Magnesium in PDB 5s52: Tubulin-Z50145861-Complex

The structure of Tubulin-Z50145861-Complex, PDB code: 5s52 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)	118.67 / 2.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.09, 161.57, 174.88, 90, 90, 90
R / Rfree (%)	23.8 / 29.7

The structure of Tubulin-Z50145861-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z50145861-Complex (pdb code 5s52). 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-Z50145861-Complex, PDB code: 5s52:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:73.0 occ:1.00 O A:HOH607 2.0 116.5 1.0 O A:HOH602 2.0 74.5 1.0 O1G A:GTP501 2.1 72.3 1.0 O A:HOH603 2.1 69.9 1.0 O1B A:GTP501 2.2 67.6 1.0 O2G A:GTP501 2.6 69.5 1.0 PG A:GTP501 2.7 64.7 1.0 NZ B:LYS254 2.9 77.2 1.0 OE1 A:GLU71 3.2 97.8 1.0 PB A:GTP501 3.2 65.8 1.0 O3B A:GTP501 3.3 75.8 1.0 O3A A:GTP501 3.6 77.3 1.0 CB A:ASP98 4.0 72.2 1.0 O3G A:GTP501 4.1 64.9 1.0 CE B:LYS254 4.2 76.2 1.0 OD2 A:ASP98 4.2 83.4 1.0 CG A:ASP98 4.3 74.3 1.0 CD A:GLU71 4.3 99.4 1.0 OD1 A:ASP69 4.5 75.3 1.0 O2B A:GTP501 4.5 65.5 1.0 O1A A:GTP501 4.8 59.3 1.0 CB A:GLN11 4.8 68.3 1.0 PA A:GTP501 4.8 60.3 1.0 OD2 A:ASP69 4.8 72.2 1.0 NE2 A:GLN11 4.9 88.0 1.0 N A:GLN11 4.9 63.0 1.0 OE2 A:GLU71 5.0 106.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:53.8 occ:1.00 O C:HOH613 2.0 66.6 1.0 O1A B:GDP501 2.3 64.5 1.0 O B:HOH601 2.4 61.4 1.0 OE1 B:GLN11 2.4 70.9 1.0 O B:HOH610 2.5 61.6 1.0 OD2 B:ASP179 3.2 74.6 1.0 CD B:GLN11 3.6 69.4 1.0 PA B:GDP501 3.7 53.0 1.0 OD1 B:ASN101 3.7 56.4 1.0 O2A B:GDP501 4.1 55.3 1.0 C5' B:GDP501 4.3 54.1 1.0 CG B:ASP179 4.3 75.2 1.0 CB B:GLN11 4.4 60.7 1.0 NE2 B:GLN11 4.5 77.3 1.0 O5' B:GDP501 4.5 56.1 1.0 OE2 C:GLU254 4.5 73.0 1.0 OE1 C:GLU254 4.5 70.1 1.0 O1B B:GDP501 4.6 63.9 1.0 CG B:GLN11 4.6 63.1 1.0 CG B:ASN101 4.8 58.9 1.0 O B:HOH632 4.8 67.2 1.0 O3B B:GDP501 4.8 49.0 1.0 CD C:GLU254 4.8 70.2 1.0 O3A B:GDP501 4.9 61.2 1.0 CB B:ASP179 4.9 75.6 1.0 C8 B:GDP501 5.0 55.0 1.0 ND2 B:ASN101 5.0 64.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:58.9 occ:1.00 O1B C:GTP501 2.3 64.5 1.0 O C:HOH618 2.4 58.2 1.0 O1G C:GTP501 2.4 63.0 1.0 O2G C:GTP501 2.5 62.0 1.0 O C:HOH610 2.6 53.4 1.0 PG C:GTP501 2.6 57.0 1.0 O3B C:GTP501 2.9 68.2 1.0 PB C:GTP501 3.2 50.7 1.0 OD1 C:ASP69 3.4 62.9 1.0 CB C:ASP98 3.5 69.7 1.0 OG1 C:THR145 3.8 55.4 1.0 O3G C:GTP501 4.1 53.9 1.0 O3A C:GTP501 4.2 60.2 1.0 CG C:GLU71 4.2 66.3 1.0 CG C:ASP69 4.3 63.5 1.0 CB C:THR145 4.3 53.4 1.0 O2B C:GTP501 4.3 59.2 1.0 OD2 C:ASP69 4.3 69.3 1.0 CG C:ASP98 4.3 75.7 1.0 NZ D:LYS254 4.4 63.9 1.0 OD2 C:ASP98 4.6 86.0 1.0 CA C:ASP98 4.6 67.4 1.0 N C:ALA99 4.8 68.3 1.0 N C:GLN11 4.8 55.0 1.0 N C:GLU71 4.9 66.9 1.0 CB C:GLU71 5.0 69.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:83.7 occ:1.00 OE1 D:GLN11 2.3 109.8 1.0 O1A D:GDP501 2.5 105.1 1.0 CD D:GLN11 3.4 108.6 1.0 PA D:GDP501 3.9 87.0 1.0 O2A D:GDP501 4.1 86.0 1.0 CB D:GLN11 4.2 100.6 1.0 NE2 D:GLN11 4.3 112.1 1.0 OD1 D:ASN101 4.4 92.6 1.0 CG D:GLN11 4.4 103.5 1.0 C5' D:GDP501 4.6 85.0 1.0 O5' D:GDP501 4.8 79.4 1.0 O1B D:GDP501 4.8 85.6 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z50145861-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z50145861-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:123.6 occ:1.00 OE2 F:GLU331 2.5 125.8 1.0 O1B F:ACP401 2.7 129.0 1.0 O3G F:ACP401 2.7 132.3 1.0 CD F:GLU331 3.4 123.5 1.0 OE1 F:GLU331 3.5 126.4 1.0 OD1 F:ASN333 3.5 125.7 1.0 PB F:ACP401 3.8 133.2 1.0 O2B F:ACP401 3.8 133.3 1.0 NZ F:LYS74 3.9 129.0 1.0 PG F:ACP401 4.2 131.0 1.0 CG F:ASN333 4.2 126.8 1.0 ND2 F:ASN333 4.3 122.8 1.0 O1G F:ACP401 4.6 129.8 1.0 C3B F:ACP401 4.7 130.2 1.0 CG F:GLU331 4.8 114.5 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