Magnesium in PDB 5s61: Tubulin-Z57472297-Complex

The structure of Tubulin-Z57472297-Complex, PDB code: 5s61 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)	62.59 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.31, 178.35, 90, 90, 90
R / Rfree (%)	21.4 / 23.9

The structure of Tubulin-Z57472297-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z57472297-Complex (pdb code 5s61). 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-Z57472297-Complex, PDB code: 5s61:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.9 occ:1.00 O1G A:GTP501 2.0 34.3 1.0 O A:HOH646 2.1 36.4 1.0 O A:HOH645 2.1 35.6 1.0 O1B A:GTP501 2.1 33.5 1.0 O A:HOH632 2.2 38.2 1.0 O A:HOH618 2.2 37.4 1.0 PG A:GTP501 3.1 36.2 1.0 PB A:GTP501 3.2 34.9 1.0 O3B A:GTP501 3.5 38.3 1.0 O2G A:GTP501 3.7 36.6 1.0 O3A A:GTP501 3.7 36.5 1.0 OE1 A:GLU71 3.8 51.2 1.0 NZ B:LYS254 4.0 45.2 1.0 OD1 A:ASP69 4.1 39.5 1.0 CB A:GLN11 4.2 36.0 1.0 OD2 A:ASP98 4.3 45.4 1.0 OD2 A:ASP69 4.3 39.6 1.0 CB A:ASP98 4.3 40.7 1.0 N A:GLN11 4.4 34.6 1.0 O3G A:GTP501 4.4 34.5 1.0 O2B A:GTP501 4.5 36.1 1.0 O1A A:GTP501 4.5 35.7 1.0 CG A:ASP69 4.6 41.0 1.0 CG A:ASP98 4.7 43.2 1.0 PA A:GTP501 4.7 36.5 1.0 O B:HOH642 4.8 50.7 1.0 NE2 A:GLN11 4.9 42.4 1.0 CA A:GLN11 4.9 37.4 1.0 CE B:LYS254 5.0 43.5 1.0 OG1 A:THR145 5.0 37.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:26.7 occ:1.00 OE1 B:GLN11 2.2 38.6 1.0 O B:HOH604 2.2 35.8 1.0 O1A B:GDP501 2.3 32.9 1.0 O B:HOH609 2.3 41.5 1.0 O C:HOH692 2.4 40.6 1.0 O B:HOH652 2.4 32.8 1.0 CD B:GLN11 3.4 41.5 1.0 PA B:GDP501 3.6 32.6 1.0 OD2 B:ASP179 3.6 40.9 1.0 O3A B:GDP501 3.9 33.3 1.0 CB B:GLN11 4.0 35.5 1.0 CG B:GLN11 4.2 40.0 1.0 O C:HOH625 4.4 40.2 1.0 NE2 B:GLN11 4.4 45.3 1.0 C5' B:GDP501 4.4 32.6 1.0 O5' B:GDP501 4.4 34.9 1.0 OD1 B:ASN101 4.5 35.4 1.0 OE1 C:GLU254 4.5 41.1 1.0 O1B B:GDP501 4.5 33.1 1.0 O B:HOH677 4.7 56.7 1.0 O2A B:GDP501 4.7 33.1 1.0 CG B:ASP179 4.7 41.6 1.0 C8 B:GDP501 4.8 37.1 1.0 PB B:GDP501 4.8 34.6 1.0 O B:HOH667 4.9 46.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.0 occ:1.00 O C:HOH642 2.0 32.2 1.0 O1G C:GTP501 2.1 31.2 1.0 O1B C:GTP501 2.1 29.6 1.0 O C:HOH639 2.1 33.5 1.0 O C:HOH746 2.1 30.0 1.0 O C:HOH662 2.2 34.4 1.0 PB C:GTP501 3.2 31.5 1.0 PG C:GTP501 3.2 33.6 1.0 O3B C:GTP501 3.6 34.6 1.0 O2G C:GTP501 3.7 32.9 1.0 O3A C:GTP501 3.7 31.5 1.0 NZ D:LYS254 3.9 33.3 1.0 OD1 C:ASP69 4.0 33.6 1.0 OE2 C:GLU71 4.1 40.1 1.0 CB C:GLN11 4.1 28.7 1.0 OD2 C:ASP69 4.2 33.8 1.0 CG C:GLU71 4.3 40.3 1.0 OD2 C:ASP98 4.4 38.4 1.0 N C:GLN11 4.4 28.8 1.0 O3G C:GTP501 4.5 32.2 1.0 O2B C:GTP501 4.5 31.5 1.0 CB C:ASP98 4.5 35.9 1.0 O1A C:GTP501 4.5 31.4 1.0 CG C:ASP69 4.5 32.0 1.0 CD C:GLU71 4.7 39.5 1.0 PA C:GTP501 4.7 33.5 1.0 CG C:ASP98 4.8 38.0 1.0 OE1 C:GLN11 4.8 39.7 1.0 CA C:GLN11 4.9 30.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.8 occ:1.00 O D:HOH610 1.8 61.0 1.0 OE1 D:GLN11 2.0 53.5 1.0 O1A D:GDP501 2.2 55.3 1.0 CD D:GLN11 3.2 57.0 1.0 PA D:GDP501 3.6 53.0 1.0 CB D:GLN11 3.9 49.8 1.0 CG D:GLN11 4.0 52.5 1.0 O3A D:GDP501 4.2 53.7 1.0 NE2 D:GLN11 4.2 61.5 1.0 O D:HOH632 4.3 65.5 1.0 C5' D:GDP501 4.4 54.0 1.0 O1B D:GDP501 4.5 47.6 1.0 O5' D:GDP501 4.5 52.0 1.0 O2A D:GDP501 4.6 49.0 1.0 OD1 D:ASN101 4.7 62.2 1.0 C8 D:GDP501 4.9 50.8 1.0 PB D:GDP501 4.9 52.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z57472297-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z57472297-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:77.6 occ:1.00 O3G F:ACP401 2.2 82.2 1.0 OE2 F:GLU331 2.4 81.8 1.0 O1B F:ACP401 2.6 88.0 1.0 OD1 F:ASN333 2.8 72.8 1.0 CD F:GLU331 3.1 77.3 1.0 OE1 F:GLU331 3.1 83.3 1.0 CG F:ASN333 3.8 69.4 1.0 PG F:ACP401 3.8 95.2 1.0 PB F:ACP401 3.8 92.4 1.0 NZ F:LYS74 4.1 94.1 1.0 O2B F:ACP401 4.2 98.7 1.0 ND2 F:ASN333 4.3 68.3 1.0 C3B F:ACP401 4.5 92.5 1.0 CG F:GLU331 4.5 69.9 1.0 O2G F:ACP401 4.6 82.0 1.0 O1G F:ACP401 4.6 90.3 1.0 O F:HOH513 4.8 60.2 1.0 CB F:ASN333 4.9 60.1 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