Magnesium in PDB 5s5v: Tubulin-Z32386228-Complex

The structure of Tubulin-Z32386228-Complex, PDB code: 5s5v 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)	72.87 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.23, 159.54, 179.08, 90, 90, 90
R / Rfree (%)	21.7 / 26.7

The structure of Tubulin-Z32386228-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Tubulin-Z32386228-Complex (pdb code 5s5v). 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-Z32386228-Complex, PDB code: 5s5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:77.2 occ:1.00 O1G A:GTP501 1.9 67.9 1.0 O A:HOH603 1.9 74.0 1.0 O A:HOH604 2.2 68.4 1.0 O1B A:GTP501 2.4 70.7 1.0 O A:HOH601 2.4 73.2 1.0 PG A:GTP501 3.1 76.1 1.0 PB A:GTP501 3.5 75.0 1.0 NZ B:LYS254 3.5 79.4 1.0 OE1 A:GLU71 3.5 90.5 1.0 O3B A:GTP501 3.7 76.6 1.0 O2G A:GTP501 3.7 72.9 1.0 O3A A:GTP501 4.1 70.9 1.0 CB A:ASP98 4.1 77.0 1.0 OD2 A:ASP98 4.3 87.7 1.0 O3G A:GTP501 4.3 73.6 1.0 CB A:GLN11 4.3 73.9 1.0 OD1 A:ASP69 4.4 77.4 1.0 NE2 A:GLN11 4.4 84.2 1.0 CG A:ASP98 4.4 77.8 1.0 CD A:GLU71 4.6 96.3 1.0 CE B:LYS254 4.6 77.6 1.0 O1A A:GTP501 4.7 71.3 1.0 OD2 A:ASP69 4.7 83.8 1.0 N A:GLN11 4.7 72.4 1.0 O2B A:GTP501 4.8 75.8 1.0 PA A:GTP501 5.0 77.0 1.0 CG A:ASP69 5.0 79.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:65.3 occ:1.00 O B:HOH601 1.9 71.4 1.0 OE1 B:GLN11 1.9 68.2 1.0 O B:HOH603 1.9 65.6 1.0 O C:HOH617 1.9 62.6 1.0 O B:HOH627 2.3 67.5 1.0 O1A B:GDP501 2.8 67.2 1.0 CD B:GLN11 3.1 67.3 1.0 NE2 B:GLN11 3.9 69.5 1.0 CB B:GLN11 4.1 64.8 1.0 CG B:GLN11 4.2 68.2 1.0 PA B:GDP501 4.2 69.1 1.0 OD2 B:ASP179 4.2 66.7 1.0 OE1 C:GLU254 4.2 66.6 1.0 O C:HOH611 4.4 64.1 1.0 O3B B:GDP501 4.5 60.2 1.0 ND2 B:ASN101 4.6 62.1 1.0 OD1 B:ASN101 4.7 70.1 1.0 O3A B:GDP501 4.7 63.2 1.0 O C:HOH664 4.8 70.3 1.0 OE2 B:GLU71 4.9 83.3 1.0 O2A B:GDP501 4.9 60.0 1.0 OE2 C:GLU254 4.9 65.0 1.0 CD C:GLU254 5.0 66.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:69.9 occ:1.00 O C:HOH630 1.9 65.2 1.0 O C:HOH626 1.9 66.8 1.0 O C:HOH613 2.0 65.6 1.0 O1G C:GTP501 2.0 62.7 1.0 O1B C:GTP501 2.1 62.7 1.0 O C:HOH610 2.2 65.4 1.0 PG C:GTP501 3.2 68.8 1.0 PB C:GTP501 3.3 70.5 1.0 O3B C:GTP501 3.6 66.4 1.0 O2G C:GTP501 3.7 64.7 1.0 OD2 C:ASP98 3.8 70.4 1.0 NZ D:LYS254 3.8 67.7 1.0 CG C:GLU71 3.9 73.0 1.0 OE2 C:GLU71 4.0 77.8 1.0 O3A C:GTP501 4.1 62.0 1.0 OD1 C:ASP69 4.1 68.1 1.0 CB C:ASP98 4.1 67.2 1.0 OD2 C:ASP69 4.3 68.5 1.0 CG C:ASP98 4.4 70.5 1.0 CD C:GLU71 4.4 74.1 1.0 O3G C:GTP501 4.5 69.4 1.0 O2B C:GTP501 4.5 63.3 1.0 CB C:GLN11 4.6 67.3 1.0 CG C:ASP69 4.6 67.8 1.0 N C:GLN11 4.7 62.6 1.0 NE2 C:GLN11 4.9 74.7 1.0 CE D:LYS254 4.9 64.9 1.0 OG1 C:THR145 5.0 63.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:94.5 occ:1.00 O D:HOH1102 1.9 98.4 1.0 OE1 D:GLN11 1.9 101.1 1.0 O1A D:GDP501 2.6 104.7 1.0 CD D:GLN11 3.1 101.3 1.0 CB D:GLN11 3.9 103.8 1.0 PA D:GDP501 3.9 97.4 1.0 NE2 D:GLN11 4.0 111.0 1.0 CG D:GLN11 4.1 104.6 1.0 O2A D:GDP501 4.1 93.9 1.0 O3B D:GDP501 4.7 102.4 1.0 OD1 D:ASN101 4.8 95.7 1.0 O1B D:GDP501 4.8 95.9 1.0 C5' D:GDP501 4.9 98.7 1.0 O3A D:GDP501 5.0 101.2 1.0 O5' D:GDP501 5.0 98.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z32386228-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z32386228-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:121.4 occ:1.00 O3G F:ACP401 2.1 133.8 1.0 O1B F:ACP401 2.4 139.1 1.0 OE2 F:GLU331 2.6 134.5 1.0 OD1 F:ASN333 2.9 119.1 1.0 PB F:ACP401 3.4 143.4 1.0 O2B F:ACP401 3.6 143.7 1.0 PG F:ACP401 3.6 139.3 1.0 CD F:GLU331 3.6 136.0 1.0 OE1 F:GLU331 3.9 141.0 1.0 CG F:ASN333 4.1 113.8 1.0 C3B F:ACP401 4.2 140.7 1.0 NZ F:LYS74 4.4 139.1 1.0 O1G F:ACP401 4.4 138.9 1.0 O2G F:ACP401 4.6 128.1 1.0 ND2 F:ASN333 4.7 117.7 1.0 O3A F:ACP401 4.8 140.3 1.0 CG F:GLU331 5.0 130.7 1.0 O1A F:ACP401 5.0 138.3 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