Magnesium in PDB 5s5m: Tubulin-Z45527714-Complex

The structure of Tubulin-Z45527714-Complex, PDB code: 5s5m 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)	55.92 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.66, 159.8, 179.1, 90, 90, 90
R / Rfree (%)	21.5 / 26.9

The structure of Tubulin-Z45527714-Complex also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z45527714-Complex (pdb code 5s5m). 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-Z45527714-Complex, PDB code: 5s5m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:71.6 occ:1.00 O1G A:GTP501 1.9 70.2 1.0 O A:HOH604 1.9 75.1 1.0 O A:HOH606 2.0 72.3 1.0 O A:HOH603 2.2 66.0 1.0 O1B A:GTP501 2.5 70.3 1.0 PG A:GTP501 3.2 72.9 1.0 OE1 A:GLU71 3.4 84.3 1.0 PB A:GTP501 3.5 68.4 1.0 NZ B:LYS254 3.5 78.0 1.0 O3B A:GTP501 3.7 79.3 1.0 O2G A:GTP501 3.8 71.4 1.0 O3A A:GTP501 3.9 73.8 1.0 CB A:GLN11 4.2 78.4 1.0 CB A:ASP98 4.3 74.8 1.0 O3G A:GTP501 4.4 72.6 1.0 OD1 A:ASP69 4.4 71.3 1.0 NE2 A:GLN11 4.5 92.0 1.0 O1A A:GTP501 4.6 75.7 1.0 CD A:GLU71 4.6 95.9 1.0 N A:GLN11 4.7 71.7 1.0 OD2 A:ASP69 4.7 80.0 1.0 CE B:LYS254 4.8 75.2 1.0 CG A:ASP98 4.8 79.4 1.0 PA A:GTP501 4.8 70.4 1.0 O2B A:GTP501 4.9 77.1 1.0 OD2 A:ASP98 4.9 83.1 1.0 CG A:ASP69 5.0 74.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:63.7 occ:1.00 OE1 B:GLN11 2.0 75.2 1.0 O C:HOH609 2.0 64.7 1.0 O B:HOH605 2.0 58.6 1.0 O1A B:GDP501 2.6 64.3 1.0 O B:HOH618 2.7 63.7 1.0 CD B:GLN11 2.9 72.7 1.0 OD2 B:ASP179 3.5 74.6 1.0 NE2 B:GLN11 3.6 80.8 1.0 CG B:GLN11 4.0 71.1 1.0 PA B:GDP501 4.1 59.5 1.0 CB B:GLN11 4.1 66.7 1.0 OE1 C:GLU254 4.4 73.9 1.0 CG B:ASP179 4.6 66.2 1.0 O3A B:GDP501 4.7 55.7 1.0 O2A B:GDP501 4.8 62.1 1.0 O3B B:GDP501 4.8 63.2 1.0 C8 B:GDP501 4.8 66.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:70.9 occ:1.00 O1G C:GTP501 1.8 63.1 1.0 O C:HOH611 1.9 68.6 1.0 O C:HOH603 2.0 65.3 1.0 O C:HOH620 2.1 73.9 1.0 O1B C:GTP501 2.3 66.4 1.0 O C:HOH602 2.5 67.5 1.0 PG C:GTP501 2.8 68.0 1.0 PB C:GTP501 3.2 63.2 1.0 O2G C:GTP501 3.2 67.4 1.0 O3B C:GTP501 3.3 70.7 1.0 OD2 C:ASP98 3.5 75.0 1.0 NZ D:LYS254 3.6 77.8 1.0 O3A C:GTP501 3.7 66.8 1.0 CB C:ASP98 3.9 67.2 1.0 O3G C:GTP501 4.1 70.0 1.0 CG C:ASP98 4.2 72.0 1.0 OD1 C:ASP69 4.2 65.9 1.0 CG C:GLU71 4.3 76.2 1.0 OE2 C:GLU71 4.5 80.1 1.0 O2B C:GTP501 4.6 67.0 1.0 CE D:LYS254 4.6 71.8 1.0 OD2 C:ASP69 4.7 79.4 1.0 CB C:GLN11 4.8 73.6 1.0 OG1 C:THR145 4.9 67.1 1.0 CG C:ASP69 4.9 69.6 1.0 PA C:GTP501 4.9 64.2 1.0 N C:GLN11 4.9 62.1 1.0 CD C:GLU71 5.0 79.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:95.7 occ:1.00 OE1 D:GLN11 2.1 106.0 1.0 O D:HOH602 2.2 83.8 1.0 O1A D:GDP501 2.8 109.8 1.0 CD D:GLN11 3.3 105.0 1.0 CB D:GLN11 3.6 109.9 1.0 O1B D:GDP501 3.9 97.9 1.0 PA D:GDP501 4.0 99.9 1.0 O2A D:GDP501 4.0 90.6 1.0 CG D:GLN11 4.1 110.8 1.0 NE2 D:GLN11 4.3 108.5 1.0 O3B D:GDP501 4.3 101.5 1.0 OD1 D:ASN101 4.5 100.6 1.0 PB D:GDP501 4.6 102.7 1.0 O3A D:GDP501 4.8 110.2 1.0 OE2 D:GLU71 4.9 143.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z45527714-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z45527714-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:135.2 occ:1.00 OE2 F:GLU331 2.5 149.5 1.0 O1B F:ACP401 2.5 150.9 1.0 O3G F:ACP401 2.6 148.0 1.0 OD1 F:ASN333 3.2 137.2 1.0 CD F:GLU331 3.3 147.2 1.0 OE1 F:GLU331 3.4 148.9 1.0 PB F:ACP401 3.6 152.4 1.0 O2B F:ACP401 3.6 154.1 1.0 NZ F:LYS74 3.8 140.2 1.0 PG F:ACP401 4.1 158.2 1.0 CG F:ASN333 4.4 132.1 1.0 C3B F:ACP401 4.6 149.4 1.0 CG F:GLU331 4.7 139.6 1.0 O1G F:ACP401 4.9 156.8 1.0 O3A F:ACP401 4.9 149.4 1.0 ND2 F:ASN333 5.0 131.0 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