Magnesium in PDB 5s5p: Tubulin-Z53825177-Complex

The structure of Tubulin-Z53825177-Complex, PDB code: 5s5p 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)	80.32 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.71, 160.63, 179.04, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Tubulin-Z53825177-Complex also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Tubulin-Z53825177-Complex (pdb code 5s5p). 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-Z53825177-Complex, PDB code: 5s5p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:86.5 occ:1.00 O A:HOH602 1.9 82.1 1.0 O1G A:GTP501 2.0 78.3 1.0 O A:HOH601 2.0 83.8 1.0 O A:HOH603 2.1 79.1 1.0 O1B A:GTP501 2.2 79.5 1.0 PG A:GTP501 3.2 78.5 1.0 PB A:GTP501 3.3 79.4 1.0 OE1 A:GLU71 3.3 96.9 1.0 O3B A:GTP501 3.5 94.3 1.0 O2G A:GTP501 3.7 76.3 1.0 NZ B:LYS254 3.9 84.0 1.0 CB A:GLN11 3.9 81.9 1.0 O3A A:GTP501 4.0 85.9 1.0 OD1 A:ASP69 4.1 85.4 1.0 N A:GLN11 4.3 83.5 1.0 OD2 A:ASP69 4.3 85.5 1.0 CB A:ASP98 4.4 85.0 1.0 O3G A:GTP501 4.4 80.2 1.0 NE2 A:GLN11 4.5 89.0 1.0 CD A:GLU71 4.6 107.8 1.0 O1A A:GTP501 4.6 78.9 1.0 O2B A:GTP501 4.6 81.5 1.0 CG A:ASP69 4.7 87.3 1.0 CA A:GLN11 4.7 82.3 1.0 CG A:ASP98 4.7 85.5 1.0 OD2 A:ASP98 4.8 90.2 1.0 PA A:GTP501 4.8 81.9 1.0 CE B:LYS254 4.9 89.1 1.0 CB A:GLU71 5.0 92.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:73.7 occ:1.00 OE1 B:GLN11 1.8 80.7 1.0 O B:HOH601 1.9 79.2 1.0 O C:HOH613 2.2 68.8 1.0 O B:HOH611 2.2 72.4 1.0 O B:HOH613 2.3 75.8 1.0 O1A B:GDP501 2.6 80.9 1.0 CD B:GLN11 3.0 80.0 1.0 CB B:GLN11 3.8 73.6 1.0 NE2 B:GLN11 3.9 83.7 1.0 CG B:GLN11 4.0 78.6 1.0 PA B:GDP501 4.0 69.7 1.0 O1B B:GDP501 4.1 71.6 1.0 OD2 B:ASP179 4.3 76.3 1.0 O2A B:GDP501 4.4 69.8 1.0 ND2 B:ASN101 4.5 73.0 1.0 OE1 C:GLU254 4.6 75.3 1.0 OD1 B:ASN101 4.7 77.6 1.0 PB B:GDP501 4.9 67.3 1.0 O3A B:GDP501 5.0 76.4 1.0 O3B B:GDP501 5.0 72.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:76.3 occ:1.00 O1G C:GTP501 1.8 72.9 1.0 O C:HOH618 1.8 80.0 1.0 O C:HOH602 2.2 72.1 1.0 O1B C:GTP501 2.4 78.0 1.0 O C:HOH601 2.6 71.3 1.0 OE2 C:GLU71 3.2 83.9 1.0 NZ D:LYS254 3.2 81.8 1.0 PG C:GTP501 3.2 65.0 1.0 OD2 C:ASP98 3.4 77.5 1.0 PB C:GTP501 3.5 75.6 1.0 O3B C:GTP501 3.8 81.7 1.0 O2G C:GTP501 4.0 70.1 1.0 O3A C:GTP501 4.0 74.0 1.0 CD C:GLU71 4.1 86.5 1.0 CG C:GLU71 4.1 85.6 1.0 CB C:ASP98 4.1 73.4 1.0 CG C:ASP98 4.2 78.8 1.0 O3G C:GTP501 4.3 75.0 1.0 CE D:LYS254 4.3 74.3 1.0 OD2 C:ASP69 4.6 80.0 1.0 OE1 C:GLN11 4.6 86.5 1.0 OD1 C:ASP69 4.7 75.7 1.0 CB C:GLN11 4.7 76.5 1.0 O2B C:GTP501 4.8 74.2 1.0 O1A C:GTP501 4.8 80.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:96.2 occ:1.00 OE1 D:GLN11 2.3 110.2 1.0 O1A D:GDP501 2.6 116.0 1.0 CD D:GLN11 3.5 109.0 1.0 PA D:GDP501 3.7 110.1 1.0 O2A D:GDP501 3.8 101.0 1.0 NE2 D:GLN11 4.2 111.5 1.0 CB D:GLN11 4.3 112.2 1.0 OD1 D:ASN101 4.4 111.8 1.0 C5' D:GDP501 4.4 106.1 1.0 CG D:GLN11 4.5 110.0 1.0 O5' D:GDP501 4.6 108.2 1.0 C8 D:GDP501 4.8 107.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z53825177-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z53825177-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:140.7 occ:1.00 OE2 F:GLU331 2.1 150.3 1.0 O3G F:ACP401 2.3 152.6 1.0 OD1 F:ASN333 2.4 140.0 1.0 O1B F:ACP401 2.8 156.4 1.0 CD F:GLU331 3.1 152.6 1.0 OE1 F:GLU331 3.4 156.6 1.0 CG F:ASN333 3.6 137.5 1.0 PG F:ACP401 3.8 158.0 1.0 PB F:ACP401 4.0 158.9 1.0 NZ F:LYS74 4.1 151.4 1.0 ND2 F:ASN333 4.2 135.7 1.0 O2B F:ACP401 4.4 153.8 1.0 CG F:GLU331 4.4 144.8 1.0 O1G F:ACP401 4.5 154.5 1.0 C3B F:ACP401 4.7 156.8 1.0 CB F:ASN333 4.8 131.9 1.0 O2G F:ACP401 4.8 149.0 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