Magnesium in PDB 5s5y: Tubulin-Z26781952-Complex

The structure of Tubulin-Z26781952-Complex, PDB code: 5s5y 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)	63.31 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.96, 158.75, 179.65, 90, 90, 90
R / Rfree (%)	20.2 / 23.1

The structure of Tubulin-Z26781952-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z26781952-Complex (pdb code 5s5y). 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-Z26781952-Complex, PDB code: 5s5y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.0 occ:1.00 O1G A:GTP501 2.0 44.2 1.0 O A:HOH633 2.0 47.0 1.0 O A:HOH624 2.1 49.5 1.0 O A:HOH622 2.1 55.6 1.0 O1B A:GTP501 2.2 44.1 1.0 O A:HOH641 2.2 50.3 1.0 PG A:GTP501 3.1 51.0 1.0 PB A:GTP501 3.3 47.8 1.0 O2G A:GTP501 3.6 49.7 1.0 O3B A:GTP501 3.6 54.3 1.0 OE1 A:GLU71 3.9 60.7 1.0 O3A A:GTP501 3.9 52.1 1.0 OD1 A:ASP69 3.9 52.3 1.0 NZ B:LYS254 3.9 60.4 1.0 OD2 A:ASP69 4.1 53.8 1.0 CB A:GLN11 4.2 49.9 1.0 CB A:ASP98 4.2 54.5 1.0 OD2 A:ASP98 4.2 65.0 1.0 N A:GLN11 4.4 51.0 1.0 O3G A:GTP501 4.4 49.1 1.0 CG A:ASP69 4.5 53.9 1.0 NE2 A:GLN11 4.6 59.0 1.0 O2B A:GTP501 4.6 53.3 1.0 CG A:ASP98 4.6 59.8 1.0 O1A A:GTP501 4.7 50.2 1.0 OG1 A:THR145 4.8 55.4 1.0 CA A:GLN11 4.9 53.7 1.0 PA A:GTP501 4.9 49.9 1.0 CE B:LYS254 4.9 59.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.6 occ:1.00 O B:HOH640 2.0 46.6 1.0 OE1 B:GLN11 2.1 50.4 1.0 O B:HOH654 2.1 51.1 1.0 O1A B:GDP501 2.2 43.2 1.0 O C:HOH743 2.3 47.8 1.0 O B:HOH614 2.3 53.3 1.0 O B:HOH651 2.6 46.0 1.0 CD B:GLN11 3.3 50.2 1.0 PA B:GDP501 3.5 41.7 1.0 O3A B:GDP501 3.8 44.4 1.0 CB B:GLN11 4.0 46.1 1.0 OD2 B:ASP179 4.0 50.6 1.0 CG B:GLN11 4.2 46.7 1.0 OD1 B:ASN101 4.2 46.3 1.0 O C:HOH747 4.2 47.3 1.0 NE2 B:GLN11 4.3 61.7 1.0 O1B B:GDP501 4.4 39.7 1.0 OE1 C:GLU254 4.4 54.2 1.0 C5' B:GDP501 4.4 46.1 1.0 O5' B:GDP501 4.5 47.7 1.0 O2A B:GDP501 4.6 43.5 1.0 PB B:GDP501 4.7 41.3 1.0 C8 B:GDP501 4.9 46.9 1.0 ND2 B:ASN101 5.0 45.1 1.0 CG B:ASN101 5.0 46.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:46.4 occ:1.00 O C:HOH731 2.0 44.3 1.0 O1G C:GTP602 2.0 41.5 1.0 O C:HOH810 2.1 45.4 1.0 O C:HOH752 2.1 44.4 1.0 O C:HOH737 2.1 43.9 1.0 O1B C:GTP602 2.1 42.4 1.0 PG C:GTP602 3.2 45.8 1.0 PB C:GTP602 3.2 40.8 1.0 O3B C:GTP602 3.5 50.1 1.0 O3A C:GTP602 3.6 45.9 1.0 O2G C:GTP602 3.7 44.1 1.0 NZ D:LYS254 3.8 48.5 1.0 OD1 C:ASP69 4.0 47.1 1.0 CB C:GLN11 4.1 44.2 1.0 OE2 C:GLU71 4.1 56.4 1.0 OD2 C:ASP69 4.2 45.4 1.0 CG C:GLU71 4.2 51.9 1.0 OD2 C:ASP98 4.3 54.6 1.0 N C:GLN11 4.3 38.7 1.0 O3G C:GTP602 4.4 42.6 1.0 O1A C:GTP602 4.5 46.5 1.0 O2B C:GTP602 4.5 45.7 1.0 CB C:ASP98 4.5 46.9 1.0 CG C:ASP69 4.6 46.2 1.0 PA C:GTP602 4.7 41.2 1.0 OE1 C:GLN11 4.7 55.6 1.0 CD C:GLU71 4.7 53.7 1.0 CG C:ASP98 4.7 49.4 1.0 CA C:GLN11 4.8 45.7 1.0 O C:HOH851 4.9 70.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:69.0 occ:1.00 OE1 D:GLN11 2.1 78.4 1.0 O D:HOH603 2.1 71.1 1.0 O1A D:GDP501 2.2 86.1 1.0 CD D:GLN11 3.3 79.2 1.0 PA D:GDP501 3.6 69.4 1.0 CB D:GLN11 3.7 69.4 1.0 O1B D:GDP501 4.0 66.8 1.0 O2A D:GDP501 4.0 66.0 1.0 CG D:GLN11 4.1 72.5 1.0 NE2 D:GLN11 4.3 75.8 1.0 O3A D:GDP501 4.4 71.6 1.0 OD1 D:ASN101 4.6 77.1 1.0 PB D:GDP501 4.6 67.8 1.0 O D:HOH622 4.7 76.9 1.0 O5' D:GDP501 4.7 71.6 1.0 C5' D:GDP501 4.8 71.2 1.0 O3B D:GDP501 4.9 74.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z26781952-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z26781952-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:97.3 occ:1.00 O3G F:ACP401 2.2 105.1 1.0 OE2 F:GLU331 2.4 104.1 1.0 O1B F:ACP401 2.6 110.6 1.0 OD1 F:ASN333 2.6 93.6 1.0 CD F:GLU331 3.2 103.2 1.0 OE1 F:GLU331 3.3 108.5 1.0 PB F:ACP401 3.7 113.8 1.0 PG F:ACP401 3.8 117.8 1.0 CG F:ASN333 3.8 87.1 1.0 O2B F:ACP401 4.0 118.4 1.0 NZ F:LYS74 4.1 108.1 1.0 C3B F:ACP401 4.4 114.0 1.0 ND2 F:ASN333 4.4 85.2 1.0 O1G F:ACP401 4.5 111.9 1.0 CG F:GLU331 4.6 93.5 1.0 O2G F:ACP401 4.7 101.1 1.0 CB F:ASN333 4.9 81.9 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