Magnesium in PDB 5s5w: Tubulin-Z53860899-Complex

The structure of Tubulin-Z53860899-Complex, PDB code: 5s5w 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)	63.19 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.87, 158.35, 178.88, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Tubulin-Z53860899-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z53860899-Complex (pdb code 5s5w). 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-Z53860899-Complex, PDB code: 5s5w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:48.7 occ:1.00 O1G A:GTP501 1.9 45.6 1.0 O A:HOH623 2.1 50.2 1.0 O A:HOH640 2.1 50.3 1.0 O A:HOH627 2.2 49.3 1.0 O A:HOH622 2.2 50.5 1.0 O1B A:GTP501 2.5 46.3 1.0 PG A:GTP501 3.2 50.2 1.0 PB A:GTP501 3.5 46.6 1.0 OE1 A:GLU71 3.6 62.0 1.0 O2G A:GTP501 3.7 51.1 1.0 O3B A:GTP501 3.7 55.3 1.0 NZ B:LYS254 3.7 60.7 1.0 O3A A:GTP501 3.9 50.4 1.0 OD2 A:ASP98 4.0 56.4 1.0 CB A:ASP98 4.0 53.9 1.0 OD1 A:ASP69 4.1 59.4 1.0 CB A:GLN11 4.3 51.6 1.0 O3G A:GTP501 4.3 49.1 1.0 CG A:ASP98 4.4 55.6 1.0 OD2 A:ASP69 4.4 56.3 1.0 NE2 A:GLN11 4.5 56.1 1.0 N A:GLN11 4.6 51.9 1.0 CD A:GLU71 4.7 67.2 1.0 CG A:ASP69 4.7 57.7 1.0 O1A A:GTP501 4.8 49.6 1.0 CE B:LYS254 4.8 58.7 1.0 O2B A:GTP501 4.8 51.3 1.0 PA A:GTP501 4.9 50.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.2 occ:1.00 O B:HOH604 1.9 60.7 1.0 O B:HOH638 1.9 50.3 1.0 O C:HOH687 2.2 38.4 1.0 OE1 B:GLN11 2.2 53.2 1.0 O1A B:GDP501 2.2 47.0 1.0 O B:HOH644 2.3 48.1 1.0 CD B:GLN11 3.4 52.9 1.0 PA B:GDP501 3.6 48.5 1.0 O3A B:GDP501 4.0 51.8 1.0 CB B:GLN11 4.0 50.8 1.0 OD2 B:ASP179 4.1 48.9 1.0 OD1 B:ASN101 4.2 48.6 1.0 O C:HOH661 4.2 51.3 1.0 CG B:GLN11 4.2 49.5 1.0 NE2 B:GLN11 4.3 62.0 1.0 OE1 C:GLU254 4.4 52.4 1.0 O1B B:GDP501 4.4 44.1 1.0 C5' B:GDP501 4.5 52.1 1.0 O5' B:GDP501 4.5 46.5 1.0 O2A B:GDP501 4.6 44.2 1.0 PB B:GDP501 4.8 47.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.8 occ:1.00 O C:HOH642 2.0 44.4 1.0 O C:HOH679 2.0 49.6 1.0 O1G C:GTP501 2.1 46.4 1.0 O C:HOH640 2.1 50.6 1.0 O1B C:GTP501 2.1 45.1 1.0 O C:HOH627 2.3 47.3 1.0 PG C:GTP501 3.3 50.4 1.0 PB C:GTP501 3.3 45.9 1.0 O3B C:GTP501 3.7 51.6 1.0 O2G C:GTP501 3.7 48.6 1.0 OE2 C:GLU71 3.8 59.7 1.0 NZ D:LYS254 3.9 45.1 1.0 O3A C:GTP501 3.9 50.3 1.0 CG C:GLU71 3.9 56.1 1.0 OD1 C:ASP69 4.0 46.1 1.0 OD2 C:ASP69 4.1 48.4 1.0 OD2 C:ASP98 4.2 54.0 1.0 CB C:ASP98 4.3 48.1 1.0 CB C:GLN11 4.3 45.2 1.0 CD C:GLU71 4.4 56.7 1.0 N C:GLN11 4.5 44.8 1.0 CG C:ASP69 4.5 51.6 1.0 O3G C:GTP501 4.5 43.0 1.0 O2B C:GTP501 4.6 51.3 1.0 CG C:ASP98 4.6 49.7 1.0 O1A C:GTP501 4.7 42.9 1.0 PA C:GTP501 4.9 48.6 1.0 NE2 C:GLN11 4.9 60.3 1.0 OG1 C:THR145 5.0 42.2 1.0 CA C:GLN11 5.0 49.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.0 occ:1.00 OE1 D:GLN11 2.0 77.4 1.0 O D:HOH615 2.2 73.4 1.0 O1A D:GDP501 2.5 82.4 1.0 CD D:GLN11 3.2 77.0 1.0 PA D:GDP501 3.8 72.7 1.0 O2A D:GDP501 4.0 72.3 1.0 CB D:GLN11 4.1 73.5 1.0 NE2 D:GLN11 4.1 74.3 1.0 CG D:GLN11 4.2 71.9 1.0 OD1 D:ASN101 4.2 83.2 1.0 O1B D:GDP501 4.3 75.2 1.0 O D:HOH606 4.6 73.7 1.0 C5' D:GDP501 4.7 71.5 1.0 O5' D:GDP501 4.8 72.4 1.0 O3A D:GDP501 4.9 81.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z53860899-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z53860899-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:101.3 occ:1.00 O3G F:ACP401 2.0 106.7 1.0 OE2 F:GLU331 2.1 104.6 1.0 O1B F:ACP401 2.5 112.6 1.0 ND2 F:ASN333 2.6 101.7 1.0 CD F:GLU331 3.0 101.2 1.0 OE1 F:GLU331 3.2 105.2 1.0 PG F:ACP401 3.6 120.6 1.0 PB F:ACP401 3.7 113.8 1.0 CG F:ASN333 3.8 94.4 1.0 O2B F:ACP401 4.1 116.4 1.0 O1G F:ACP401 4.2 116.3 1.0 OD1 F:ASN333 4.3 95.2 1.0 C3B F:ACP401 4.3 112.6 1.0 CG F:GLU331 4.4 89.7 1.0 NZ F:LYS74 4.5 100.7 1.0 O2G F:ACP401 4.6 103.3 1.0 O1A F:ACP401 4.9 107.9 1.0 CB F:ASN333 4.9 84.6 1.0 O3A F:ACP401 5.0 111.0 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