Magnesium in PDB 5s5e: Tubulin-Z1515654336-Complex

The structure of Tubulin-Z1515654336-Complex, PDB code: 5s5e 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)	29.76 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.407, 159.503, 179.362, 90, 90, 90
R / Rfree (%)	18.7 / 22.7

The structure of Tubulin-Z1515654336-Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-Z1515654336-Complex (pdb code 5s5e). 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-Z1515654336-Complex, PDB code: 5s5e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.4 occ:1.00 O A:HOH617 2.1 41.1 1.0 O A:HOH605 2.1 45.0 1.0 O A:HOH633 2.1 42.4 1.0 O1G A:GTP501 2.1 42.0 1.0 O1B A:GTP501 2.3 38.8 1.0 PG A:GTP501 3.3 42.3 1.0 OE1 A:GLU71 3.3 60.2 1.0 PB A:GTP501 3.4 39.2 1.0 O3B A:GTP501 3.7 50.6 1.0 O2G A:GTP501 3.8 41.2 1.0 NZ B:LYS254 3.8 62.5 1.0 O3A A:GTP501 4.0 41.8 1.0 CB A:GLN11 4.2 43.4 1.0 OD1 A:ASP69 4.2 51.2 1.0 OD2 A:ASP69 4.3 52.2 1.0 CB A:ASP98 4.3 49.9 1.0 NE2 A:GLN11 4.4 59.0 1.0 O1A A:GTP501 4.5 41.6 1.0 N A:GLN11 4.5 41.8 1.0 OD2 A:ASP98 4.5 63.0 1.0 O3G A:GTP501 4.5 42.5 1.0 CD A:GLU71 4.6 64.2 1.0 CG A:ASP69 4.7 51.0 1.0 O2B A:GTP501 4.7 44.3 1.0 CG A:ASP98 4.7 54.8 1.0 PA A:GTP501 4.8 38.8 1.0 CA A:GLN11 4.9 46.1 1.0 CE B:LYS254 5.0 58.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.6 occ:1.00 O B:HOH601 1.8 38.5 1.0 O B:HOH620 1.9 46.0 1.0 O B:HOH628 2.1 44.1 1.0 O1A B:GDP501 2.3 34.1 1.0 OE1 B:GLN11 2.3 47.6 1.0 O C:HOH656 2.4 37.2 1.0 CD B:GLN11 3.5 47.0 1.0 PA B:GDP501 3.5 37.0 1.0 O1B B:GDP501 3.8 33.3 1.0 O3A B:GDP501 3.8 38.7 1.0 CB B:GLN11 3.9 40.2 1.0 OD1 B:ASN101 4.2 42.7 1.0 CG B:GLN11 4.3 43.1 1.0 PB B:GDP501 4.4 33.6 1.0 O2A B:GDP501 4.5 37.4 1.0 NE2 B:GLN11 4.5 50.1 1.0 OD2 B:ASP179 4.5 44.5 1.0 O5' B:GDP501 4.6 36.5 1.0 OE1 C:GLU254 4.6 50.2 1.0 C5' B:GDP501 4.7 39.8 1.0 O B:HOH623 4.7 34.7 1.0 ND2 B:ASN101 4.8 40.0 1.0 CG B:ASN101 4.9 42.0 1.0 O C:HOH625 4.9 45.5 1.0 O3B B:GDP501 5.0 36.3 1.0 OE2 B:GLU71 5.0 61.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.1 occ:1.00 O1G C:GTP501 1.9 32.6 1.0 O C:HOH654 2.0 39.1 1.0 O C:HOH620 2.0 38.6 1.0 O C:HOH650 2.1 36.4 1.0 O C:HOH614 2.1 41.7 1.0 O1B C:GTP501 2.2 36.0 1.0 PG C:GTP501 3.0 36.2 1.0 PB C:GTP501 3.3 33.2 1.0 O3B C:GTP501 3.5 41.1 1.0 O2G C:GTP501 3.5 35.0 1.0 OD2 C:ASP98 3.7 47.8 1.0 O3A C:GTP501 3.8 39.4 1.0 NZ D:LYS254 3.8 44.1 1.0 OE2 C:GLU71 4.0 50.1 1.0 CG C:GLU71 4.1 45.2 1.0 OD1 C:ASP69 4.2 42.2 1.0 CB C:ASP98 4.3 41.6 1.0 O3G C:GTP501 4.3 34.1 1.0 OD2 C:ASP69 4.4 42.6 1.0 CG C:ASP98 4.4 46.3 1.0 CB C:GLN11 4.5 38.0 1.0 CD C:GLU71 4.5 45.8 1.0 O2B C:GTP501 4.6 37.4 1.0 N C:GLN11 4.7 35.1 1.0 CG C:ASP69 4.7 42.3 1.0 O1A C:GTP501 4.8 36.9 1.0 CE D:LYS254 4.9 43.1 1.0 PA C:GTP501 4.9 36.6 1.0 OE1 C:GLN11 5.0 49.9 1.0 O D:HOH614 5.0 53.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:64.5 occ:1.00 O D:HOH604 2.3 61.9 1.0 OE1 D:GLN11 2.3 69.3 1.0 O1A D:GDP501 2.5 75.8 1.0 CD D:GLN11 3.3 69.8 1.0 CB D:GLN11 3.6 63.4 1.0 O1B D:GDP501 3.8 55.5 1.0 PA D:GDP501 3.9 60.6 1.0 CG D:GLN11 4.1 65.2 1.0 NE2 D:GLN11 4.3 71.2 1.0 O2A D:GDP501 4.4 59.9 1.0 OD1 D:ASN101 4.5 66.3 1.0 PB D:GDP501 4.5 62.6 1.0 O3B D:GDP501 4.5 66.7 1.0 O3A D:GDP501 4.6 61.7 1.0 OE2 D:GLU71 4.6 103.6 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:79.1 occ:1.00 O3G F:ACP401 2.2 100.2 1.0 OE2 F:GLU331 2.4 96.3 1.0 O1B F:ACP401 2.5 105.5 1.0 OD1 F:ASN333 2.7 89.1 1.0 CD F:GLU331 3.2 92.6 1.0 OE1 F:GLU331 3.3 99.4 1.0 PB F:ACP401 3.7 109.0 1.0 PG F:ACP401 3.7 115.2 1.0 CG F:ASN333 3.9 83.1 1.0 O2B F:ACP401 3.9 110.7 1.0 NZ F:LYS74 4.0 106.3 1.0 C3B F:ACP401 4.4 107.0 1.0 ND2 F:ASN333 4.5 82.8 1.0 O1G F:ACP401 4.5 106.2 1.0 CG F:GLU331 4.6 80.2 1.0 O2G F:ACP401 4.7 95.8 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