Magnesium in PDB 5s67: Tubulin-Z1896597864-Complex

The structure of Tubulin-Z1896597864-Complex, PDB code: 5s67 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)	62.75 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.9, 158.96, 179.98, 90, 90, 90
R / Rfree (%)	21 / 23.8

The structure of Tubulin-Z1896597864-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1896597864-Complex (pdb code 5s67). 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-Z1896597864-Complex, PDB code: 5s67:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.7 occ:1.00 O A:HOH622 2.0 52.1 1.0 O1G A:GTP501 2.0 43.0 1.0 O A:HOH628 2.1 48.6 1.0 O1B A:GTP501 2.1 41.1 1.0 O A:HOH649 2.2 45.5 1.0 O A:HOH625 2.2 51.8 1.0 PG A:GTP501 3.2 46.4 1.0 PB A:GTP501 3.3 45.8 1.0 O3B A:GTP501 3.6 55.7 1.0 O2G A:GTP501 3.7 46.5 1.0 OE1 A:GLU71 3.8 65.0 1.0 O3A A:GTP501 3.9 49.0 1.0 NZ B:LYS254 3.9 54.7 1.0 OD1 A:ASP69 4.0 52.1 1.0 OD2 A:ASP69 4.2 52.7 1.0 CB A:GLN11 4.2 46.5 1.0 CB A:ASP98 4.3 53.4 1.0 OD2 A:ASP98 4.4 62.1 1.0 N A:GLN11 4.4 45.6 1.0 O3G A:GTP501 4.5 46.2 1.0 O A:HOH659 4.5 58.3 1.0 O2B A:GTP501 4.5 51.4 1.0 CG A:ASP69 4.5 54.5 1.0 O1A A:GTP501 4.6 44.9 1.0 CG A:ASP98 4.6 54.7 1.0 NE2 A:GLN11 4.7 57.3 1.0 PA A:GTP501 4.8 47.5 1.0 CA A:GLN11 4.9 47.2 1.0 CE B:LYS254 5.0 52.6 1.0 CD A:GLU71 5.0 70.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:38.0 occ:1.00 O B:HOH637 2.0 49.6 1.0 OE1 B:GLN11 2.1 49.4 1.0 O C:HOH638 2.1 49.1 1.0 O1A B:GDP501 2.3 45.6 1.0 O B:HOH648 2.4 49.8 1.0 O B:HOH606 2.4 50.2 1.0 CD B:GLN11 3.3 51.0 1.0 PA B:GDP501 3.6 43.8 1.0 O3A B:GDP501 3.9 43.1 1.0 OD2 B:ASP179 4.0 50.7 1.0 CB B:GLN11 4.0 43.8 1.0 CG B:GLN11 4.2 47.7 1.0 NE2 B:GLN11 4.3 55.9 1.0 O C:HOH648 4.4 51.2 1.0 C5' B:GDP501 4.4 45.9 1.0 OE1 C:GLU254 4.5 53.0 1.0 OD1 B:ASN101 4.5 47.7 1.0 O5' B:GDP501 4.5 44.9 1.0 O1B B:GDP501 4.5 37.5 1.0 O2A B:GDP501 4.6 42.3 1.0 PB B:GDP501 4.9 42.0 1.0 CG B:ASP179 4.9 51.5 1.0 C8 B:GDP501 4.9 49.9 1.0 ND2 B:ASN101 5.0 45.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.9 occ:1.00 O1G C:GTP501 2.0 37.9 1.0 O C:HOH671 2.0 42.4 1.0 O C:HOH724 2.1 42.2 1.0 O C:HOH659 2.1 40.5 1.0 O1B C:GTP501 2.1 38.3 1.0 O C:HOH669 2.2 43.0 1.0 PG C:GTP501 3.2 42.5 1.0 PB C:GTP501 3.3 39.6 1.0 O3B C:GTP501 3.6 46.7 1.0 O3A C:GTP501 3.7 41.3 1.0 O2G C:GTP501 3.7 40.5 1.0 NZ D:LYS254 3.9 46.6 1.0 OE2 C:GLU71 4.1 53.3 1.0 OD1 C:ASP69 4.1 44.5 1.0 CB C:GLN11 4.2 38.8 1.0 CG C:GLU71 4.2 49.3 1.0 OD2 C:ASP69 4.2 38.6 1.0 OD2 C:ASP98 4.3 51.8 1.0 N C:GLN11 4.4 37.4 1.0 O3G C:GTP501 4.4 40.7 1.0 CB C:ASP98 4.5 45.0 1.0 O2B C:GTP501 4.6 42.9 1.0 O1A C:GTP501 4.6 39.6 1.0 CG C:ASP69 4.6 42.7 1.0 CD C:GLU71 4.6 51.5 1.0 OE1 C:GLN11 4.7 53.0 1.0 PA C:GTP501 4.7 40.7 1.0 CG C:ASP98 4.8 49.9 1.0 CA C:GLN11 4.9 40.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.5 occ:1.00 O D:HOH607 1.9 63.3 1.0 OE1 D:GLN11 2.1 68.1 1.0 O1A D:GDP501 2.2 74.0 1.0 CD D:GLN11 3.3 72.6 1.0 PA D:GDP501 3.6 68.2 1.0 CB D:GLN11 4.0 66.9 1.0 CG D:GLN11 4.2 71.4 1.0 NE2 D:GLN11 4.3 70.9 1.0 O3A D:GDP501 4.3 64.0 1.0 C5' D:GDP501 4.4 69.3 1.0 O D:HOH625 4.4 73.1 1.0 O1B D:GDP501 4.4 60.6 1.0 O2A D:GDP501 4.5 67.8 1.0 O5' D:GDP501 4.5 66.6 1.0 OD1 D:ASN101 4.6 73.6 1.0 PB D:GDP501 4.9 60.6 1.0 C8 D:GDP501 5.0 67.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1896597864-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1896597864-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:82.3 occ:1.00 O3G F:ACP401 2.0 89.7 1.0 OE2 F:GLU331 2.2 88.4 1.0 O1B F:ACP401 2.4 96.5 1.0 OD1 F:ASN333 2.8 83.2 1.0 CD F:GLU331 3.1 85.2 1.0 OE1 F:GLU331 3.2 90.4 1.0 PB F:ACP401 3.5 97.0 1.0 PG F:ACP401 3.6 105.9 1.0 NZ F:LYS74 3.8 96.3 1.0 CG F:ASN333 3.9 78.0 1.0 O2B F:ACP401 3.9 102.7 1.0 C3B F:ACP401 4.2 95.6 1.0 ND2 F:ASN333 4.4 75.8 1.0 O2G F:ACP401 4.4 85.8 1.0 CG F:GLU331 4.5 77.3 1.0 O1G F:ACP401 4.5 100.0 1.0 O3A F:ACP401 4.9 99.0 1.0 O1A F:ACP401 5.0 90.7 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