Magnesium in PDB 5s5x: Tubulin-Z45705015-Complex

The structure of Tubulin-Z45705015-Complex, PDB code: 5s5x 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)	63.41 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.96, 159.13, 178.6, 90, 90, 90
R / Rfree (%)	20.7 / 24.3

The structure of Tubulin-Z45705015-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z45705015-Complex (pdb code 5s5x). 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-Z45705015-Complex, PDB code: 5s5x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.6 occ:1.00 O1G A:GTP501 2.0 47.6 1.0 O A:HOH606 2.1 56.2 1.0 O A:HOH630 2.1 45.5 1.0 O A:HOH648 2.2 49.4 1.0 O A:HOH605 2.2 47.4 1.0 O1B A:GTP501 2.3 45.2 1.0 PG A:GTP501 3.2 49.5 1.0 PB A:GTP501 3.3 46.2 1.0 OE1 A:GLU71 3.5 70.6 1.0 O3B A:GTP501 3.6 54.6 1.0 O2G A:GTP501 3.7 49.7 1.0 O3A A:GTP501 3.7 51.2 1.0 NZ B:LYS254 3.8 65.5 1.0 CB A:GLN11 4.1 46.5 1.0 OD1 A:ASP69 4.1 56.4 1.0 OD2 A:ASP69 4.2 53.1 1.0 OD2 A:ASP98 4.2 58.1 1.0 CB A:ASP98 4.3 55.4 1.0 N A:GLN11 4.4 46.6 1.0 O3G A:GTP501 4.4 47.8 1.0 O1A A:GTP501 4.5 49.0 1.0 NE2 A:GLN11 4.5 57.5 1.0 CG A:ASP69 4.6 54.3 1.0 CG A:ASP98 4.6 56.9 1.0 O2B A:GTP501 4.7 47.7 1.0 PA A:GTP501 4.7 50.8 1.0 CD A:GLU71 4.8 72.9 1.0 CA A:GLN11 4.8 49.5 1.0 O B:HOH624 4.9 59.5 1.0 CE B:LYS254 4.9 60.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.5 occ:1.00 O B:HOH604 1.7 58.4 1.0 O B:HOH640 2.0 56.1 1.0 O1A B:GDP501 2.2 44.1 1.0 O B:HOH654 2.2 50.9 1.0 O C:HOH642 2.3 47.1 1.0 OE1 B:GLN11 2.5 52.9 1.0 PA B:GDP501 3.5 45.3 1.0 CD B:GLN11 3.6 49.5 1.0 O3A B:GDP501 3.8 49.4 1.0 CB B:GLN11 4.1 44.9 1.0 OD1 B:ASN101 4.1 48.8 1.0 OD2 B:ASP179 4.2 55.4 1.0 O1B B:GDP501 4.2 43.8 1.0 CG B:GLN11 4.4 46.4 1.0 C5' B:GDP501 4.4 53.1 1.0 O5' B:GDP501 4.4 50.0 1.0 OE1 C:GLU254 4.4 59.9 1.0 O C:HOH616 4.5 52.6 1.0 O2A B:GDP501 4.5 45.5 1.0 PB B:GDP501 4.6 44.2 1.0 ND2 B:ASN101 4.6 51.9 1.0 O C:HOH727 4.6 69.5 1.0 NE2 B:GLN11 4.6 57.7 1.0 CG B:ASN101 4.8 50.9 1.0 O B:HOH638 5.0 49.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:49.6 occ:1.00 O C:HOH659 2.0 44.3 1.0 O1G C:GTP501 2.0 42.7 1.0 O C:HOH636 2.0 42.1 1.0 O C:HOH687 2.1 47.3 1.0 O C:HOH652 2.1 45.2 1.0 O1B C:GTP501 2.2 39.3 1.0 PG C:GTP501 3.1 43.8 1.0 PB C:GTP501 3.3 41.3 1.0 O3B C:GTP501 3.6 47.7 1.0 O2G C:GTP501 3.6 42.4 1.0 O3A C:GTP501 3.7 46.1 1.0 NZ D:LYS254 3.9 50.1 1.0 OD1 C:ASP69 4.1 40.7 1.0 OD2 C:ASP98 4.2 50.0 1.0 OE2 C:GLU71 4.2 53.8 1.0 CG C:GLU71 4.2 54.0 1.0 OD2 C:ASP69 4.2 42.4 1.0 CB C:GLN11 4.2 43.0 1.0 N C:GLN11 4.4 41.4 1.0 O3G C:GTP501 4.4 39.0 1.0 CB C:ASP98 4.5 44.1 1.0 O2B C:GTP501 4.6 48.3 1.0 CG C:ASP69 4.6 43.1 1.0 O C:HOH656 4.6 69.8 1.0 O1A C:GTP501 4.6 44.0 1.0 CG C:ASP98 4.7 48.7 1.0 CD C:GLU71 4.7 54.1 1.0 PA C:GTP501 4.8 43.4 1.0 OE1 C:GLN11 4.8 59.1 1.0 CA C:GLN11 4.9 44.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:63.4 occ:1.00 O D:HOH603 1.9 68.4 1.0 OE1 D:GLN11 2.0 74.1 1.0 O1A D:GDP501 2.4 81.4 1.0 CD D:GLN11 3.2 73.3 1.0 PA D:GDP501 3.8 66.0 1.0 CB D:GLN11 4.0 65.8 1.0 NE2 D:GLN11 4.0 76.1 1.0 CG D:GLN11 4.1 69.2 1.0 O2A D:GDP501 4.4 65.5 1.0 C5' D:GDP501 4.6 71.0 1.0 O1B D:GDP501 4.6 63.2 1.0 O5' D:GDP501 4.7 70.4 1.0 OD1 D:ASN101 4.8 72.0 1.0 O3A D:GDP501 4.8 68.1 1.0 C8 D:GDP501 4.9 67.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z45705015-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z45705015-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:95.2 occ:1.00 O3G F:ACP401 2.1 102.5 1.0 OE2 F:GLU331 2.3 98.2 1.0 O1B F:ACP401 2.6 108.9 1.0 OD1 F:ASN333 2.8 94.2 1.0 CD F:GLU331 3.1 96.9 1.0 OE1 F:GLU331 3.3 103.3 1.0 PG F:ACP401 3.7 117.2 1.0 PB F:ACP401 3.7 109.7 1.0 CG F:ASN333 3.9 87.6 1.0 O2B F:ACP401 3.9 115.0 1.0 NZ F:LYS74 4.0 113.0 1.0 C3B F:ACP401 4.3 111.1 1.0 O1G F:ACP401 4.4 109.1 1.0 ND2 F:ASN333 4.5 86.4 1.0 CG F:GLU331 4.5 86.4 1.0 O2G F:ACP401 4.6 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