Magnesium in PDB 5s5h: Tubulin-Z2074076908-Complex

The structure of Tubulin-Z2074076908-Complex, PDB code: 5s5h 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)	90.54 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.91, 158.89, 179.24, 90, 90, 90
R / Rfree (%)	21.6 / 27

The structure of Tubulin-Z2074076908-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Tubulin-Z2074076908-Complex (pdb code 5s5h). 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-Z2074076908-Complex, PDB code: 5s5h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:76.3 occ:1.00 O A:HOH614 1.9 75.1 1.0 O1G A:GTP501 2.0 63.6 1.0 O A:HOH602 2.0 67.9 1.0 O A:HOH609 2.1 74.0 1.0 O1B A:GTP501 2.1 68.8 1.0 PB A:GTP501 3.2 67.7 1.0 PG A:GTP501 3.3 65.5 1.0 O3B A:GTP501 3.6 77.2 1.0 OE1 A:GLU71 3.7 92.7 1.0 NZ B:LYS254 3.7 83.0 1.0 O3A A:GTP501 3.8 72.4 1.0 CB A:GLN11 3.9 71.0 1.0 NE2 A:GLN11 4.0 82.7 1.0 O2G A:GTP501 4.0 68.5 1.0 OD1 A:ASP69 4.2 73.2 1.0 OD2 A:ASP69 4.3 78.4 1.0 O1A A:GTP501 4.4 69.8 1.0 O3G A:GTP501 4.4 62.0 1.0 N A:GLN11 4.4 67.8 1.0 O2B A:GTP501 4.5 75.7 1.0 CB A:ASP98 4.6 71.8 1.0 PA A:GTP501 4.6 67.7 1.0 CG A:ASP69 4.7 77.0 1.0 CA A:GLN11 4.8 72.2 1.0 OD2 A:ASP98 4.8 89.4 1.0 CG A:ASP98 4.9 76.6 1.0 CE B:LYS254 4.9 72.3 1.0 CD A:GLU71 4.9 100.4 1.0 CD A:GLN11 4.9 79.7 1.0 O2A A:GTP501 5.0 68.1 1.0 CG A:GLN11 5.0 76.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:58.4 occ:1.00 O B:HOH626 1.8 66.5 1.0 OE1 B:GLN11 1.8 72.1 1.0 O B:HOH604 2.2 55.8 1.0 O1A B:GDP501 2.5 62.5 1.0 O C:HOH651 2.6 56.5 1.0 CD B:GLN11 2.8 70.7 1.0 O B:HOH616 2.8 58.2 1.0 NE2 B:GLN11 3.4 78.1 1.0 OD2 B:ASP179 3.4 65.7 1.0 O C:HOH607 3.8 65.5 1.0 CG B:GLN11 3.9 65.5 1.0 PA B:GDP501 4.0 53.1 1.0 CB B:GLN11 4.0 62.5 1.0 O3A B:GDP501 4.5 55.5 1.0 CG B:ASP179 4.6 64.9 1.0 C5' B:GDP501 4.6 64.0 1.0 C8 B:GDP501 4.7 61.8 1.0 OE1 C:GLU254 4.7 65.1 1.0 O5' B:GDP501 4.8 57.5 1.0 O2A B:GDP501 4.9 55.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:70.0 occ:1.00 O C:HOH625 1.9 65.4 1.0 O C:HOH635 2.0 61.7 1.0 O1G C:GTP501 2.0 61.5 1.0 O C:HOH617 2.1 63.2 1.0 O C:HOH612 2.2 61.2 1.0 O1B C:GTP501 2.3 61.0 1.0 PG C:GTP501 3.3 63.6 1.0 PB C:GTP501 3.5 61.7 1.0 O2G C:GTP501 3.7 58.1 1.0 OD2 C:ASP98 3.8 64.0 1.0 O3B C:GTP501 3.8 66.8 1.0 CG C:GLU71 3.8 80.5 1.0 OE2 C:GLU71 3.8 80.7 1.0 NZ D:LYS254 3.9 66.2 1.0 O3A C:GTP501 4.0 64.1 1.0 OD1 C:ASP69 4.2 63.4 1.0 OD2 C:ASP69 4.2 65.5 1.0 CD C:GLU71 4.3 80.2 1.0 CB C:ASP98 4.3 63.4 1.0 CB C:GLN11 4.4 59.0 1.0 CG C:ASP98 4.4 63.1 1.0 O3G C:GTP501 4.5 60.1 1.0 N C:GLN11 4.6 60.1 1.0 CG C:ASP69 4.7 65.8 1.0 OE1 C:GLN11 4.7 76.1 1.0 O2B C:GTP501 4.7 64.1 1.0 O1A C:GTP501 4.9 68.0 1.0 CE D:LYS254 5.0 65.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:89.7 occ:1.00 OE1 D:GLN11 2.2 94.7 1.0 O D:HOH605 2.4 83.7 1.0 O1A D:GDP501 2.4 102.3 1.0 CD D:GLN11 3.4 93.8 1.0 PA D:GDP501 3.7 90.4 1.0 O2A D:GDP501 3.9 83.2 1.0 CB D:GLN11 3.9 98.0 1.0 OD1 D:ASN101 4.1 97.2 1.0 O3B D:GDP501 4.1 102.1 1.0 CG D:GLN11 4.3 97.2 1.0 NE2 D:GLN11 4.3 103.7 1.0 O1B D:GDP501 4.3 89.2 1.0 PB D:GDP501 4.6 94.0 1.0 O3A D:GDP501 4.7 94.2 1.0 O5' D:GDP501 4.9 90.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2074076908-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2074076908-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:123.3 occ:1.00 OE2 F:GLU331 2.3 138.0 1.0 O1B F:ACP401 2.3 142.1 1.0 O3G F:ACP401 2.6 134.9 1.0 CD F:GLU331 3.1 139.4 1.0 OD1 F:ASN333 3.1 124.4 1.0 OE1 F:GLU331 3.1 144.4 1.0 PB F:ACP401 3.6 141.9 1.0 NZ F:LYS74 3.7 138.4 1.0 O2B F:ACP401 3.9 135.8 1.0 PG F:ACP401 4.0 141.9 1.0 CG F:ASN333 4.2 118.9 1.0 C3B F:ACP401 4.5 139.5 1.0 CG F:GLU331 4.5 132.4 1.0 O1G F:ACP401 4.6 136.8 1.0 O1A F:ACP401 4.8 136.1 1.0 O3A F:ACP401 4.8 139.8 1.0 ND2 F:ASN333 4.8 113.8 1.0 CE F:LYS74 4.9 138.8 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