Magnesium in PDB 5s5c: Tubulin-Z44592329-Complex

The structure of Tubulin-Z44592329-Complex, PDB code: 5s5c 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)	67.93 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.22, 159.9, 177.91, 90, 90, 90
R / Rfree (%)	20.7 / 24.4

The structure of Tubulin-Z44592329-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z44592329-Complex (pdb code 5s5c). 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-Z44592329-Complex, PDB code: 5s5c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z44592329-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z44592329-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:53.2 occ:1.00 O A:HOH606 2.0 48.3 1.0 O A:HOH612 2.1 52.6 1.0 O A:HOH635 2.1 52.0 1.0 O1G A:GTP501 2.1 51.1 1.0 O A:HOH609 2.1 56.8 1.0 O1B A:GTP501 2.2 50.1 1.0 PG A:GTP501 3.3 51.5 1.0 PB A:GTP501 3.3 50.0 1.0 OE1 A:GLU71 3.6 68.6 1.0 O3B A:GTP501 3.7 58.8 1.0 O2G A:GTP501 3.8 49.8 1.0 NZ B:LYS254 3.8 63.3 1.0 O3A A:GTP501 3.9 54.6 1.0 CB A:GLN11 4.0 54.5 1.0 OD1 A:ASP69 4.0 61.2 1.0 OD2 A:ASP69 4.2 62.8 1.0 N A:GLN11 4.3 53.4 1.0 NE2 A:GLN11 4.4 61.6 1.0 CB A:ASP98 4.4 60.2 1.0 O1A A:GTP501 4.5 56.4 1.0 O3G A:GTP501 4.5 51.4 1.0 OD2 A:ASP98 4.6 69.8 1.0 CG A:ASP69 4.6 62.0 1.0 O2B A:GTP501 4.6 55.7 1.0 CG A:ASP98 4.7 60.9 1.0 PA A:GTP501 4.8 48.7 1.0 CA A:GLN11 4.8 56.9 1.0 CD A:GLU71 4.8 75.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z44592329-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z44592329-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.5 occ:1.00 O B:HOH622 2.1 51.6 1.0 OE1 B:GLN11 2.1 58.2 1.0 O C:HOH666 2.1 53.4 1.0 O B:HOH653 2.2 56.5 1.0 O1A B:GDP501 2.2 47.1 1.0 O B:HOH637 2.6 53.9 1.0 CD B:GLN11 3.3 56.6 1.0 PA B:GDP501 3.6 49.4 1.0 OD2 B:ASP179 4.0 55.7 1.0 CB B:GLN11 4.0 48.8 1.0 O C:HOH672 4.1 66.0 1.0 CG B:GLN11 4.1 51.7 1.0 O3A B:GDP501 4.1 51.8 1.0 OD1 B:ASN101 4.3 52.9 1.0 NE2 B:GLN11 4.3 63.4 1.0 O1B B:GDP501 4.4 48.9 1.0 C5' B:GDP501 4.5 53.1 1.0 OE1 C:GLU254 4.5 65.4 1.0 O5' B:GDP501 4.5 48.8 1.0 O2A B:GDP501 4.6 48.0 1.0 PB B:GDP501 4.9 50.6 1.0 C8 B:GDP501 4.9 53.5 1.0 CG B:ASP179 4.9 54.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z44592329-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z44592329-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:52.3 occ:1.00 O1G C:GTP501 2.0 47.1 1.0 O C:HOH707 2.0 48.8 1.0 O C:HOH649 2.1 44.0 1.0 O C:HOH652 2.2 49.2 1.0 O1B C:GTP501 2.2 42.5 1.0 O C:HOH612 2.3 49.1 1.0 PG C:GTP501 3.1 45.2 1.0 PB C:GTP501 3.2 46.7 1.0 O3B C:GTP501 3.5 56.2 1.0 O3A C:GTP501 3.7 54.1 1.0 O2G C:GTP501 3.7 48.6 1.0 NZ D:LYS254 3.8 55.9 1.0 OE2 C:GLU71 4.1 62.0 1.0 OD2 C:ASP98 4.1 56.5 1.0 OD1 C:ASP69 4.2 47.9 1.0 CB C:GLN11 4.2 48.1 1.0 CG C:GLU71 4.2 62.1 1.0 OD2 C:ASP69 4.4 50.0 1.0 O3G C:GTP501 4.4 43.5 1.0 N C:GLN11 4.5 45.3 1.0 CB C:ASP98 4.5 51.0 1.0 O2B C:GTP501 4.6 49.1 1.0 O1A C:GTP501 4.6 48.5 1.0 CD C:GLU71 4.7 62.2 1.0 OE1 C:GLN11 4.7 60.5 1.0 CG C:ASP98 4.7 53.2 1.0 CG C:ASP69 4.7 49.4 1.0 PA C:GTP501 4.7 43.7 1.0 CE D:LYS254 4.9 52.5 1.0 CA C:GLN11 4.9 53.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z44592329-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z44592329-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:76.5 occ:1.00 O D:HOH608 1.9 83.9 1.0 OE1 D:GLN11 2.0 84.2 1.0 O1A D:GDP501 2.3 89.5 1.0 CD D:GLN11 3.2 83.0 1.0 PA D:GDP501 3.8 77.6 1.0 CB D:GLN11 4.0 77.7 1.0 NE2 D:GLN11 4.1 83.6 1.0 CG D:GLN11 4.2 80.4 1.0 O D:HOH618 4.2 79.6 1.0 O2A D:GDP501 4.2 71.2 1.0 O1B D:GDP501 4.5 70.4 1.0 C5' D:GDP501 4.5 78.3 1.0 O5' D:GDP501 4.7 78.0 1.0 OD1 D:ASN101 4.7 87.9 1.0 O3A D:GDP501 4.8 82.4 1.0 C8 D:GDP501 4.9 70.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z44592329-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z44592329-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:95.9 occ:1.00 O3G F:ACP401 2.3 109.9 1.0 OE2 F:GLU331 2.4 111.2 1.0 O1B F:ACP401 2.6 115.2 1.0 OD1 F:ASN333 2.8 99.5 1.0 CD F:GLU331 3.3 112.5 1.0 OE1 F:GLU331 3.4 119.0 1.0 PB F:ACP401 3.7 113.8 1.0 PG F:ACP401 3.8 122.3 1.0 CG F:ASN333 3.9 93.5 1.0 O2B F:ACP401 4.0 120.0 1.0 NZ F:LYS74 4.2 117.1 1.0 ND2 F:ASN333 4.3 95.7 1.0 C3B F:ACP401 4.5 117.2 1.0 O1G F:ACP401 4.6 116.0 1.0 CG F:GLU331 4.7 102.7 1.0 O2G F:ACP401 4.7 109.1 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