Magnesium in PDB 5s5a: Tubulin-Z1449748885-Complex

The structure of Tubulin-Z1449748885-Complex, PDB code: 5s5a 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)	63.08 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.59, 158.16, 179.51, 90, 90, 90
R / Rfree (%)	20.6 / 23.7

The structure of Tubulin-Z1449748885-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1449748885-Complex (pdb code 5s5a). 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-Z1449748885-Complex, PDB code: 5s5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:53.4 occ:1.00 O A:HOH604 1.9 54.6 1.0 O A:HOH625 2.1 55.9 1.0 O A:HOH608 2.1 48.6 1.0 O A:HOH611 2.2 54.7 1.0 O1G A:GTP501 2.2 46.1 1.0 O1B A:GTP501 2.3 48.9 1.0 PG A:GTP501 3.4 52.4 1.0 PB A:GTP501 3.4 49.6 1.0 OE1 A:GLU71 3.5 66.4 1.0 O3B A:GTP501 3.8 53.2 1.0 NZ B:LYS254 3.8 69.7 1.0 CB A:GLN11 3.9 50.3 1.0 O3A A:GTP501 4.0 51.7 1.0 O2G A:GTP501 4.0 50.9 1.0 OD1 A:ASP69 4.0 56.2 1.0 OD2 A:ASP69 4.1 56.6 1.0 NE2 A:GLN11 4.2 62.5 1.0 N A:GLN11 4.3 52.3 1.0 OD2 A:ASP98 4.3 67.1 1.0 CG A:ASP69 4.5 59.4 1.0 CB A:ASP98 4.5 55.2 1.0 O1A A:GTP501 4.6 46.8 1.0 O3G A:GTP501 4.6 49.2 1.0 CA A:GLN11 4.7 53.6 1.0 O2B A:GTP501 4.7 53.8 1.0 CD A:GLU71 4.7 67.9 1.0 PA A:GTP501 4.8 48.5 1.0 CG A:ASP98 4.9 58.5 1.0 CD A:GLN11 5.0 60.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:45.9 occ:1.00 O B:HOH605 1.8 58.9 1.0 O B:HOH615 2.2 55.4 1.0 O1A B:GDP501 2.2 51.0 1.0 O C:HOH682 2.3 57.3 1.0 O B:HOH632 2.4 50.2 1.0 OE1 B:GLN11 2.5 61.0 1.0 PA B:GDP501 3.5 50.1 1.0 CD B:GLN11 3.7 59.2 1.0 OD1 B:ASN101 3.9 52.4 1.0 O3A B:GDP501 3.9 48.4 1.0 OD2 B:ASP179 4.1 58.2 1.0 CB B:GLN11 4.2 50.5 1.0 OE1 C:GLU254 4.3 65.0 1.0 O1B B:GDP501 4.3 43.1 1.0 C5' B:GDP501 4.4 52.1 1.0 O5' B:GDP501 4.4 48.0 1.0 CG B:GLN11 4.4 54.4 1.0 O C:HOH630 4.6 53.0 1.0 O2A B:GDP501 4.6 48.1 1.0 CG B:ASN101 4.7 55.5 1.0 ND2 B:ASN101 4.7 53.6 1.0 NE2 B:GLN11 4.7 60.5 1.0 PB B:GDP501 4.8 45.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.5 occ:1.00 O C:HOH659 1.9 44.7 1.0 O C:HOH629 2.0 46.3 1.0 O1B C:GTP501 2.0 42.5 1.0 O1G C:GTP501 2.0 43.0 1.0 O C:HOH706 2.1 48.0 1.0 O C:HOH643 2.2 47.5 1.0 PG C:GTP501 3.1 44.7 1.0 PB C:GTP501 3.1 44.4 1.0 O3B C:GTP501 3.5 51.0 1.0 O2G C:GTP501 3.6 47.8 1.0 O3A C:GTP501 3.7 48.5 1.0 NZ D:LYS254 3.8 54.9 1.0 OE2 C:GLU71 4.1 56.2 1.0 OD1 C:ASP69 4.1 49.5 1.0 CB C:GLN11 4.2 46.1 1.0 OD2 C:ASP98 4.3 51.6 1.0 OD2 C:ASP69 4.3 48.5 1.0 CG C:GLU71 4.3 52.7 1.0 O2B C:GTP501 4.4 48.5 1.0 O3G C:GTP501 4.4 44.8 1.0 N C:GLN11 4.4 43.5 1.0 O1A C:GTP501 4.5 48.3 1.0 O C:HOH675 4.5 64.7 1.0 CB C:ASP98 4.6 50.6 1.0 CG C:ASP69 4.7 48.5 1.0 PA C:GTP501 4.7 45.6 1.0 CD C:GLU71 4.7 56.3 1.0 OE1 C:GLN11 4.8 55.5 1.0 CG C:ASP98 4.8 52.6 1.0 CE D:LYS254 4.9 53.8 1.0 CA C:GLN11 4.9 46.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.6 occ:1.00 O D:HOH604 1.9 70.7 1.0 OE1 D:GLN11 2.3 80.2 1.0 O1A D:GDP501 2.3 83.8 1.0 CD D:GLN11 3.4 79.8 1.0 PA D:GDP501 3.8 72.7 1.0 OD1 D:ASN101 4.2 76.2 1.0 CB D:GLN11 4.2 73.4 1.0 CG D:GLN11 4.3 77.5 1.0 NE2 D:GLN11 4.4 82.5 1.0 O2A D:GDP501 4.4 72.2 1.0 O D:HOH605 4.4 80.4 1.0 O1B D:GDP501 4.5 74.2 1.0 O3A D:GDP501 4.7 70.5 1.0 C5' D:GDP501 4.7 74.5 1.0 O5' D:GDP501 4.8 70.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1449748885-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1449748885-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:99.7 occ:1.00 O3G F:ACP401 2.2 107.4 1.0 O1B F:ACP401 2.3 115.1 1.0 OE2 F:GLU331 2.5 101.2 1.0 OD1 F:ASN333 2.7 98.3 1.0 OE1 F:GLU331 2.8 103.1 1.0 CD F:GLU331 3.0 98.7 1.0 PB F:ACP401 3.5 119.5 1.0 NZ F:LYS74 3.6 115.3 1.0 PG F:ACP401 3.7 124.2 1.0 CG F:ASN333 3.9 93.5 1.0 O2B F:ACP401 3.9 123.0 1.0 C3B F:ACP401 4.3 118.4 1.0 CG F:GLU331 4.5 88.0 1.0 ND2 F:ASN333 4.5 90.4 1.0 O2G F:ACP401 4.6 108.1 1.0 O1A F:ACP401 4.6 109.8 1.0 O1G F:ACP401 4.6 118.2 1.0 CE F:LYS74 4.7 110.6 1.0 O3A F:ACP401 4.8 120.0 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