Magnesium in PDB 5s5i: Tubulin-Z295848548-Complex

The structure of Tubulin-Z295848548-Complex, PDB code: 5s5i 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)	62.66 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.89, 158.87, 179.47, 90, 90, 90
R / Rfree (%)	21.2 / 25.9

The structure of Tubulin-Z295848548-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z295848548-Complex (pdb code 5s5i). 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-Z295848548-Complex, PDB code: 5s5i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.4 occ:1.00 O1G A:GTP501 2.0 55.0 1.0 O A:HOH612 2.0 68.6 1.0 O A:HOH625 2.1 57.3 1.0 O A:HOH609 2.2 66.2 1.0 O A:HOH607 2.3 57.9 1.0 O1B A:GTP501 2.3 57.0 1.0 PG A:GTP501 3.2 57.3 1.0 PB A:GTP501 3.3 53.2 1.0 O3B A:GTP501 3.5 65.4 1.0 OE1 A:GLU71 3.7 72.5 1.0 O2G A:GTP501 3.8 56.4 1.0 NZ B:LYS254 3.8 74.2 1.0 O3A A:GTP501 3.9 61.5 1.0 CB A:GLN11 4.0 63.3 1.0 NE2 A:GLN11 4.0 73.8 1.0 OD1 A:ASP69 4.3 59.9 1.0 O1A A:GTP501 4.3 56.3 1.0 O3G A:GTP501 4.4 56.5 1.0 CB A:ASP98 4.4 67.8 1.0 N A:GLN11 4.5 56.6 1.0 OD2 A:ASP69 4.5 72.3 1.0 OD2 A:ASP98 4.6 75.6 1.0 O2B A:GTP501 4.6 58.0 1.0 PA A:GTP501 4.7 57.2 1.0 CG A:ASP98 4.8 65.5 1.0 CE B:LYS254 4.8 66.0 1.0 CG A:ASP69 4.8 65.1 1.0 CA A:GLN11 4.8 60.7 1.0 CD A:GLU71 4.9 79.0 1.0 CD A:GLN11 5.0 69.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:53.4 occ:1.00 OE1 B:GLN11 1.9 68.7 1.0 O B:HOH633 1.9 58.0 1.0 O C:HOH641 2.1 50.6 1.0 O1A B:GDP501 2.2 56.0 1.0 O B:HOH647 2.7 52.5 1.0 CD B:GLN11 3.1 67.2 1.0 PA B:GDP501 3.7 49.7 1.0 OD2 B:ASP179 3.8 58.9 1.0 CB B:GLN11 3.8 59.7 1.0 NE2 B:GLN11 3.9 72.8 1.0 CG B:GLN11 4.0 62.4 1.0 O3A B:GDP501 4.2 56.5 1.0 O C:HOH624 4.2 55.5 1.0 OD1 B:ASN101 4.4 54.2 1.0 OE1 C:GLU254 4.5 62.4 1.0 O1B B:GDP501 4.5 51.0 1.0 C5' B:GDP501 4.5 54.5 1.0 O5' B:GDP501 4.6 50.7 1.0 O2A B:GDP501 4.6 47.9 1.0 CG B:ASP179 4.8 60.9 1.0 C8 B:GDP501 4.9 57.0 1.0 PB B:GDP501 4.9 48.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:57.4 occ:1.00 O C:HOH666 1.9 53.8 1.0 O C:HOH646 2.0 56.4 1.0 O C:HOH611 2.0 52.0 1.0 O1G C:GTP501 2.2 51.0 1.0 O1B C:GTP501 2.2 51.3 1.0 O C:HOH635 2.4 52.4 1.0 PB C:GTP501 3.4 51.0 1.0 PG C:GTP501 3.5 56.4 1.0 OE2 C:GLU71 3.6 68.2 1.0 NZ D:LYS254 3.8 54.8 1.0 O3B C:GTP501 3.9 54.1 1.0 O3A C:GTP501 3.9 58.2 1.0 CG C:GLU71 3.9 64.3 1.0 O2G C:GTP501 4.0 49.5 1.0 OD1 C:ASP69 4.2 48.7 1.0 CB C:GLN11 4.2 53.8 1.0 CD C:GLU71 4.2 63.8 1.0 OD2 C:ASP69 4.3 60.5 1.0 OD2 C:ASP98 4.3 60.2 1.0 OE1 C:GLN11 4.4 66.2 1.0 N C:GLN11 4.5 48.9 1.0 CB C:ASP98 4.5 55.0 1.0 O C:HOH680 4.6 77.5 1.0 O1A C:GTP501 4.6 54.1 1.0 CG C:ASP98 4.6 55.7 1.0 O2B C:GTP501 4.7 49.4 1.0 O3G C:GTP501 4.7 52.8 1.0 CG C:ASP69 4.7 51.8 1.0 PA C:GTP501 4.8 46.5 1.0 CA C:GLN11 4.9 52.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:76.4 occ:1.00 O D:HOH603 1.9 81.2 1.0 OE1 D:GLN11 2.1 84.1 1.0 O1A D:GDP501 2.5 90.2 1.0 CD D:GLN11 3.2 83.0 1.0 CB D:GLN11 3.8 84.8 1.0 PA D:GDP501 3.8 80.7 1.0 O2A D:GDP501 4.1 75.8 1.0 CG D:GLN11 4.1 86.3 1.0 NE2 D:GLN11 4.1 86.1 1.0 O1B D:GDP501 4.4 83.5 1.0 O3B D:GDP501 4.7 81.2 1.0 OD1 D:ASN101 4.7 82.6 1.0 O3A D:GDP501 4.9 87.6 1.0 PB D:GDP501 4.9 79.5 1.0 C5' D:GDP501 4.9 82.9 1.0 O5' D:GDP501 4.9 83.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z295848548-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z295848548-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:114.5 occ:1.00 O1B F:ACP401 2.2 130.4 1.0 OE2 F:GLU331 2.4 122.9 1.0 O3G F:ACP401 2.4 121.7 1.0 OD1 F:ASN333 3.1 120.8 1.0 OE1 F:GLU331 3.1 129.6 1.0 CD F:GLU331 3.1 123.0 1.0 PB F:ACP401 3.5 130.4 1.0 O2B F:ACP401 3.8 131.2 1.0 NZ F:LYS74 3.8 140.8 1.0 PG F:ACP401 3.9 130.9 1.0 CG F:ASN333 4.0 111.5 1.0 C3B F:ACP401 4.3 128.9 1.0 ND2 F:ASN333 4.5 109.7 1.0 CG F:GLU331 4.6 110.3 1.0 O1G F:ACP401 4.7 127.5 1.0 O3A F:ACP401 4.7 128.3 1.0 O1A F:ACP401 4.8 122.6 1.0 O2G F:ACP401 5.0 116.9 1.0 CE F:LYS74 5.0 131.8 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