Magnesium in PDB 5s63: Tubulin-Z2241115980-Complex

The structure of Tubulin-Z2241115980-Complex, PDB code: 5s63 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)	62.78 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.22, 159.1, 179.66, 90, 90, 90
R / Rfree (%)	21.3 / 26.8

The structure of Tubulin-Z2241115980-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2241115980-Complex (pdb code 5s63). 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-Z2241115980-Complex, PDB code: 5s63:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:58.5 occ:1.00 O A:HOH615 1.9 60.9 1.0 O A:HOH607 2.0 57.6 1.0 O1G A:GTP501 2.0 56.7 1.0 O A:HOH605 2.1 54.1 1.0 O1B A:GTP501 2.2 56.9 1.0 O A:HOH619 2.3 60.5 1.0 PG A:GTP501 3.1 56.2 1.0 PB A:GTP501 3.3 51.4 1.0 O3B A:GTP501 3.5 63.1 1.0 O2G A:GTP501 3.6 56.6 1.0 OE1 A:GLU71 3.6 72.0 1.0 O3A A:GTP501 3.9 57.5 1.0 CB A:GLN11 4.0 52.6 1.0 OD1 A:ASP69 4.1 62.0 1.0 NE2 A:GLN11 4.1 65.6 1.0 NZ B:LYS254 4.2 65.9 1.0 N A:GLN11 4.3 53.7 1.0 OD2 A:ASP69 4.3 62.5 1.0 O3G A:GTP501 4.4 57.3 1.0 CB A:ASP98 4.5 62.0 1.0 O2B A:GTP501 4.6 59.4 1.0 O1A A:GTP501 4.6 54.0 1.0 CG A:ASP69 4.6 62.3 1.0 CA A:GLN11 4.7 57.5 1.0 CD A:GLU71 4.8 76.4 1.0 PA A:GTP501 4.8 55.2 1.0 CG A:ASP98 4.9 62.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.3 occ:1.00 OE1 B:GLN11 1.9 57.6 1.0 O B:HOH607 2.0 47.7 1.0 O B:HOH629 2.0 50.3 1.0 O B:HOH601 2.1 55.1 1.0 O1A B:GDP501 2.2 48.7 1.0 O C:HOH745 2.3 39.4 1.0 CD B:GLN11 3.1 55.7 1.0 PA B:GDP501 3.5 39.2 1.0 CB B:GLN11 3.8 48.9 1.0 O3A B:GDP501 3.9 43.4 1.0 CG B:GLN11 4.0 51.5 1.0 OD2 B:ASP179 4.0 55.7 1.0 NE2 B:GLN11 4.0 58.6 1.0 O1B B:GDP501 4.3 45.7 1.0 O2A B:GDP501 4.5 44.5 1.0 OD1 B:ASN101 4.5 53.6 1.0 OE1 C:GLU254 4.5 57.6 1.0 O5' B:GDP501 4.6 50.4 1.0 C5' B:GDP501 4.7 48.5 1.0 PB B:GDP501 4.7 43.5 1.0 ND2 B:ASN101 4.8 49.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:55.9 occ:1.00 O C:HOH755 1.8 56.5 1.0 O C:HOH752 1.9 51.3 1.0 O1G C:GTP602 1.9 44.1 1.0 O C:HOH743 2.1 52.3 1.0 O C:HOH733 2.3 51.9 1.0 O1B C:GTP602 2.3 49.8 1.0 PG C:GTP602 3.0 47.9 1.0 PB C:GTP602 3.2 42.2 1.0 O2G C:GTP602 3.4 47.9 1.0 O3B C:GTP602 3.4 52.7 1.0 O3A C:GTP602 3.6 52.0 1.0 OD2 C:ASP98 3.7 56.0 1.0 NZ D:LYS254 3.8 53.3 1.0 OD1 C:ASP69 4.2 53.7 1.0 CG C:GLU71 4.2 63.2 1.0 OE2 C:GLU71 4.3 65.4 1.0 CB C:ASP98 4.3 56.3 1.0 O3G C:GTP602 4.3 49.9 1.0 OD2 C:ASP69 4.4 54.2 1.0 CG C:ASP98 4.4 57.1 1.0 CB C:GLN11 4.5 51.8 1.0 O2B C:GTP602 4.6 51.2 1.0 N C:GLN11 4.6 48.5 1.0 CG C:ASP69 4.7 54.1 1.0 CD C:GLU71 4.7 65.5 1.0 OG1 C:THR145 4.7 53.2 1.0 PA C:GTP602 4.8 49.1 1.0 OE1 C:GLN11 4.9 66.0 1.0 CE D:LYS254 4.9 52.1 1.0 O1A C:GTP602 5.0 53.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.6 occ:1.00 OE1 D:GLN11 2.0 83.3 1.0 O1A D:GDP501 2.3 88.2 1.0 CD D:GLN11 3.3 85.7 1.0 PA D:GDP501 3.6 77.9 1.0 O2A D:GDP501 3.8 74.6 1.0 CB D:GLN11 4.0 80.7 1.0 CG D:GLN11 4.2 83.8 1.0 NE2 D:GLN11 4.2 83.5 1.0 OD1 D:ASN101 4.3 78.6 1.0 C5' D:GDP501 4.4 74.4 1.0 O1B D:GDP501 4.4 72.4 1.0 O5' D:GDP501 4.5 76.3 1.0 O3A D:GDP501 4.8 78.4 1.0 PB D:GDP501 5.0 78.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2241115980-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2241115980-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:99.2 occ:1.00 O1B F:ACP401 2.4 121.0 1.0 O3G F:ACP401 2.5 111.9 1.0 OE2 F:GLU331 2.7 114.6 1.0 OD1 F:ASN333 3.1 101.2 1.0 OE1 F:GLU331 3.2 120.4 1.0 CD F:GLU331 3.3 114.1 1.0 PB F:ACP401 3.5 127.8 1.0 NZ F:LYS74 3.7 111.3 1.0 O2B F:ACP401 3.7 125.0 1.0 PG F:ACP401 4.0 125.3 1.0 CG F:ASN333 4.3 97.9 1.0 C3B F:ACP401 4.5 121.7 1.0 O1G F:ACP401 4.6 121.8 1.0 O3A F:ACP401 4.8 120.6 1.0 CG F:GLU331 4.8 101.1 1.0 ND2 F:ASN333 4.8 93.4 1.0 CE F:LYS74 4.9 110.7 1.0 O1A F:ACP401 5.0 114.2 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