Magnesium in PDB 5s5g: Tubulin-Z1129283193-Complex

The structure of Tubulin-Z1129283193-Complex, PDB code: 5s5g 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)	72.26 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.645, 157.922, 179.187, 90, 90, 90
R / Rfree (%)	21.8 / 27.1

The structure of Tubulin-Z1129283193-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1129283193-Complex (pdb code 5s5g). 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-Z1129283193-Complex, PDB code: 5s5g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.0 occ:1.00 O A:HOH604 1.9 29.3 1.0 O A:HOH616 2.2 28.0 1.0 O1G A:GTP501 2.2 27.9 1.0 O A:HOH614 2.3 29.9 1.0 O1B A:GTP501 2.7 25.6 1.0 OE1 A:GLU71 3.0 44.0 1.0 NZ B:LYS254 3.5 44.3 1.0 PG A:GTP501 3.6 28.7 1.0 PB A:GTP501 3.9 25.2 1.0 O2G A:GTP501 4.0 26.4 1.0 CB A:ASP98 4.1 34.0 1.0 NE2 A:GLN11 4.1 38.3 1.0 O3B A:GTP501 4.2 31.5 1.0 OD2 A:ASP98 4.2 39.7 1.0 CD A:GLU71 4.3 42.7 1.0 O3A A:GTP501 4.4 25.8 1.0 CB A:GLN11 4.4 28.7 1.0 OD1 A:ASP69 4.5 33.3 1.0 CG A:ASP98 4.5 39.1 1.0 OD2 A:ASP69 4.6 37.6 1.0 CE B:LYS254 4.6 42.4 1.0 O3G A:GTP501 4.7 27.1 1.0 O1A A:GTP501 4.7 27.4 1.0 O B:HOH608 4.8 37.2 1.0 N A:GLN11 4.9 27.9 1.0 OE2 A:GLU71 5.0 49.8 1.0 CG A:ASP69 5.0 35.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:25.0 occ:1.00 O B:HOH612 1.8 23.4 1.0 OE1 B:GLN11 1.9 32.0 1.0 O B:HOH621 2.2 23.3 1.0 O C:HOH675 2.3 26.3 1.0 O1A B:GDP501 2.4 22.1 1.0 CD B:GLN11 2.9 32.1 1.0 OD2 B:ASP179 3.4 27.9 1.0 NE2 B:GLN11 3.7 34.6 1.0 PA B:GDP501 3.8 21.1 1.0 CG B:GLN11 4.0 32.8 1.0 CB B:GLN11 4.0 27.6 1.0 O3A B:GDP501 4.5 23.6 1.0 O C:HOH608 4.5 30.2 1.0 C5' B:GDP501 4.6 23.9 1.0 CG B:ASP179 4.6 28.0 1.0 C8 B:GDP501 4.7 23.4 1.0 OD1 B:ASN101 4.7 25.5 1.0 O1B B:GDP501 4.7 22.7 1.0 O5' B:GDP501 4.7 20.2 1.0 O2A B:GDP501 4.8 22.2 1.0 OE1 C:GLU254 4.9 34.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:24.3 occ:1.00 O C:HOH613 1.9 21.5 1.0 O C:HOH642 2.0 24.3 1.0 O C:HOH623 2.1 19.6 1.0 O1G C:GTP501 2.1 17.3 1.0 O1B C:GTP501 2.7 18.0 1.0 PG C:GTP501 3.4 18.2 1.0 OE2 C:GLU71 3.4 31.5 1.0 NZ D:LYS254 3.5 31.0 1.0 OD2 C:ASP98 3.6 27.2 1.0 CG C:GLU71 3.7 30.6 1.0 O2G C:GTP501 3.7 22.7 1.0 PB C:GTP501 3.8 15.8 1.0 CD C:GLU71 4.0 32.5 1.0 O3B C:GTP501 4.0 22.5 1.0 CB C:ASP98 4.1 27.0 1.0 O3A C:GTP501 4.2 23.5 1.0 CG C:ASP98 4.3 28.5 1.0 OD1 C:ASP69 4.4 25.4 1.0 O D:HOH621 4.5 35.7 1.0 OD2 C:ASP69 4.5 23.4 1.0 O3G C:GTP501 4.5 19.3 1.0 O C:HOH695 4.6 38.8 1.0 CE D:LYS254 4.6 30.2 1.0 OE1 C:GLN11 4.7 40.5 1.0 CB C:GLN11 4.7 24.4 1.0 CG C:ASP69 4.9 23.8 1.0 CB C:GLU71 5.0 31.7 1.0 O1A C:GTP501 5.0 22.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.9 occ:1.00 O D:HOH605 2.5 35.4 1.0 OE1 D:GLN11 2.6 59.3 1.0 O1A D:GDP501 2.8 56.9 1.0 CD D:GLN11 3.4 58.3 1.0 O1B D:GDP501 3.7 47.9 1.0 CB D:GLN11 3.8 52.6 1.0 PA D:GDP501 4.1 45.4 1.0 NE2 D:GLN11 4.1 60.8 1.0 CG D:GLN11 4.2 54.4 1.0 OE2 D:GLU71 4.2 96.5 1.0 O3B D:GDP501 4.4 49.2 1.0 O2A D:GDP501 4.4 46.0 1.0 OD1 D:ASN101 4.5 51.5 1.0 PB D:GDP501 4.5 45.0 1.0 O3A D:GDP501 4.8 47.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1129283193-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1129283193-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:64.5 occ:1.00 OE2 F:GLU331 2.4 74.1 1.0 O3G F:ACP401 2.6 82.6 1.0 O1B F:ACP401 2.6 86.0 1.0 OE1 F:GLU331 2.8 77.0 1.0 CD F:GLU331 3.0 71.5 1.0 OD1 F:ASN333 3.3 71.1 1.0 NZ F:LYS74 3.7 81.7 1.0 PB F:ACP401 3.9 94.6 1.0 PG F:ACP401 4.1 99.2 1.0 CG F:ASN333 4.2 63.5 1.0 O2B F:ACP401 4.3 87.6 1.0 CG F:GLU331 4.4 62.8 1.0 C3B F:ACP401 4.7 92.9 1.0 ND2 F:ASN333 4.8 62.4 1.0 O2G F:ACP401 4.9 76.9 1.0 CE F:LYS74 4.9 78.5 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