Magnesium in PDB 5s5d: Tubulin-Z32400357-Complex

The structure of Tubulin-Z32400357-Complex, PDB code: 5s5d 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)	63.42 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.07, 159.08, 179.22, 90, 90, 90
R / Rfree (%)	20 / 22.7

The structure of Tubulin-Z32400357-Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-Z32400357-Complex (pdb code 5s5d). 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-Z32400357-Complex, PDB code: 5s5d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.9 occ:1.00 O1G A:GTP501 2.0 37.1 1.0 O A:HOH659 2.1 36.8 1.0 O A:HOH708 2.1 35.4 1.0 O A:HOH622 2.1 35.1 1.0 O1B A:GTP501 2.1 31.4 1.0 O A:HOH637 2.2 35.8 1.0 PG A:GTP501 3.2 36.6 1.0 PB A:GTP501 3.2 33.7 1.0 O3B A:GTP501 3.6 31.5 1.0 O3A A:GTP501 3.7 33.7 1.0 O2G A:GTP501 3.8 35.5 1.0 NZ B:LYS254 3.8 44.0 1.0 OE1 A:GLU71 4.0 53.4 1.0 OD1 A:ASP69 4.1 38.2 1.0 CB A:GLN11 4.1 34.4 1.0 OD2 A:ASP69 4.2 39.4 1.0 CB A:ASP98 4.3 37.9 1.0 OD2 A:ASP98 4.3 43.6 1.0 N A:GLN11 4.3 33.3 1.0 O1A A:GTP501 4.4 33.9 1.0 O3G A:GTP501 4.5 33.9 1.0 O2B A:GTP501 4.6 34.0 1.0 O A:HOH625 4.6 55.4 1.0 CG A:ASP69 4.6 39.7 1.0 CG A:ASP98 4.7 38.6 1.0 PA A:GTP501 4.7 35.8 1.0 NE2 A:GLN11 4.8 41.4 1.0 CA A:GLN11 4.8 35.0 1.0 CE B:LYS254 4.9 42.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:28.1 occ:1.00 OE1 B:GLN11 2.2 39.7 1.0 O B:HOH665 2.3 33.9 1.0 O B:HOH701 2.3 45.5 1.0 O1A B:GDP501 2.3 31.8 1.0 O C:HOH671 2.4 36.6 1.0 O B:HOH634 2.4 37.7 1.0 O B:HOH670 2.5 34.1 1.0 CD B:GLN11 3.4 36.8 1.0 PA B:GDP501 3.6 31.5 1.0 O3A B:GDP501 3.8 33.8 1.0 CB B:GLN11 4.0 32.2 1.0 OD2 B:ASP179 4.1 35.2 1.0 CG B:GLN11 4.2 33.3 1.0 OE1 C:GLU254 4.4 41.8 1.0 O C:HOH637 4.4 40.4 1.0 NE2 B:GLN11 4.4 42.2 1.0 O1B B:GDP501 4.5 32.1 1.0 OD1 B:ASN101 4.5 35.0 1.0 C5' B:GDP501 4.5 31.1 1.0 O5' B:GDP501 4.5 33.6 1.0 O2A B:GDP501 4.7 32.8 1.0 PB B:GDP501 4.8 31.7 1.0 C8 B:GDP501 4.9 36.6 1.0 O B:HOH720 5.0 47.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.5 occ:1.00 O C:HOH654 2.1 31.2 1.0 O C:HOH808 2.1 32.5 1.0 O1B C:GTP501 2.1 28.8 1.0 O C:HOH653 2.1 35.1 1.0 O1G C:GTP501 2.1 31.3 1.0 O C:HOH724 2.2 32.3 1.0 PB C:GTP501 3.2 32.0 1.0 PG C:GTP501 3.2 32.3 1.0 O3B C:GTP501 3.5 30.7 1.0 O2G C:GTP501 3.7 34.5 1.0 O3A C:GTP501 3.8 32.5 1.0 NZ D:LYS254 3.9 35.5 1.0 OD1 C:ASP69 4.1 33.9 1.0 OE2 C:GLU71 4.1 42.8 1.0 CB C:GLN11 4.1 29.1 1.0 OD2 C:ASP69 4.1 35.3 1.0 CG C:GLU71 4.3 43.1 1.0 N C:GLN11 4.4 28.9 1.0 OD2 C:ASP98 4.4 40.7 1.0 O2B C:GTP501 4.5 30.5 1.0 O1A C:GTP501 4.5 33.3 1.0 O3G C:GTP501 4.5 32.3 1.0 CB C:ASP98 4.5 33.6 1.0 CG C:ASP69 4.5 33.5 1.0 CD C:GLU71 4.7 43.7 1.0 PA C:GTP501 4.7 31.4 1.0 OE1 C:GLN11 4.8 39.5 1.0 CG C:ASP98 4.8 38.8 1.0 O C:HOH644 4.8 42.5 1.0 CA C:GLN11 4.9 31.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:52.0 occ:1.00 O D:HOH655 2.0 54.1 1.0 OE1 D:GLN11 2.1 55.9 1.0 O1A D:GDP501 2.1 59.7 1.0 O D:HOH630 2.6 54.5 1.0 CD D:GLN11 3.3 59.4 1.0 PA D:GDP501 3.5 52.1 1.0 CB D:GLN11 4.0 51.3 1.0 O3A D:GDP501 4.1 52.5 1.0 CG D:GLN11 4.2 56.8 1.0 NE2 D:GLN11 4.2 61.7 1.0 O1B D:GDP501 4.3 50.6 1.0 C5' D:GDP501 4.4 54.4 1.0 O5' D:GDP501 4.4 51.2 1.0 OD1 D:ASN101 4.5 62.2 1.0 O2A D:GDP501 4.5 48.8 1.0 PB D:GDP501 4.8 50.1 1.0 C8 D:GDP501 5.0 49.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z32400357-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z32400357-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:77.2 occ:1.00 O3G F:ACP401 2.3 83.3 1.0 OE2 F:GLU331 2.5 81.8 1.0 O1B F:ACP401 2.6 87.1 1.0 OD1 F:ASN333 2.7 77.6 1.0 OE1 F:GLU331 3.1 80.5 1.0 CD F:GLU331 3.2 77.8 1.0 NZ F:LYS74 3.6 91.4 1.0 CG F:ASN333 3.8 68.9 1.0 PB F:ACP401 3.8 91.7 1.0 PG F:ACP401 3.9 99.5 1.0 O2B F:ACP401 4.1 95.8 1.0 ND2 F:ASN333 4.4 64.0 1.0 C3B F:ACP401 4.6 93.2 1.0 O1G F:ACP401 4.6 90.7 1.0 CG F:GLU331 4.6 67.4 1.0 CE F:LYS74 4.9 90.8 1.0 O2G F:ACP401 4.9 83.0 1.0 CB F:ASN333 4.9 60.4 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