Magnesium in PDB 5s4v: Tubulin-Z57040482-Complex

The structure of Tubulin-Z57040482-Complex, PDB code: 5s4v 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)	63.02 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.42, 158.06, 178.36, 90, 90, 90
R / Rfree (%)	20.5 / 24.2

The structure of Tubulin-Z57040482-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z57040482-Complex (pdb code 5s4v). 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-Z57040482-Complex, PDB code: 5s4v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.9 occ:1.00 O1G A:GTP501 2.0 45.3 1.0 O A:HOH626 2.1 46.2 1.0 O A:HOH640 2.1 51.7 1.0 O A:HOH637 2.1 49.4 1.0 O A:HOH607 2.2 50.8 1.0 O1B A:GTP501 2.3 46.4 1.0 PG A:GTP501 3.2 53.5 1.0 PB A:GTP501 3.3 49.6 1.0 O3B A:GTP501 3.6 58.7 1.0 O2G A:GTP501 3.7 50.7 1.0 O3A A:GTP501 3.7 56.3 1.0 OE1 A:GLU71 3.7 65.4 1.0 NZ B:LYS254 3.9 58.0 1.0 OD2 A:ASP98 4.1 63.6 1.0 OD1 A:ASP69 4.1 57.8 1.0 CB A:ASP98 4.1 54.5 1.0 CB A:GLN11 4.2 50.1 1.0 OD2 A:ASP69 4.3 54.5 1.0 NE2 A:GLN11 4.4 65.0 1.0 O3G A:GTP501 4.4 48.7 1.0 CG A:ASP98 4.4 57.3 1.0 N A:GLN11 4.4 50.3 1.0 CG A:ASP69 4.7 57.3 1.0 O2B A:GTP501 4.7 51.6 1.0 O1A A:GTP501 4.7 53.3 1.0 PA A:GTP501 4.8 47.4 1.0 CA A:GLN11 4.9 52.2 1.0 CD A:GLU71 4.9 71.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:44.7 occ:1.00 O B:HOH632 1.9 55.0 1.0 OE1 B:GLN11 2.1 50.8 1.0 O B:HOH651 2.2 48.8 1.0 O1A B:GDP501 2.3 45.4 1.0 O B:HOH610 2.3 55.5 1.0 O C:HOH688 2.3 46.2 1.0 CD B:GLN11 3.3 49.6 1.0 PA B:GDP501 3.6 48.0 1.0 O3A B:GDP501 4.0 47.1 1.0 CB B:GLN11 4.0 47.6 1.0 OD2 B:ASP179 4.0 56.3 1.0 CG B:GLN11 4.1 47.9 1.0 NE2 B:GLN11 4.3 51.9 1.0 O1B B:GDP501 4.3 48.0 1.0 OD1 B:ASN101 4.4 45.5 1.0 O C:HOH626 4.6 56.0 1.0 O2A B:GDP501 4.6 46.4 1.0 C5' B:GDP501 4.6 49.6 1.0 O5' B:GDP501 4.6 44.1 1.0 OE1 C:GLU254 4.7 55.1 1.0 PB B:GDP501 4.8 45.3 1.0 C8 B:GDP501 4.9 50.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.0 occ:1.00 O1G C:GTP501 1.9 50.4 1.0 O C:HOH710 2.0 49.9 1.0 O C:HOH615 2.1 49.5 1.0 O C:HOH631 2.1 50.6 1.0 O1B C:GTP501 2.1 47.0 1.0 O C:HOH616 2.1 45.8 1.0 PG C:GTP501 3.1 45.6 1.0 PB C:GTP501 3.2 46.0 1.0 O3B C:GTP501 3.4 53.3 1.0 O2G C:GTP501 3.6 48.4 1.0 O3A C:GTP501 3.7 51.3 1.0 NZ D:LYS254 3.8 55.3 1.0 OD2 C:ASP98 4.1 58.1 1.0 OD1 C:ASP69 4.2 50.7 1.0 CB C:GLN11 4.3 49.4 1.0 OD2 C:ASP69 4.3 47.8 1.0 CG C:GLU71 4.3 57.0 1.0 OE2 C:GLU71 4.3 62.0 1.0 O3G C:GTP501 4.3 47.4 1.0 O2B C:GTP501 4.5 48.5 1.0 CB C:ASP98 4.5 52.0 1.0 O1A C:GTP501 4.5 51.2 1.0 N C:GLN11 4.5 43.0 1.0 O C:HOH722 4.5 70.7 1.0 CG C:ASP98 4.7 55.1 1.0 CG C:ASP69 4.7 49.4 1.0 PA C:GTP501 4.7 47.1 1.0 OE1 C:GLN11 4.7 57.1 1.0 CD C:GLU71 4.8 58.6 1.0 CE D:LYS254 4.8 54.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.5 occ:1.00 OE1 D:GLN11 2.1 79.2 1.0 O D:HOH606 2.2 74.1 1.0 O1A D:GDP501 2.3 81.5 1.0 CD D:GLN11 3.3 78.1 1.0 O1B D:GDP501 3.7 68.7 1.0 CB D:GLN11 3.7 72.1 1.0 PA D:GDP501 3.7 69.5 1.0 CG D:GLN11 4.1 77.7 1.0 O2A D:GDP501 4.3 67.3 1.0 NE2 D:GLN11 4.3 80.8 1.0 OD1 D:ASN101 4.3 79.3 1.0 O3A D:GDP501 4.4 70.6 1.0 PB D:GDP501 4.4 67.1 1.0 O3B D:GDP501 4.7 74.7 1.0 O5' D:GDP501 4.9 72.1 1.0 OE2 D:GLU71 4.9 112.1 1.0 C5' D:GDP501 5.0 75.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z57040482-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z57040482-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:104.0 occ:1.00 O3G F:ACP401 2.2 110.2 1.0 OE2 F:GLU331 2.2 102.9 1.0 O1B F:ACP401 2.5 111.7 1.0 OD1 F:ASN333 2.7 103.3 1.0 CD F:GLU331 3.0 102.7 1.0 OE1 F:GLU331 3.1 109.4 1.0 PB F:ACP401 3.6 116.6 1.0 PG F:ACP401 3.7 124.3 1.0 NZ F:LYS74 3.8 109.0 1.0 CG F:ASN333 3.9 97.2 1.0 O2B F:ACP401 3.9 116.5 1.0 C3B F:ACP401 4.3 116.1 1.0 O1G F:ACP401 4.4 114.9 1.0 CG F:GLU331 4.4 91.9 1.0 ND2 F:ASN333 4.5 95.2 1.0 O2G F:ACP401 4.7 107.6 1.0 CE F:LYS74 4.9 110.5 1.0 O1A F:ACP401 4.9 113.1 1.0 O3A F:ACP401 5.0 117.3 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