Magnesium in PDB 5s5j: Tubulin-Z1148747945-Complex

The structure of Tubulin-Z1148747945-Complex, PDB code: 5s5j 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)	62.71 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.77, 159.73, 179.63, 90, 90, 90
R / Rfree (%)	20.5 / 23.8

The structure of Tubulin-Z1148747945-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1148747945-Complex (pdb code 5s5j). 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-Z1148747945-Complex, PDB code: 5s5j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.5 occ:1.00 O1G A:GTP501 2.0 44.4 1.0 O A:HOH635 2.1 48.7 1.0 O A:HOH605 2.2 50.3 1.0 O1B A:GTP501 2.2 40.6 1.0 O A:HOH606 2.2 45.9 1.0 O A:HOH616 2.3 50.2 1.0 PG A:GTP501 3.2 50.7 1.0 PB A:GTP501 3.3 44.4 1.0 O3B A:GTP501 3.6 54.7 1.0 O2G A:GTP501 3.7 43.9 1.0 OE1 A:GLU71 3.7 57.3 1.0 O3A A:GTP501 3.8 49.3 1.0 NZ B:LYS254 3.9 62.0 1.0 OD1 A:ASP69 4.0 52.1 1.0 OD2 A:ASP69 4.1 56.6 1.0 CB A:GLN11 4.2 46.3 1.0 CB A:ASP98 4.3 52.7 1.0 N A:GLN11 4.4 50.3 1.0 O3G A:GTP501 4.4 45.0 1.0 CG A:ASP69 4.5 54.9 1.0 OD2 A:ASP98 4.5 63.4 1.0 NE2 A:GLN11 4.5 60.0 1.0 O2B A:GTP501 4.6 49.0 1.0 O1A A:GTP501 4.6 49.0 1.0 CG A:ASP98 4.8 55.7 1.0 PA A:GTP501 4.8 42.9 1.0 CA A:GLN11 4.9 50.6 1.0 CD A:GLU71 4.9 67.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.2 occ:1.00 OE1 B:GLN11 2.1 52.6 1.0 O B:HOH634 2.1 43.9 1.0 O C:HOH651 2.2 47.0 1.0 O1A B:GDP501 2.3 44.6 1.0 O B:HOH607 2.5 48.7 1.0 O B:HOH648 2.6 42.6 1.0 CD B:GLN11 3.3 50.8 1.0 PA B:GDP501 3.7 39.7 1.0 OD2 B:ASP179 3.9 47.7 1.0 O3A B:GDP501 4.0 42.0 1.0 CB B:GLN11 4.1 43.7 1.0 CG B:GLN11 4.2 46.1 1.0 NE2 B:GLN11 4.2 56.5 1.0 OD1 B:ASN101 4.3 46.3 1.0 O C:HOH721 4.3 47.5 1.0 OE1 C:GLU254 4.4 50.0 1.0 C5' B:GDP501 4.4 43.6 1.0 O5' B:GDP501 4.5 42.7 1.0 O1B B:GDP501 4.6 38.8 1.0 O2A B:GDP501 4.7 39.6 1.0 CG B:ASP179 4.9 45.8 1.0 C8 B:GDP501 4.9 46.2 1.0 ND2 B:ASN101 4.9 41.4 1.0 PB B:GDP501 5.0 40.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.7 occ:1.00 O1G C:GTP501 2.0 38.5 1.0 O C:HOH686 2.0 41.2 1.0 O C:HOH640 2.0 38.2 1.0 O1B C:GTP501 2.0 37.8 1.0 O C:HOH641 2.1 40.6 1.0 O C:HOH654 2.3 43.7 1.0 PB C:GTP501 3.1 37.5 1.0 PG C:GTP501 3.1 42.3 1.0 O3B C:GTP501 3.5 45.1 1.0 O3A C:GTP501 3.6 43.1 1.0 O2G C:GTP501 3.7 41.8 1.0 NZ D:LYS254 4.0 50.5 1.0 OD1 C:ASP69 4.0 44.8 1.0 OE2 C:GLU71 4.1 50.3 1.0 CB C:GLN11 4.1 39.3 1.0 OD2 C:ASP69 4.2 39.9 1.0 N C:GLN11 4.3 37.5 1.0 OD2 C:ASP98 4.3 46.4 1.0 O3G C:GTP501 4.4 40.2 1.0 CG C:GLU71 4.4 50.4 1.0 O1A C:GTP501 4.4 42.5 1.0 O2B C:GTP501 4.4 43.2 1.0 CG C:ASP69 4.5 43.2 1.0 PA C:GTP501 4.6 40.1 1.0 OE1 C:GLN11 4.6 54.5 1.0 CB C:ASP98 4.6 45.2 1.0 CD C:GLU71 4.7 50.9 1.0 CA C:GLN11 4.8 40.8 1.0 CG C:ASP98 4.8 46.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:73.7 occ:1.00 OE1 D:GLN11 1.9 77.5 1.0 O D:HOH602 2.0 70.2 1.0 O1A D:GDP501 2.5 82.4 1.0 CD D:GLN11 3.1 76.2 1.0 O D:HOH624 3.9 74.4 1.0 PA D:GDP501 4.0 71.9 1.0 NE2 D:GLN11 4.0 78.6 1.0 CB D:GLN11 4.1 70.4 1.0 CG D:GLN11 4.1 75.3 1.0 O2A D:GDP501 4.5 66.6 1.0 C5' D:GDP501 4.6 71.4 1.0 C8 D:GDP501 4.9 66.8 1.0 O5' D:GDP501 4.9 69.0 1.0 O1B D:GDP501 4.9 64.1 1.0 OD1 D:ASN101 5.0 73.0 1.0 O3A D:GDP501 5.0 71.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1148747945-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1148747945-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:94.5 occ:1.00 O3G F:ACP401 2.1 102.5 1.0 O1B F:ACP401 2.3 107.6 1.0 OE2 F:GLU331 2.3 98.0 1.0 OD1 F:ASN333 2.8 92.4 1.0 CD F:GLU331 3.2 96.2 1.0 OE1 F:GLU331 3.4 99.0 1.0 PB F:ACP401 3.5 111.2 1.0 PG F:ACP401 3.6 118.8 1.0 CG F:ASN333 3.9 89.3 1.0 NZ F:LYS74 3.9 104.4 1.0 O2B F:ACP401 3.9 115.7 1.0 O1G F:ACP401 4.2 111.5 1.0 C3B F:ACP401 4.2 111.1 1.0 ND2 F:ASN333 4.4 84.4 1.0 CG F:GLU331 4.6 85.0 1.0 O2G F:ACP401 4.7 99.0 1.0 O1A F:ACP401 4.7 103.7 1.0 O3A F:ACP401 4.8 109.5 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