Magnesium in PDB 5s5b: Tubulin-Z906021418-Complex

The structure of Tubulin-Z906021418-Complex, PDB code: 5s5b 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)	63.37 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.02, 158.92, 179.41, 90, 90, 90
R / Rfree (%)	20.9 / 24.4

The structure of Tubulin-Z906021418-Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z906021418-Complex (pdb code 5s5b). 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-Z906021418-Complex, PDB code: 5s5b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.5 occ:1.00 O1G A:GTP501 2.0 45.1 1.0 O A:HOH606 2.0 50.9 1.0 O A:HOH632 2.1 48.8 1.0 O A:HOH631 2.2 48.4 1.0 O A:HOH621 2.2 51.5 1.0 O1B A:GTP501 2.2 44.1 1.0 PG A:GTP501 3.2 47.7 1.0 PB A:GTP501 3.4 43.0 1.0 OE1 A:GLU71 3.6 67.9 1.0 O3B A:GTP501 3.6 54.0 1.0 O2G A:GTP501 3.7 47.5 1.0 NZ B:LYS254 3.8 61.1 1.0 O3A A:GTP501 3.9 51.7 1.0 OD1 A:ASP69 4.1 54.2 1.0 CB A:GLN11 4.1 47.3 1.0 CB A:ASP98 4.1 53.6 1.0 OD2 A:ASP69 4.2 58.6 1.0 N A:GLN11 4.4 48.3 1.0 O3G A:GTP501 4.5 49.3 1.0 OD2 A:ASP98 4.5 65.1 1.0 CG A:ASP69 4.5 55.6 1.0 O1A A:GTP501 4.6 49.5 1.0 O2B A:GTP501 4.6 50.1 1.0 CG A:ASP98 4.7 58.7 1.0 NE2 A:GLN11 4.7 57.5 1.0 O B:HOH632 4.8 59.0 1.0 CE B:LYS254 4.8 55.4 1.0 CD A:GLU71 4.8 67.8 1.0 PA A:GTP501 4.8 48.5 1.0 CA A:GLN11 4.8 49.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.9 occ:1.00 O B:HOH603 1.9 59.3 1.0 OE1 B:GLN11 2.1 50.3 1.0 O C:HOH686 2.2 45.1 1.0 O B:HOH637 2.2 47.4 1.0 O1A B:GDP501 2.2 43.3 1.0 O B:HOH659 2.3 45.8 1.0 CD B:GLN11 3.3 50.7 1.0 PA B:GDP501 3.5 43.8 1.0 O3A B:GDP501 3.9 43.4 1.0 OD2 B:ASP179 3.9 49.1 1.0 CB B:GLN11 4.0 46.7 1.0 CG B:GLN11 4.2 48.1 1.0 OD1 B:ASN101 4.3 45.0 1.0 NE2 B:GLN11 4.3 56.9 1.0 O1B B:GDP501 4.3 41.5 1.0 O C:HOH712 4.4 60.3 1.0 C5' B:GDP501 4.4 45.0 1.0 O5' B:GDP501 4.4 44.2 1.0 OE1 C:GLU254 4.5 55.1 1.0 O2A B:GDP501 4.6 44.2 1.0 PB B:GDP501 4.8 38.7 1.0 ND2 B:ASN101 4.8 47.7 1.0 CG B:ASP179 4.9 49.4 1.0 CG B:ASN101 4.9 47.6 1.0 C8 B:GDP501 4.9 48.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:44.2 occ:1.00 O C:HOH680 2.0 46.0 1.0 O1G C:GTP501 2.0 44.3 1.0 O1B C:GTP501 2.0 42.4 1.0 O C:HOH630 2.1 46.0 1.0 O C:HOH688 2.1 46.1 1.0 O C:HOH643 2.1 49.1 1.0 PG C:GTP501 3.1 43.2 1.0 PB C:GTP501 3.1 42.3 1.0 O3B C:GTP501 3.4 47.9 1.0 O2G C:GTP501 3.6 45.9 1.0 O3A C:GTP501 3.7 49.2 1.0 NZ D:LYS254 3.9 47.2 1.0 OD2 C:ASP98 3.9 53.4 1.0 OD1 C:ASP69 4.0 48.8 1.0 OE2 C:GLU71 4.1 58.2 1.0 CG C:GLU71 4.2 56.8 1.0 OD2 C:ASP69 4.3 41.8 1.0 CB C:ASP98 4.4 48.7 1.0 CB C:GLN11 4.4 45.7 1.0 O3G C:GTP501 4.4 44.7 1.0 O2B C:GTP501 4.4 43.4 1.0 N C:GLN11 4.5 42.4 1.0 CG C:ASP98 4.6 50.3 1.0 CG C:ASP69 4.6 46.4 1.0 O1A C:GTP501 4.6 45.0 1.0 CD C:GLU71 4.7 58.3 1.0 PA C:GTP501 4.8 43.9 1.0 OE1 C:GLN11 4.9 56.0 1.0 OG1 C:THR145 4.9 49.3 1.0 CE D:LYS254 5.0 48.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:71.9 occ:1.00 O D:HOH603 1.9 74.4 1.0 OE1 D:GLN11 2.0 73.1 1.0 O1A D:GDP501 2.2 88.7 1.0 CD D:GLN11 3.1 76.9 1.0 PA D:GDP501 3.5 74.7 1.0 CB D:GLN11 3.8 71.0 1.0 O2A D:GDP501 3.9 69.4 1.0 CG D:GLN11 3.9 71.1 1.0 O D:HOH631 4.1 74.1 1.0 NE2 D:GLN11 4.1 73.2 1.0 O1B D:GDP501 4.3 69.1 1.0 C5' D:GDP501 4.4 73.1 1.0 O5' D:GDP501 4.5 70.6 1.0 O3A D:GDP501 4.7 73.5 1.0 C8 D:GDP501 4.8 69.8 1.0 OD1 D:ASN101 4.8 80.4 1.0 PB D:GDP501 5.0 70.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z906021418-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z906021418-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:98.4 occ:1.00 O3G F:ACP401 2.3 103.1 1.0 OE2 F:GLU331 2.4 101.4 1.0 O1B F:ACP401 2.5 113.1 1.0 OD1 F:ASN333 2.8 94.0 1.0 CD F:GLU331 3.2 100.2 1.0 OE1 F:GLU331 3.4 104.2 1.0 PB F:ACP401 3.6 115.5 1.0 PG F:ACP401 3.7 117.5 1.0 O2B F:ACP401 3.8 118.0 1.0 CG F:ASN333 3.9 88.0 1.0 NZ F:LYS74 4.1 112.5 1.0 C3B F:ACP401 4.3 114.4 1.0 O1G F:ACP401 4.4 109.1 1.0 ND2 F:ASN333 4.4 85.6 1.0 CG F:GLU331 4.7 88.3 1.0 O2G F:ACP401 4.8 102.3 1.0 O3A F:ACP401 5.0 114.6 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