Magnesium in PDB 5s62: Tubulin-Z100642432-Complex

The structure of Tubulin-Z100642432-Complex, PDB code: 5s62 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)	63.60 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.48, 159.44, 179.83, 90, 90, 90
R / Rfree (%)	21.1 / 26.7

The structure of Tubulin-Z100642432-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	4 atoms
Bromine	(Br)	1 atom

The binding sites of Magnesium atom in the Tubulin-Z100642432-Complex (pdb code 5s62). 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-Z100642432-Complex, PDB code: 5s62:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:81.6 occ:1.00 O A:HOH602 1.9 71.4 1.0 O A:HOH603 2.0 72.2 1.0 O A:HOH604 2.1 67.9 1.0 O1G A:GTP501 2.1 65.0 1.0 O1B A:GTP501 2.5 71.6 1.0 OE1 A:GLU71 3.0 92.5 1.0 PG A:GTP501 3.4 70.7 1.0 NZ B:LYS254 3.4 79.6 1.0 PB A:GTP501 3.6 70.2 1.0 O3B A:GTP501 3.8 83.5 1.0 O2G A:GTP501 3.9 72.3 1.0 CD A:GLU71 4.2 94.2 1.0 CB A:ASP98 4.2 79.2 1.0 OD2 A:ASP98 4.3 83.6 1.0 O3A A:GTP501 4.3 68.7 1.0 OD1 A:ASP69 4.4 77.8 1.0 CB A:GLN11 4.4 72.5 1.0 CG A:ASP98 4.5 80.3 1.0 OD2 A:ASP69 4.6 76.8 1.0 O3G A:GTP501 4.6 68.6 1.0 CE B:LYS254 4.6 73.8 1.0 O1A A:GTP501 4.7 67.8 1.0 NE2 A:GLN11 4.8 83.7 1.0 OE2 A:GLU71 4.8 101.7 1.0 O2B A:GTP501 4.9 77.8 1.0 N A:GLN11 4.9 71.5 1.0 CG A:ASP69 4.9 78.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:74.8 occ:1.00 O B:HOH603 1.9 75.0 1.0 OE1 B:GLN11 1.9 77.3 1.0 O B:HOH607 2.1 80.9 1.0 O C:HOH615 2.2 74.9 1.0 O1A B:GDP501 2.2 76.3 1.0 O B:HOH619 2.3 69.7 1.0 CD B:GLN11 3.1 75.4 1.0 PA B:GDP501 3.7 66.0 1.0 OD2 B:ASP179 3.8 68.7 1.0 NE2 B:GLN11 3.9 78.3 1.0 CB B:GLN11 3.9 68.8 1.0 CG B:GLN11 4.1 70.5 1.0 OD1 B:ASN101 4.3 77.0 1.0 OE1 C:GLU254 4.4 86.3 1.0 O2A B:GDP501 4.4 57.9 1.0 O3A B:GDP501 4.5 76.7 1.0 ND2 B:ASN101 4.6 80.4 1.0 O3B B:GDP501 4.6 68.8 1.0 C5' B:GDP501 4.7 72.0 1.0 O5' B:GDP501 4.7 68.4 1.0 O1B B:GDP501 4.9 72.2 1.0 CG B:ASN101 4.9 72.1 1.0 PB B:GDP501 4.9 62.1 1.0 CG B:ASP179 4.9 70.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.5 occ:1.00 O C:HOH611 1.8 60.7 1.0 O1G C:GTP501 2.0 57.0 1.0 O C:HOH608 2.2 56.5 1.0 O C:HOH605 2.4 56.5 1.0 O1B C:GTP501 2.9 63.1 1.0 PG C:GTP501 3.4 69.9 1.0 OD2 C:ASP98 3.4 70.8 1.0 NZ D:LYS254 3.5 73.5 1.0 OE2 C:GLU71 3.6 76.2 1.0 CG C:GLU71 3.7 74.6 1.0 O2G C:GTP501 3.9 60.9 1.0 PB C:GTP501 3.9 64.9 1.0 CG C:ASP98 4.0 69.3 1.0 CB C:ASP98 4.0 66.0 1.0 O3B C:GTP501 4.1 75.4 1.0 CD C:GLU71 4.2 79.0 1.0 O3A C:GTP501 4.3 62.2 1.0 O3G C:GTP501 4.5 62.4 1.0 OD1 C:ASP69 4.5 63.8 1.0 OD2 C:ASP69 4.6 66.7 1.0 CE D:LYS254 4.6 69.5 1.0 OE1 C:GLN11 4.7 82.3 1.0 CB C:GLN11 4.7 71.4 1.0 OD1 C:ASP98 4.9 75.5 1.0 CG C:ASP69 5.0 63.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:104.4 occ:1.00 OE1 D:GLN11 2.0 103.9 1.0 O D:HOH603 2.4 93.1 1.0 O1A D:GDP501 2.6 109.2 1.0 CD D:GLN11 3.2 103.5 1.0 CB D:GLN11 3.9 105.4 1.0 PA D:GDP501 3.9 95.1 1.0 NE2 D:GLN11 4.1 109.8 1.0 CG D:GLN11 4.1 104.9 1.0 O2A D:GDP501 4.2 91.7 1.0 O1B D:GDP501 4.2 99.4 1.0 OD1 D:ASN101 4.3 116.7 1.0 O3B D:GDP501 4.7 106.3 1.0 PB D:GDP501 4.9 100.4 1.0 O3A D:GDP501 4.9 103.6 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:133.6 occ:1.00 O1B F:ACP401 2.6 153.0 1.0 OE2 F:GLU331 2.8 141.9 1.0 O3G F:ACP401 2.9 144.7 1.0 OD1 F:ASN333 3.5 136.8 1.0 OE1 F:GLU331 3.6 142.2 1.0 CD F:GLU331 3.6 139.9 1.0 PB F:ACP401 3.7 160.3 1.0 NZ F:LYS74 3.7 148.0 1.0 O2B F:ACP401 3.7 151.7 1.0 PG F:ACP401 4.4 161.4 1.0 CG F:ASN333 4.6 131.1 1.0 C3B F:ACP401 4.7 158.2 1.0 O3A F:ACP401 4.9 152.8 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