.0 OE1 B:GLN11 2.1 52.1 1.0 O C:HOH676 2.1 40.8 1.0 O B:HOH655 2.4 40.8 1.0 O1A B:GDP501 2.4 40.2 1.0 O B:HOH610 2.6 50.7 1.0 CD B:GLN11 3.3 48.1 1.0 PA B:GDP501 3.8 35.6 1.0 OD2 B:ASP179 3.8 49.4 1.0 CB B:GLN11 4.1 41.7 1.0 NE2 B:GLN11 4.2 55.1 1.0 CG B:GLN11 4.2 44.0 1.0 O3A B:GDP501 4.2 40.4 1.0 O C:HOH628 4.4 47.5 1.0 OD1 B:ASN101 4.5 48.4 1.0 OE1 C:GLU254 4.5 57.0 1.0 O1B B:GDP501 4.6 39.4 1.0 C5' B:GDP501 4.6 41.2 1.0 O C:HOH694 4.7 61.0 1.0 O5' B:GDP501 4.7 39.1 1.0 O2A B:GDP501 4.8 38.9 1.0 CG B:ASP179 4.8 50.0 1.0 C8 B:GDP501 4.9 44.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.5 occ:1.00 O C:HOH646 1.9 32.4 1.0 O C:HOH608 2.0 33.8 1.0 O C:HOH670 2.0 31.5 1.0 O1G C:GTP501 2.1 29.7 1.0 O1B C:GTP501 2.1 31.4 1.0 O C:HOH650 2.2 43.0 1.0 PG C:GTP501 3.2 35.1 1.0 PB C:GTP501 3.3 32.2 1.0 O3B C:GTP501 3.6 39.0 1.0 O2G C:GTP501 3.6 35.9 1.0 OE2 C:GLU71 3.8 44.5 1.0 NZ D:LYS254 3.9 40.8 1.0 O3A C:GTP501 4.0 37.9 1.0 OD1 C:ASP69 4.0 36.1 1.0 CG C:GLU71 4.0 44.6 1.0 OD2 C:ASP98 4.1 43.7 1.0 OD2 C:ASP69 4.2 36.4 1.0 CB C:GLN11 4.3 37.5 1.0 CD C:GLU71 4.4 43.5 1.0 CB C:ASP98 4.4 37.1 1.0 O C:HOH605 4.4 57.2 1.0 O3G C:GTP501 4.5 35.3 1.0 N C:GLN11 4.5 32.6 1.0 CG C:ASP69 4.5 37.0 1.0 O2B C:GTP501 4.5 34.8 1.0 CG C:ASP98 4.7 41.9 1.0 O1A C:GTP501 4.8 35.0 1.0 OE1 C:GLN11 4.8 53.5 1.0 PA C:GTP501 4.9 33.8 1.0 CE D:LYS254 5.0 41.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:70.0 occ:1.00 OE1 D:GLN11 1.9 75.9 1.0 O D:HOH602 2.2 55.3 1.0 O1A D:GDP501 2.8 79.9 1.0 CD D:GLN11 2.9 75.2 1.0 NE2 D:GLN11 3.6 86.0 1.0 CB D:GLN11 3.6 70.8 1.0 CG D:GLN11 3.8 73.0 1.0 PA D:GDP501 4.0 63.2 1.0 O2A D:GDP501 4.1 60.5 1.0 O1B D:GDP501 4.3 66.2 1.0 O D:HOH625 4.6 63.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z198194394-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z198194394-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:86.3 occ:1.00 O1B F:ACP401 2.2 103.3 1.0 OE2 F:GLU331 2.5 93.2 1.0 O3G F:ACP401 2.5 95.2 1.0 OD1 F:ASN333 3.0 88.7 1.0 CD F:GLU331 3.2 88.0 1.0 OE1 F:GLU331 3.2 90.5 1.0 PB F:ACP401 3.5 104.9 1.0 O2B F:ACP401 3.7 107.9 1.0 NZ F:LYS74 3.9 92.0 1.0 PG F:ACP401 4.0 111.7 1.0 CG F:ASN333 4.1 82.8 1.0 C3B F:ACP401 4.4 104.9 1.0 ND2 F:ASN333 4.6 84.7 1.0 CG F:GLU331 4.7 79.4 1.0 O3A F:ACP401 4.7 101.7 1.0 O1G F:ACP401 4.7 107.7 1.0 O1A F:ACP401 4.9 96.8 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