Magnesium in PDB 5s4t: Tubulin-Z328695024-Complex

The structure of Tubulin-Z328695024-Complex, PDB code: 5s4t 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)	62.53 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.77, 158.42, 179.05, 90, 90, 90
R / Rfree (%)	20.6 / 24.6

The structure of Tubulin-Z328695024-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z328695024-Complex (pdb code 5s4t). 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-Z328695024-Complex, PDB code: 5s4t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:53.2 occ:1.00 O A:HOH618 2.0 53.8 1.0 O A:HOH609 2.0 60.7 1.0 O1G A:GTP501 2.1 46.0 1.0 O A:HOH626 2.2 49.9 1.0 O A:HOH639 2.2 53.6 1.0 O1B A:GTP501 2.2 46.5 1.0 PG A:GTP501 3.2 54.3 1.0 PB A:GTP501 3.3 48.9 1.0 O3B A:GTP501 3.6 56.5 1.0 O2G A:GTP501 3.7 49.7 1.0 O3A A:GTP501 3.7 53.9 1.0 OE1 A:GLU71 3.8 70.6 1.0 CB A:GLN11 4.0 51.5 1.0 OD1 A:ASP69 4.1 58.9 1.0 NZ B:LYS254 4.1 62.6 1.0 OD2 A:ASP69 4.1 57.5 1.0 N A:GLN11 4.3 49.9 1.0 NE2 A:GLN11 4.3 62.2 1.0 OD2 A:ASP98 4.4 67.6 1.0 CB A:ASP98 4.4 55.5 1.0 O3G A:GTP501 4.5 50.0 1.0 CG A:ASP69 4.5 59.5 1.0 O1A A:GTP501 4.6 54.1 1.0 O2B A:GTP501 4.6 53.5 1.0 CA A:GLN11 4.7 53.3 1.0 PA A:GTP501 4.7 56.1 1.0 CG A:ASP98 4.8 59.8 1.0 O B:HOH635 5.0 65.8 1.0 CD A:GLU71 5.0 69.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.3 occ:1.00 O B:HOH620 2.0 54.7 1.0 O1A B:GDP501 2.2 47.2 1.0 O C:HOH664 2.3 49.6 1.0 O B:HOH664 2.3 61.0 1.0 OE1 B:GLN11 2.3 54.7 1.0 O B:HOH638 2.4 48.5 1.0 O B:HOH604 2.9 60.2 1.0 CD B:GLN11 3.5 51.4 1.0 PA B:GDP501 3.5 48.0 1.0 O3A B:GDP501 3.8 45.9 1.0 OD2 B:ASP179 3.9 56.7 1.0 CB B:GLN11 4.1 47.9 1.0 OD1 B:ASN101 4.1 50.7 1.0 CG B:GLN11 4.3 50.7 1.0 O1B B:GDP501 4.3 46.4 1.0 O C:HOH660 4.4 61.2 1.0 C5' B:GDP501 4.4 50.6 1.0 O5' B:GDP501 4.4 49.4 1.0 OE1 C:GLU254 4.5 63.8 1.0 NE2 B:GLN11 4.5 60.1 1.0 O2A B:GDP501 4.6 45.7 1.0 PB B:GDP501 4.7 48.5 1.0 ND2 B:ASN101 4.9 53.4 1.0 CG B:ASP179 4.9 55.5 1.0 C8 B:GDP501 5.0 53.0 1.0 CG B:ASN101 5.0 53.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:51.6 occ:1.00 O C:HOH629 2.0 48.2 1.0 O1G C:GTP501 2.1 44.3 1.0 O C:HOH630 2.1 46.3 1.0 O C:HOH650 2.1 48.8 1.0 O C:HOH704 2.1 47.2 1.0 O1B C:GTP501 2.1 43.5 1.0 PG C:GTP501 3.2 51.1 1.0 PB C:GTP501 3.2 42.3 1.0 O3B C:GTP501 3.6 53.0 1.0 O2G C:GTP501 3.6 47.9 1.0 O3A C:GTP501 3.7 49.8 1.0 NZ D:LYS254 3.9 54.4 1.0 OE2 C:GLU71 4.0 62.2 1.0 OD1 C:ASP69 4.0 51.5 1.0 OD2 C:ASP69 4.1 45.8 1.0 OD2 C:ASP98 4.2 58.0 1.0 CG C:GLU71 4.2 55.3 1.0 CB C:GLN11 4.2 46.3 1.0 N C:GLN11 4.3 41.2 1.0 O3G C:GTP501 4.5 44.7 1.0 O2B C:GTP501 4.5 51.0 1.0 CB C:ASP98 4.5 49.3 1.0 CG C:ASP69 4.5 46.4 1.0 CD C:GLU71 4.6 57.9 1.0 O1A C:GTP501 4.6 48.9 1.0 OE1 C:GLN11 4.7 64.0 1.0 PA C:GTP501 4.7 40.6 1.0 CG C:ASP98 4.7 51.3 1.0 O C:HOH696 4.8 65.5 1.0 CA C:GLN11 4.9 44.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.4 occ:1.00 OE1 D:GLN11 1.9 75.3 1.0 O D:HOH602 2.1 70.6 1.0 O1A D:GDP501 2.5 90.4 1.0 CD D:GLN11 3.1 77.9 1.0 CB D:GLN11 3.5 73.4 1.0 PA D:GDP501 3.7 75.3 1.0 O1B D:GDP501 3.8 71.2 1.0 CG D:GLN11 3.8 74.5 1.0 O2A D:GDP501 3.9 72.7 1.0 NE2 D:GLN11 4.1 77.7 1.0 PB D:GDP501 4.6 74.3 1.0 O3A D:GDP501 4.6 82.8 1.0 O3B D:GDP501 4.6 81.6 1.0 OD1 D:ASN101 4.7 78.9 1.0 CA D:GLN11 4.9 74.8 1.0 O5' D:GDP501 5.0 79.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z328695024-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z328695024-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:96.2 occ:1.00 OE2 F:GLU331 2.1 105.0 1.0 O3G F:ACP401 2.2 110.1 1.0 O1B F:ACP401 2.4 113.3 1.0 OD1 F:ASN333 2.7 99.0 1.0 CD F:GLU331 2.9 103.3 1.0 OE1 F:GLU331 3.0 109.6 1.0 PB F:ACP401 3.6 116.1 1.0 NZ F:LYS74 3.6 109.8 1.0 PG F:ACP401 3.7 125.8 1.0 CG F:ASN333 3.8 92.5 1.0 O2B F:ACP401 3.9 120.0 1.0 C3B F:ACP401 4.3 118.5 1.0 O1G F:ACP401 4.4 116.1 1.0 ND2 F:ASN333 4.4 93.3 1.0 CG F:GLU331 4.4 90.5 1.0 O F:HOH514 4.5 82.2 1.0 O2G F:ACP401 4.7 110.8 1.0 O1A F:ACP401 4.8 112.9 1.0 O3A F:ACP401 4.9 118.5 1.0 CE F:LYS74 4.9 112.1 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