Magnesium in PDB 5s4z: Tubulin-Z28290384-Complex

The structure of Tubulin-Z28290384-Complex, PDB code: 5s4z 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)	63.53 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.26, 178.54, 90, 90, 90
R / Rfree (%)	20.5 / 24.2

The structure of Tubulin-Z28290384-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Tubulin-Z28290384-Complex (pdb code 5s4z). 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-Z28290384-Complex, PDB code: 5s4z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.1 occ:1.00 O A:HOH616 2.0 38.8 1.0 O1G A:GTP501 2.0 32.7 1.0 O A:HOH653 2.0 37.7 1.0 O A:HOH601 2.1 42.5 1.0 O A:HOH682 2.1 37.2 1.0 O1B A:GTP501 2.1 33.9 1.0 PG A:GTP501 3.2 39.9 1.0 PB A:GTP501 3.2 33.9 1.0 OE1 A:GLU71 3.6 63.0 1.0 O3B A:GTP501 3.6 42.2 1.0 O2G A:GTP501 3.7 38.2 1.0 O3A A:GTP501 3.7 41.9 1.0 NZ B:LYS254 3.9 49.6 1.0 OD1 A:ASP69 4.0 38.7 1.0 OD2 A:ASP69 4.1 38.6 1.0 CB A:GLN11 4.1 36.4 1.0 N A:GLN11 4.3 35.1 1.0 CB A:ASP98 4.3 42.5 1.0 OD2 A:ASP98 4.4 52.5 1.0 CG A:ASP69 4.5 43.0 1.0 O3G A:GTP501 4.5 40.1 1.0 NE2 A:GLN11 4.5 47.9 1.0 CD A:GLU71 4.5 58.3 1.0 O2B A:GTP501 4.5 38.5 1.0 O1A A:GTP501 4.6 40.1 1.0 CG A:ASP98 4.7 49.7 1.0 PA A:GTP501 4.8 41.4 1.0 CA A:GLN11 4.8 37.8 1.0 CE B:LYS254 4.8 45.6 1.0 OE2 A:GLU71 4.9 65.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.7 occ:1.00 O B:HOH618 2.1 41.0 1.0 OE1 B:GLN11 2.1 45.4 1.0 O C:HOH731 2.2 44.0 1.0 O B:HOH612 2.3 43.7 1.0 O1A B:GDP501 2.3 36.2 1.0 O B:HOH643 2.5 39.7 1.0 CD B:GLN11 3.3 45.0 1.0 PA B:GDP501 3.6 33.7 1.0 OD2 B:ASP179 3.8 42.4 1.0 O3A B:GDP501 3.9 36.5 1.0 CB B:GLN11 4.0 38.6 1.0 CG B:GLN11 4.1 40.6 1.0 O C:HOH707 4.2 43.9 1.0 NE2 B:GLN11 4.3 52.1 1.0 C5' B:GDP501 4.4 39.9 1.0 OD1 B:ASN101 4.4 42.5 1.0 O1B B:GDP501 4.5 36.2 1.0 O5' B:GDP501 4.5 41.2 1.0 OE1 C:GLU254 4.5 46.3 1.0 O2A B:GDP501 4.7 38.1 1.0 CG B:ASP179 4.8 45.2 1.0 PB B:GDP501 4.9 37.1 1.0 C8 B:GDP501 4.9 40.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.5 occ:1.00 O C:HOH642 2.0 35.5 1.0 O C:HOH654 2.1 33.5 1.0 O1G C:GTP501 2.1 32.3 1.0 O C:HOH709 2.1 35.5 1.0 O1B C:GTP501 2.2 30.8 1.0 PB C:GTP501 3.2 33.7 1.0 PG C:GTP501 3.3 37.2 1.0 O3A C:GTP501 3.6 35.4 1.0 O3B C:GTP501 3.6 38.4 1.0 NZ D:LYS254 3.7 42.6 1.0 O2G C:GTP501 3.8 35.5 1.0 OE2 C:GLU71 4.1 45.2 1.0 CB C:GLN11 4.1 31.8 1.0 OD1 C:ASP69 4.2 39.4 1.0 CG C:GLU71 4.3 47.4 1.0 OD2 C:ASP69 4.3 31.1 1.0 OD2 C:ASP98 4.4 43.7 1.0 N C:GLN11 4.4 32.2 1.0 O1A C:GTP501 4.4 33.8 1.0 O3G C:GTP501 4.5 33.0 1.0 OE1 C:GLN11 4.5 42.2 1.0 O2B C:GTP501 4.5 39.6 1.0 PA C:GTP501 4.6 35.7 1.0 CB C:ASP98 4.7 37.8 1.0 CD C:GLU71 4.7 44.9 1.0 CG C:ASP69 4.7 34.8 1.0 CA C:GLN11 4.9 33.8 1.0 CG C:ASP98 4.9 39.7 1.0 CE D:LYS254 4.9 45.1 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:53.0 occ:1.00 OE1 D:GLN11 2.0 60.3 1.0 O1A D:GDP501 2.1 62.2 1.0 O D:HOH614 2.1 54.5 1.0 O D:HOH660 2.5 60.6 1.0 O D:HOH638 2.6 55.3 1.0 CD D:GLN11 3.2 60.4 1.0 PA D:GDP501 3.6 54.2 1.0 CB D:GLN11 4.0 54.5 1.0 CG D:GLN11 4.1 55.6 1.0 NE2 D:GLN11 4.2 61.0 1.0 O3A D:GDP501 4.3 58.8 1.0 C5' D:GDP501 4.4 58.1 1.0 O1B D:GDP501 4.4 52.0 1.0 O2A D:GDP501 4.4 49.6 1.0 O D:HOH656 4.5 64.1 1.0 O5' D:GDP501 4.5 58.2 1.0 O D:HOH661 4.7 66.8 1.0 OD1 D:ASN101 4.8 64.7 1.0 C8 D:GDP501 4.9 54.0 1.0 PB D:GDP501 5.0 53.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z28290384-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z28290384-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:71.7 occ:1.00 O3G F:ACP401 2.1 87.0 1.0 OE2 F:GLU331 2.2 82.8 1.0 OD1 F:ASN333 2.5 76.3 1.0 O1B F:ACP401 2.7 90.2 1.0 CD F:GLU331 2.9 82.2 1.0 OE1 F:GLU331 3.0 89.8 1.0 CG F:ASN333 3.6 71.4 1.0 PG F:ACP401 3.7 102.1 1.0 PB F:ACP401 3.8 91.6 1.0 ND2 F:ASN333 4.1 68.6 1.0 NZ F:LYS74 4.2 92.3 1.0 O2B F:ACP401 4.2 98.4 1.0 CG F:GLU331 4.4 73.0 1.0 C3B F:ACP401 4.5 92.9 1.0 O1G F:ACP401 4.5 92.9 1.0 O2G F:ACP401 4.6 82.9 1.0 CB F:ASN333 4.8 61.5 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