Magnesium in PDB 5s55: Tubulin-Z106307058-Complex

The structure of Tubulin-Z106307058-Complex, PDB code: 5s55 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)	62.68 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.64, 158.15, 180.17, 90, 90, 90
R / Rfree (%)	20.6 / 23.6

The structure of Tubulin-Z106307058-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z106307058-Complex (pdb code 5s55). 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-Z106307058-Complex, PDB code: 5s55:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.0 occ:1.00 O A:HOH612 2.0 45.9 1.0 O1G A:GTP501 2.0 40.5 1.0 O A:HOH644 2.1 48.1 1.0 O A:HOH645 2.1 46.8 1.0 O1B A:GTP501 2.2 41.0 1.0 O A:HOH609 2.2 42.6 1.0 PG A:GTP501 3.2 47.6 1.0 PB A:GTP501 3.3 44.5 1.0 O3B A:GTP501 3.6 49.1 1.0 O2G A:GTP501 3.8 44.6 1.0 O3A A:GTP501 3.8 48.1 1.0 OE1 A:GLU71 3.8 62.8 1.0 NZ B:LYS254 4.0 56.8 1.0 CB A:GLN11 4.0 45.2 1.0 OD1 A:ASP69 4.0 50.0 1.0 OD2 A:ASP69 4.1 53.0 1.0 N A:GLN11 4.2 45.7 1.0 CB A:ASP98 4.3 50.3 1.0 O3G A:GTP501 4.4 41.3 1.0 OD2 A:ASP98 4.5 59.2 1.0 CG A:ASP69 4.5 54.3 1.0 OE1 A:GLN11 4.6 56.2 1.0 O1A A:GTP501 4.6 46.0 1.0 O2B A:GTP501 4.6 47.4 1.0 O B:HOH608 4.7 61.6 1.0 CA A:GLN11 4.7 44.9 1.0 PA A:GTP501 4.8 44.6 1.0 CG A:ASP98 4.8 50.0 1.0 CE B:LYS254 5.0 51.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.8 occ:1.00 O B:HOH636 1.9 43.5 1.0 O C:HOH648 2.1 48.2 1.0 OE1 B:GLN11 2.2 52.5 1.0 O1A B:GDP501 2.3 43.7 1.0 O B:HOH610 2.4 52.2 1.0 O B:HOH637 2.4 47.5 1.0 CD B:GLN11 3.4 51.2 1.0 PA B:GDP501 3.6 42.1 1.0 O3A B:GDP501 3.9 44.8 1.0 OD2 B:ASP179 3.9 47.6 1.0 CB B:GLN11 4.1 45.0 1.0 OD1 B:ASN101 4.1 48.2 1.0 NE2 B:GLN11 4.3 59.5 1.0 CG B:GLN11 4.3 47.1 1.0 O C:HOH690 4.4 55.2 1.0 O1B B:GDP501 4.4 41.3 1.0 OE1 C:GLU254 4.4 52.9 1.0 C5' B:GDP501 4.4 46.1 1.0 O5' B:GDP501 4.4 42.1 1.0 O2A B:GDP501 4.6 40.7 1.0 ND2 B:ASN101 4.7 43.8 1.0 PB B:GDP501 4.8 41.2 1.0 CG B:ASN101 4.9 49.5 1.0 CG B:ASP179 4.9 48.6 1.0 C8 B:GDP501 5.0 46.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.3 occ:1.00 O C:HOH651 1.9 44.1 1.0 O C:HOH666 2.0 40.8 1.0 O C:HOH613 2.1 44.3 1.0 O1B C:GTP501 2.1 37.5 1.0 O1G C:GTP501 2.2 36.2 1.0 O C:HOH668 2.2 42.7 1.0 PB C:GTP501 3.3 39.9 1.0 PG C:GTP501 3.3 42.7 1.0 O3B C:GTP501 3.7 43.3 1.0 O2G C:GTP501 3.7 41.1 1.0 O3A C:GTP501 3.8 42.2 1.0 OD1 C:ASP69 3.9 46.0 1.0 OE2 C:GLU71 4.0 51.9 1.0 OD2 C:ASP69 4.0 42.2 1.0 NZ D:LYS254 4.1 43.7 1.0 CB C:GLN11 4.1 39.7 1.0 CG C:GLU71 4.1 51.2 1.0 OD2 C:ASP98 4.2 47.2 1.0 N C:GLN11 4.3 38.7 1.0 CG C:ASP69 4.4 47.4 1.0 O2B C:GTP501 4.5 42.8 1.0 O C:HOH696 4.5 68.4 1.0 CB C:ASP98 4.5 41.7 1.0 CD C:GLU71 4.5 51.2 1.0 NE2 C:GLN11 4.5 53.5 1.0 O3G C:GTP501 4.6 36.6 1.0 CA C:GLN11 4.8 39.6 1.0 O1A C:GTP501 4.8 45.8 1.0 CG C:ASP98 4.8 43.5 1.0 PA C:GTP501 4.8 40.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.1 occ:1.00 O D:HOH603 1.9 65.1 1.0 O1A D:GDP501 2.1 81.6 1.0 OE1 D:GLN11 2.1 71.6 1.0 CD D:GLN11 3.3 70.2 1.0 PA D:GDP501 3.6 66.3 1.0 O2A D:GDP501 4.1 64.2 1.0 CB D:GLN11 4.1 65.4 1.0 O D:HOH610 4.1 71.7 1.0 CG D:GLN11 4.2 68.4 1.0 NE2 D:GLN11 4.3 72.5 1.0 C5' D:GDP501 4.4 69.9 1.0 O5' D:GDP501 4.5 67.1 1.0 O1B D:GDP501 4.6 62.7 1.0 O3A D:GDP501 4.6 69.2 1.0 OD1 D:ASN101 4.6 70.2 1.0 C8 D:GDP501 4.7 64.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z106307058-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z106307058-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:80.8 occ:1.00 O1B F:ACP401 2.0 99.4 1.0 O3G F:ACP401 2.3 93.5 1.0 OE2 F:GLU331 2.5 91.5 1.0 ND2 F:ASN333 2.8 85.5 1.0 OE1 F:GLU331 2.9 93.6 1.0 CD F:GLU331 3.1 89.3 1.0 PB F:ACP401 3.3 103.5 1.0 O2B F:ACP401 3.6 98.6 1.0 PG F:ACP401 3.7 113.8 1.0 NZ F:LYS74 3.7 102.7 1.0 CG F:ASN333 3.9 82.8 1.0 C3B F:ACP401 4.1 103.5 1.0 OD1 F:ASN333 4.2 83.8 1.0 O3A F:ACP401 4.6 104.2 1.0 CG F:GLU331 4.6 80.5 1.0 O2G F:ACP401 4.6 89.7 1.0 O1A F:ACP401 4.6 97.7 1.0 O1G F:ACP401 4.6 106.2 1.0 CE F:LYS74 4.7 96.2 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