Magnesium in PDB 5s59: Tubulin-Z1324080698-Complex

The structure of Tubulin-Z1324080698-Complex, PDB code: 5s59 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)	59.84 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.56, 158.9, 179.33, 90, 90, 90
R / Rfree (%)	22 / 26.8

The structure of Tubulin-Z1324080698-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1324080698-Complex (pdb code 5s59). 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-Z1324080698-Complex, PDB code: 5s59:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:74.7 occ:1.00 O A:HOH615 2.0 69.3 1.0 O A:HOH606 2.0 70.7 1.0 O1G A:GTP501 2.0 68.3 1.0 O A:HOH610 2.1 70.4 1.0 O1B A:GTP501 2.3 71.8 1.0 OE1 A:GLU71 3.2 86.0 1.0 PG A:GTP501 3.3 69.3 1.0 PB A:GTP501 3.6 64.6 1.0 NZ B:LYS254 3.6 80.1 1.0 O2G A:GTP501 3.7 69.9 1.0 O3B A:GTP501 3.8 72.8 1.0 CB A:ASP98 4.1 74.1 1.0 O3A A:GTP501 4.2 66.6 1.0 CB A:GLN11 4.2 73.2 1.0 OD1 A:ASP69 4.3 70.2 1.0 CD A:GLU71 4.4 89.0 1.0 OE1 A:GLN11 4.4 88.4 1.0 OD2 A:ASP98 4.4 83.1 1.0 O3G A:GTP501 4.5 69.5 1.0 OD2 A:ASP69 4.5 78.0 1.0 CG A:ASP98 4.6 76.9 1.0 O1A A:GTP501 4.7 70.9 1.0 N A:GLN11 4.7 63.8 1.0 CE B:LYS254 4.7 72.1 1.0 O2B A:GTP501 4.7 69.8 1.0 CG A:ASP69 4.9 71.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:75.3 occ:1.00 O B:HOH602 1.8 77.0 1.0 O B:HOH629 2.0 68.8 1.0 O1A B:GDP501 2.1 70.9 1.0 O B:HOH612 2.1 72.6 1.0 O B:HOH614 2.2 65.6 1.0 OE1 B:GLN11 2.3 80.5 1.0 PA B:GDP501 3.4 62.3 1.0 CD B:GLN11 3.4 78.5 1.0 O3A B:GDP501 3.7 63.9 1.0 OD1 B:ASN101 3.8 69.8 1.0 CB B:GLN11 3.8 70.7 1.0 O3B B:GDP501 4.0 65.1 1.0 OD2 B:ASP179 4.1 74.3 1.0 CG B:GLN11 4.2 73.1 1.0 O2A B:GDP501 4.2 63.5 1.0 NE2 B:GLN11 4.4 81.5 1.0 PB B:GDP501 4.4 61.0 1.0 O5' B:GDP501 4.5 66.1 1.0 OE1 C:GLU254 4.5 81.8 1.0 ND2 B:ASN101 4.6 75.2 1.0 CG B:ASN101 4.6 70.8 1.0 C5' B:GDP501 4.6 68.0 1.0 O1B B:GDP501 4.8 71.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:68.6 occ:1.00 O C:HOH619 1.9 66.6 1.0 O1G C:GTP501 2.0 63.3 1.0 O C:HOH605 2.1 64.8 1.0 O C:HOH623 2.2 70.0 1.0 O1B C:GTP501 2.2 64.3 1.0 O C:HOH612 2.3 62.7 1.0 PG C:GTP501 3.1 64.2 1.0 PB C:GTP501 3.4 60.8 1.0 O2G C:GTP501 3.5 64.2 1.0 O3B C:GTP501 3.6 68.4 1.0 NZ D:LYS254 3.8 69.1 1.0 OD2 C:ASP98 3.8 68.3 1.0 O3A C:GTP501 4.0 66.0 1.0 CG C:GLU71 4.1 80.3 1.0 OE2 C:GLU71 4.1 84.5 1.0 OD1 C:ASP69 4.2 62.1 1.0 CB C:ASP98 4.3 68.9 1.0 OD2 C:ASP69 4.3 66.6 1.0 O3G C:GTP501 4.4 63.7 1.0 CB C:GLN11 4.5 64.3 1.0 CG C:ASP98 4.5 69.6 1.0 O2B C:GTP501 4.6 67.0 1.0 CD C:GLU71 4.6 82.8 1.0 N C:GLN11 4.7 56.6 1.0 CG C:ASP69 4.7 63.2 1.0 NE2 C:GLN11 4.7 73.9 1.0 CE D:LYS254 4.8 66.9 1.0 O1A C:GTP501 5.0 70.1 1.0 PA C:GTP501 5.0 58.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:91.4 occ:1.00 O D:HOH601 2.0 85.8 1.0 OE1 D:GLN11 2.4 91.9 1.0 O1A D:GDP501 2.5 100.6 1.0 CD D:GLN11 3.2 92.8 1.0 CB D:GLN11 3.6 93.2 1.0 PA D:GDP501 3.7 91.3 1.0 O2A D:GDP501 3.8 89.5 1.0 O1B D:GDP501 4.0 93.8 1.0 CG D:GLN11 4.0 93.7 1.0 NE2 D:GLN11 4.0 94.9 1.0 O3B D:GDP501 4.6 100.9 1.0 PB D:GDP501 4.6 94.7 1.0 O3A D:GDP501 4.6 93.4 1.0 OD1 D:ASN101 4.7 94.6 1.0 OE2 D:GLU71 4.9 129.4 1.0 O5' D:GDP501 4.9 91.2 1.0 CA D:GLN11 5.0 94.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:124.9 occ:1.00 O1B F:ACP401 2.5 134.5 1.0 O3G F:ACP401 2.7 131.4 1.0 OE2 F:GLU331 2.8 124.9 1.0 ND2 F:ASN333 3.3 123.0 1.0 O2B F:ACP401 3.5 138.2 1.0 PB F:ACP401 3.5 139.4 1.0 OE1 F:GLU331 3.6 125.8 1.0 CD F:GLU331 3.6 123.6 1.0 NZ F:LYS74 3.9 132.6 1.0 PG F:ACP401 4.1 139.2 1.0 C3B F:ACP401 4.4 136.5 1.0 CG F:ASN333 4.6 119.2 1.0 O1G F:ACP401 4.9 138.4 1.0 O3A F:ACP401 4.9 136.5 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