Magnesium in PDB 5s5f: Tubulin-Z87615031-Complex

The structure of Tubulin-Z87615031-Complex, PDB code: 5s5f 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)	72.43 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.828, 158.374, 179.214, 90, 90, 90
R / Rfree (%)	23.6 / 26.2

The structure of Tubulin-Z87615031-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z87615031-Complex (pdb code 5s5f). 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-Z87615031-Complex, PDB code: 5s5f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.5 occ:1.00 O A:HOH610 2.1 30.6 1.0 O1G A:GTP501 2.1 31.1 1.0 O A:HOH625 2.1 30.7 1.0 O A:HOH657 2.2 32.3 1.0 O A:HOH654 2.2 29.0 1.0 O1B A:GTP501 2.3 31.1 1.0 PG A:GTP501 3.3 30.5 1.0 PB A:GTP501 3.4 27.2 1.0 OE1 A:GLU71 3.6 45.2 1.0 O3B A:GTP501 3.7 32.6 1.0 O2G A:GTP501 3.7 29.6 1.0 NZ B:LYS254 3.9 40.4 1.0 O3A A:GTP501 3.9 29.6 1.0 OD1 A:ASP69 4.0 34.6 1.0 CB A:GLN11 4.2 29.2 1.0 OD2 A:ASP69 4.2 35.9 1.0 CB A:ASP98 4.3 34.2 1.0 OD2 A:ASP98 4.4 38.0 1.0 N A:GLN11 4.5 30.0 1.0 NE2 A:GLN11 4.5 37.5 1.0 O3G A:GTP501 4.5 26.4 1.0 CG A:ASP69 4.6 35.8 1.0 O1A A:GTP501 4.6 30.1 1.0 CD A:GLU71 4.7 45.0 1.0 O2B A:GTP501 4.7 30.1 1.0 CG A:ASP98 4.7 35.8 1.0 O B:HOH640 4.8 46.5 1.0 PA A:GTP501 4.9 27.1 1.0 CA A:GLN11 4.9 32.8 1.0 CE B:LYS254 4.9 37.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.0 occ:1.00 O B:HOH630 2.0 27.1 1.0 OE1 B:GLN11 2.1 27.4 1.0 O B:HOH661 2.2 26.6 1.0 O1A B:GDP501 2.2 25.4 1.0 O B:HOH663 2.5 25.6 1.0 O B:HOH617 2.5 27.9 1.0 CD B:GLN11 3.3 29.2 1.0 PA B:GDP501 3.5 22.2 1.0 O3A B:GDP501 3.9 25.1 1.0 OD2 B:ASP179 3.9 30.1 1.0 CB B:GLN11 4.0 23.8 1.0 CG B:GLN11 4.1 27.3 1.0 NE2 B:GLN11 4.3 33.1 1.0 OD1 B:ASN101 4.4 26.3 1.0 C5' B:GDP501 4.4 26.0 1.0 O5' B:GDP501 4.4 24.7 1.0 O C:HOH665 4.5 34.7 1.0 O1B B:GDP501 4.5 21.6 1.0 O2A B:GDP501 4.5 24.9 1.0 OE1 C:GLU254 4.6 39.0 1.0 C8 B:GDP501 4.8 28.9 1.0 PB B:GDP501 4.9 24.5 1.0 CG B:ASP179 4.9 31.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.1 occ:1.00 O C:HOH689 1.9 20.6 1.0 O C:HOH700 2.0 26.3 1.0 O1G C:GTP501 2.0 21.7 1.0 O C:HOH658 2.1 24.9 1.0 O C:HOH702 2.1 23.9 1.0 O1B C:GTP501 2.2 21.7 1.0 PG C:GTP501 3.2 24.8 1.0 PB C:GTP501 3.3 22.0 1.0 O3B C:GTP501 3.6 24.8 1.0 O2G C:GTP501 3.7 23.3 1.0 O3A C:GTP501 3.8 25.0 1.0 NZ D:LYS254 4.0 28.6 1.0 OE2 C:GLU71 4.0 32.5 1.0 OD1 C:ASP69 4.1 24.6 1.0 CG C:GLU71 4.1 31.1 1.0 CB C:GLN11 4.2 22.2 1.0 OD2 C:ASP69 4.2 24.8 1.0 OD2 C:ASP98 4.4 30.6 1.0 N C:GLN11 4.4 19.6 1.0 CB C:ASP98 4.4 27.9 1.0 O3G C:GTP501 4.5 21.9 1.0 O2B C:GTP501 4.6 23.3 1.0 CD C:GLU71 4.6 31.7 1.0 O1A C:GTP501 4.6 25.4 1.0 CG C:ASP69 4.6 27.0 1.0 O C:HOH638 4.7 30.3 1.0 OE1 C:GLN11 4.7 37.9 1.0 CG C:ASP98 4.7 30.4 1.0 PA C:GTP501 4.8 24.3 1.0 O C:HOH698 4.8 47.9 1.0 O D:HOH613 4.9 36.5 1.0 CA C:GLN11 4.9 24.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:47.9 occ:1.00 O D:HOH605 2.0 43.8 1.0 OE1 D:GLN11 2.0 49.6 1.0 O1A D:GDP501 2.3 54.4 1.0 CD D:GLN11 3.3 48.6 1.0 PA D:GDP501 3.7 43.1 1.0 CB D:GLN11 4.0 45.6 1.0 CG D:GLN11 4.2 45.9 1.0 NE2 D:GLN11 4.2 50.9 1.0 O2A D:GDP501 4.5 42.4 1.0 O3A D:GDP501 4.5 44.2 1.0 O1B D:GDP501 4.5 43.3 1.0 O D:HOH623 4.6 54.7 1.0 C5' D:GDP501 4.7 45.6 1.0 OD1 D:ASN101 4.7 54.0 1.0 O5' D:GDP501 4.7 44.6 1.0 C8 D:GDP501 4.9 45.1 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z87615031-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z87615031-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:70.0 occ:1.00 O3G F:ACP401 2.3 78.7 1.0 O1B F:ACP401 2.4 84.9 1.0 OE2 F:GLU331 2.4 73.2 1.0 OD1 F:ASN333 2.7 68.7 1.0 OE1 F:GLU331 3.1 76.0 1.0 CD F:GLU331 3.1 70.7 1.0 PB F:ACP401 3.6 86.8 1.0 NZ F:LYS74 3.8 84.3 1.0 CG F:ASN333 3.8 62.6 1.0 PG F:ACP401 3.9 94.6 1.0 O2B F:ACP401 4.0 91.2 1.0 C3B F:ACP401 4.4 86.4 1.0 ND2 F:ASN333 4.4 61.0 1.0 CG F:GLU331 4.6 61.3 1.0 O1G F:ACP401 4.7 88.3 1.0 O2G F:ACP401 4.8 72.4 1.0 O3A F:ACP401 4.9 87.3 1.0 CE F:LYS74 5.0 80.5 1.0 CB F:ASN333 5.0 55.4 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