Magnesium in PDB 5s4l: Tubulin-Z1891773393-Complex

The structure of Tubulin-Z1891773393-Complex, PDB code: 5s4l 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)	63.66 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.37, 159.78, 178.97, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Z1891773393-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1891773393-Complex (pdb code 5s4l). 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-Z1891773393-Complex, PDB code: 5s4l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.1 occ:1.00 O1G A:GTP501 2.0 43.8 1.0 O A:HOH611 2.0 50.5 1.0 O A:HOH607 2.1 46.0 1.0 O A:HOH637 2.1 47.8 1.0 O1B A:GTP501 2.1 46.6 1.0 O A:HOH617 2.1 52.2 1.0 PG A:GTP501 3.1 55.1 1.0 PB A:GTP501 3.2 46.6 1.0 O3B A:GTP501 3.5 56.3 1.0 O2G A:GTP501 3.5 50.3 1.0 OE1 A:GLU71 3.6 70.6 1.0 O3A A:GTP501 3.8 52.4 1.0 NZ B:LYS254 3.9 59.2 1.0 OD1 A:ASP69 3.9 55.0 1.0 OD2 A:ASP69 4.2 58.1 1.0 CB A:ASP98 4.2 56.5 1.0 CB A:GLN11 4.2 49.2 1.0 O3G A:GTP501 4.4 51.1 1.0 N A:GLN11 4.4 51.1 1.0 CG A:ASP69 4.5 59.4 1.0 OD2 A:ASP98 4.5 66.7 1.0 O2B A:GTP501 4.5 50.3 1.0 NE2 A:GLN11 4.6 54.0 1.0 O1A A:GTP501 4.6 50.8 1.0 CG A:ASP98 4.6 59.5 1.0 PA A:GTP501 4.8 50.0 1.0 CD A:GLU71 4.8 76.0 1.0 CE B:LYS254 4.9 56.9 1.0 CA A:GLN11 4.9 50.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.1 occ:1.00 O B:HOH601 1.8 58.1 1.0 O B:HOH623 2.1 51.7 1.0 OE1 B:GLN11 2.2 59.8 1.0 O C:HOH669 2.2 47.5 1.0 O1A B:GDP501 2.2 46.3 1.0 O B:HOH650 2.3 47.2 1.0 CD B:GLN11 3.4 58.7 1.0 PA B:GDP501 3.5 50.6 1.0 O3A B:GDP501 3.8 47.3 1.0 OD2 B:ASP179 4.0 56.2 1.0 CB B:GLN11 4.0 51.2 1.0 OD1 B:ASN101 4.1 51.5 1.0 CG B:GLN11 4.2 54.1 1.0 O1B B:GDP501 4.3 43.2 1.0 NE2 B:GLN11 4.4 62.2 1.0 O5' B:GDP501 4.4 48.8 1.0 C5' B:GDP501 4.4 52.9 1.0 O2A B:GDP501 4.6 46.7 1.0 OE1 C:GLU254 4.6 59.0 1.0 PB B:GDP501 4.7 47.6 1.0 O C:HOH646 4.7 52.8 1.0 O C:HOH687 4.9 62.3 1.0 ND2 B:ASN101 4.9 52.0 1.0 CG B:ASN101 4.9 51.3 1.0 O B:HOH635 5.0 50.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.7 occ:1.00 O C:HOH677 1.9 46.3 1.0 O C:HOH640 2.0 45.1 1.0 O C:HOH613 2.1 45.9 1.0 O1B C:GTP501 2.1 41.6 1.0 O1G C:GTP501 2.1 41.0 1.0 O C:HOH680 2.2 45.1 1.0 PB C:GTP501 3.2 42.5 1.0 PG C:GTP501 3.2 45.7 1.0 O3B C:GTP501 3.5 47.7 1.0 O3A C:GTP501 3.6 47.2 1.0 O2G C:GTP501 3.6 44.4 1.0 OD1 C:ASP69 4.0 42.2 1.0 NZ D:LYS254 4.0 44.4 1.0 OE2 C:GLU71 4.1 56.4 1.0 CB C:GLN11 4.1 40.8 1.0 OD2 C:ASP69 4.2 43.3 1.0 CG C:GLU71 4.2 54.5 1.0 N C:GLN11 4.3 42.3 1.0 OD2 C:ASP98 4.4 53.5 1.0 O2B C:GTP501 4.5 47.0 1.0 O3G C:GTP501 4.5 42.1 1.0 CB C:ASP98 4.5 46.4 1.0 CG C:ASP69 4.5 47.6 1.0 OE1 C:GLN11 4.6 54.2 1.0 O1A C:GTP501 4.6 44.8 1.0 CD C:GLU71 4.6 52.9 1.0 PA C:GTP501 4.7 44.0 1.0 CG C:ASP98 4.8 48.0 1.0 CA C:GLN11 4.8 45.5 1.0 OG1 C:THR145 5.0 46.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:66.9 occ:1.00 O1A D:GDP501 2.2 78.2 1.0 O D:HOH603 2.2 67.6 1.0 OE1 D:GLN11 2.2 69.8 1.0 CD D:GLN11 3.4 71.2 1.0 PA D:GDP501 3.6 67.6 1.0 CB D:GLN11 3.8 66.2 1.0 O1B D:GDP501 3.9 64.5 1.0 CG D:GLN11 4.1 71.1 1.0 O3A D:GDP501 4.3 65.0 1.0 O2A D:GDP501 4.3 66.0 1.0 NE2 D:GLN11 4.3 71.6 1.0 OD1 D:ASN101 4.6 70.8 1.0 PB D:GDP501 4.6 68.0 1.0 O5' D:GDP501 4.7 63.9 1.0 C5' D:GDP501 4.7 67.9 1.0 O D:HOH620 4.7 73.6 1.0 O3B D:GDP501 4.9 70.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1891773393-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1891773393-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:84.9 occ:1.00 OE2 F:GLU331 2.3 92.8 1.0 O1B F:ACP401 2.5 102.6 1.0 O3G F:ACP401 2.6 94.0 1.0 OD1 F:ASN333 2.9 88.2 1.0 CD F:GLU331 3.1 91.3 1.0 OE1 F:GLU331 3.1 97.1 1.0 NZ F:LYS74 3.6 105.0 1.0 PB F:ACP401 3.7 102.1 1.0 CG F:ASN333 4.0 85.6 1.0 O2B F:ACP401 4.0 108.2 1.0 PG F:ACP401 4.1 107.3 1.0 CG F:GLU331 4.6 83.3 1.0 ND2 F:ASN333 4.6 82.9 1.0 C3B F:ACP401 4.6 99.1 1.0 CE F:LYS74 4.8 103.1 1.0 O2G F:ACP401 4.9 91.5 1.0 O3A F:ACP401 4.9 104.4 1.0 O1G F:ACP401 5.0 101.2 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