Magnesium in PDB 5s66: Tubulin-Z2856434929-Complex

The structure of Tubulin-Z2856434929-Complex, PDB code: 5s66 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)	68.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.69, 157.88, 178.85, 90, 90, 90
R / Rfree (%)	21.4 / 24.4

The binding sites of Magnesium atom in the Tubulin-Z2856434929-Complex (pdb code 5s66). 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-Z2856434929-Complex, PDB code: 5s66:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434929-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434929-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.1 occ:1.00 O A:HOH625 2.0 46.2 1.0 O A:HOH626 2.0 46.1 1.0 O1B A:GTP501 2.0 43.9 1.0 O2G A:GTP501 2.1 41.1 1.0 O A:HOH638 2.1 44.3 1.0 O A:HOH628 2.1 48.4 1.0 PB A:GTP501 3.1 43.6 1.0 PG A:GTP501 3.2 41.9 1.0 O3B A:GTP501 3.5 48.2 1.0 O3A A:GTP501 3.6 46.1 1.0 O3G A:GTP501 3.6 46.2 1.0 NZ B:LYS254 3.8 56.7 1.0 CB A:GLN11 4.0 46.3 1.0 OE2 A:GLU71 4.0 59.8 1.0 OD1 A:ASP69 4.1 51.6 1.0 OD2 A:ASP69 4.2 52.8 1.0 OD2 A:ASP98 4.3 55.5 1.0 N A:GLN11 4.3 45.5 1.0 O2A A:GTP501 4.4 44.6 1.0 O2B A:GTP501 4.4 45.1 1.0 CB A:ASP98 4.5 52.1 1.0 O1G A:GTP501 4.5 45.5 1.0 OE1 A:GLN11 4.6 52.7 1.0 PA A:GTP501 4.6 43.3 1.0 CG A:ASP69 4.6 53.8 1.0 CA A:GLN11 4.7 48.2 1.0 CG A:ASP98 4.8 54.4 1.0 CE B:LYS254 4.8 54.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434929-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434929-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:38.8 occ:1.00 O B:HOH620 2.1 49.7 1.0 O B:HOH612 2.1 57.2 1.0 OE1 B:GLN11 2.2 48.5 1.0 O1A B:GDP501 2.3 44.0 1.0 O C:HOH658 2.3 44.6 1.0 O B:HOH634 2.4 47.5 1.0 CD B:GLN11 3.4 48.5 1.0 PA B:GDP501 3.6 45.9 1.0 O3A B:GDP501 3.9 42.8 1.0 OD2 B:ASP179 4.1 52.4 1.0 CB B:GLN11 4.1 42.1 1.0 ND2 B:ASN101 4.2 44.2 1.0 CG B:GLN11 4.3 48.5 1.0 NE2 B:GLN11 4.3 56.2 1.0 OE1 C:GLU254 4.4 53.2 1.0 C5' B:GDP501 4.5 46.7 1.0 O1B B:GDP501 4.5 40.0 1.0 O5' B:GDP501 4.5 41.6 1.0 O2A B:GDP501 4.7 41.8 1.0 PB B:GDP501 4.8 38.6 1.0 OD1 B:ASN101 4.9 52.9 1.0 CG B:ASP179 5.0 48.9 1.0 CG B:ASN101 5.0 47.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434929-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434929-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.0 occ:1.00 O C:HOH631 1.9 39.6 1.0 O C:HOH623 2.0 41.4 1.0 O1G C:GTP501 2.1 40.3 1.0 O C:HOH704 2.1 40.8 1.0 O C:HOH645 2.1 42.3 1.0 O2B C:GTP501 2.2 38.4 1.0 PG C:GTP501 3.2 45.3 1.0 PB C:GTP501 3.3 42.2 1.0 O3G C:GTP501 3.6 42.9 1.0 O3B C:GTP501 3.7 42.4 1.0 O3A C:GTP501 3.8 44.0 1.0 NZ D:LYS254 3.9 46.0 1.0 OE1 C:GLU71 4.1 51.2 1.0 OD2 C:ASP69 4.1 40.6 1.0 OD1 C:ASP69 4.1 44.4 1.0 CB C:GLN11 4.2 40.1 1.0 CG C:GLU71 4.2 47.8 1.0 OD2 C:ASP98 4.2 48.2 1.0 N C:GLN11 4.4 38.0 1.0 CB C:ASP98 4.5 44.8 1.0 CG C:ASP69 4.5 42.3 1.0 O2G C:GTP501 4.5 39.5 1.0 O1B C:GTP501 4.6 41.0 1.0 NE2 C:GLN11 4.6 48.5 1.0 CD C:GLU71 4.6 48.5 1.0 O1A C:GTP501 4.7 42.1 1.0 CG C:ASP98 4.7 44.9 1.0 PA C:GTP501 4.8 39.0 1.0 CA C:GLN11 4.9 39.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434929-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434929-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:64.7 occ:1.00 O1A D:GDP501 2.0 74.9 1.0 O D:HOH636 2.0 65.9 1.0 OE1 D:GLN11 2.1 68.2 1.0 CD D:GLN11 3.3 70.2 1.0 PA D:GDP501 3.5 62.7 1.0 CB D:GLN11 4.0 64.4 1.0 CG D:GLN11 4.1 66.0 1.0 C5' D:GDP501 4.2 67.5 1.0 O2A D:GDP501 4.3 65.5 1.0 NE2 D:GLN11 4.3 68.3 1.0 O D:HOH632 4.3 64.9 1.0 O5' D:GDP501 4.4 66.8 1.0 O1B D:GDP501 4.4 60.6 1.0 O3A D:GDP501 4.4 67.4 1.0 OD1 D:ASN101 4.5 75.9 1.0 C8 D:GDP501 4.8 63.4 1.0 PB D:GDP501 4.9 65.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434929-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434929-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:89.2 occ:1.00 O3G F:ACP401 2.4 90.7 1.0 OE1 F:GLU331 2.5 84.4 1.0 ND2 F:ASN333 2.7 84.6 1.0 O1B F:ACP401 2.7 95.0 1.0 OE2 F:GLU331 3.0 90.0 1.0 CD F:GLU331 3.1 84.3 1.0 NZ F:LYS74 3.1 99.3 1.0 PG F:ACP401 3.8 104.7 1.0 CG F:ASN333 3.9 81.2 1.0 PB F:ACP401 3.9 96.3 1.0 CE F:LYS74 4.2 97.0 1.0 O1G F:ACP401 4.2 97.8 1.0 CG A:GLU450 4.2 85.9 1.0 O2B F:ACP401 4.4 102.1 1.0 OD1 F:ASN333 4.5 82.6 1.0 C3B F:ACP401 4.5 96.8 1.0 CG F:GLU331 4.6 77.5 1.0 CD A:GLU450 4.7 85.0 1.0 CB A:GLU450 4.9 83.6 1.0 OE1 A:GLU450 4.9 85.2 1.0 O2G F:ACP401 5.0 94.0 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