Magnesium in PDB 5s54: Tubulin-Z2856434816-Complex

The structure of Tubulin-Z2856434816-Complex, PDB code: 5s54 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)	71.96 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.33, 157.15, 179.17, 90, 90, 90
R / Rfree (%)	20.6 / 25

The structure of Tubulin-Z2856434816-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434816-Complex (pdb code 5s54). 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-Z2856434816-Complex, PDB code: 5s54:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:60.9 occ:1.00 O A:HOH609 2.0 63.9 1.0 O A:HOH611 2.1 51.8 1.0 O A:HOH621 2.1 57.6 1.0 O A:HOH630 2.2 59.9 1.0 O1B A:GTP501 2.2 59.0 1.0 O1G A:GTP501 2.3 52.6 1.0 PB A:GTP501 3.5 59.7 1.0 PG A:GTP501 3.5 59.6 1.0 OE1 A:GLU71 3.6 78.1 1.0 NZ B:LYS254 3.9 70.3 1.0 O3B A:GTP501 3.9 70.4 1.0 CB A:GLN11 3.9 61.8 1.0 NE2 A:GLN11 4.0 69.0 1.0 OD1 A:ASP69 4.1 65.4 1.0 O2G A:GTP501 4.1 58.9 1.0 O3A A:GTP501 4.1 60.3 1.0 OD2 A:ASP69 4.2 67.0 1.0 N A:GLN11 4.4 58.4 1.0 CB A:ASP98 4.5 62.4 1.0 O1A A:GTP501 4.5 58.8 1.0 CG A:ASP69 4.6 64.0 1.0 O2B A:GTP501 4.7 64.2 1.0 CA A:GLN11 4.7 63.9 1.0 O3G A:GTP501 4.8 52.9 1.0 CD A:GLU71 4.8 80.3 1.0 CD A:GLN11 4.8 61.8 1.0 OD2 A:ASP98 4.8 78.2 1.0 CG A:GLN11 4.9 64.3 1.0 PA A:GTP501 4.9 61.7 1.0 CG A:ASP98 5.0 67.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:59.1 occ:1.00 O C:HOH687 2.1 54.9 1.0 O B:HOH617 2.2 65.3 1.0 OE1 B:GLN11 2.3 64.8 1.0 O1A B:GDP501 2.3 54.1 1.0 O B:HOH628 2.3 54.7 1.0 CD B:GLN11 3.5 63.3 1.0 PA B:GDP501 3.6 53.3 1.0 OD2 B:ASP179 4.0 66.6 1.0 OD1 B:ASN101 4.0 65.0 1.0 O3A B:GDP501 4.0 55.6 1.0 CB B:GLN11 4.1 55.5 1.0 CG B:GLN11 4.4 57.4 1.0 C5' B:GDP501 4.4 55.6 1.0 O1B B:GDP501 4.5 52.6 1.0 NE2 B:GLN11 4.5 68.1 1.0 O5' B:GDP501 4.5 50.7 1.0 OE1 C:GLU254 4.6 83.0 1.0 O2A B:GDP501 4.7 49.9 1.0 OE2 C:GLU254 4.8 80.3 1.0 ND2 B:ASN101 4.8 68.3 1.0 CG B:ASN101 4.8 62.0 1.0 PB B:GDP501 4.9 54.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:60.8 occ:1.00 O1G C:GTP501 2.0 47.2 1.0 O1B C:GTP501 2.1 47.6 1.0 O C:HOH616 2.1 51.4 1.0 O C:HOH624 2.1 56.8 1.0 O C:HOH620 2.1 55.8 1.0 O C:HOH663 2.2 54.2 1.0 PG C:GTP501 3.2 56.0 1.0 PB C:GTP501 3.3 50.9 1.0 O3B C:GTP501 3.7 56.5 1.0 NZ D:LYS254 3.7 62.8 1.0 O2G C:GTP501 3.8 52.2 1.0 OE2 C:GLU71 3.9 66.7 1.0 O3A C:GTP501 3.9 51.8 1.0 OD2 C:ASP98 4.1 59.8 1.0 CB C:GLN11 4.1 47.7 1.0 CG C:GLU71 4.2 65.0 1.0 OD1 C:ASP69 4.3 59.4 1.0 OD2 C:ASP69 4.3 56.1 1.0 CB C:ASP98 4.4 54.9 1.0 N C:GLN11 4.5 44.9 1.0 O3G C:GTP501 4.5 48.7 1.0 O2B C:GTP501 4.5 51.2 1.0 CD C:GLU71 4.5 64.4 1.0 OE1 C:GLN11 4.6 63.6 1.0 O1A C:GTP501 4.6 47.8 1.0 CG C:ASP98 4.7 56.0 1.0 CG C:ASP69 4.7 57.9 1.0 PA C:GTP501 4.8 53.9 1.0 CA C:GLN11 4.9 49.0 1.0 CE D:LYS254 5.0 61.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.7 occ:1.00 O D:HOH601 1.9 69.8 1.0 OE1 D:GLN11 2.0 82.2 1.0 O1A D:GDP501 2.4 95.8 1.0 CD D:GLN11 3.1 81.7 1.0 O D:HOH617 3.4 77.6 1.0 PA D:GDP501 3.6 80.5 1.0 O2A D:GDP501 3.9 74.2 1.0 NE2 D:GLN11 4.0 87.8 1.0 CB D:GLN11 4.0 78.8 1.0 CG D:GLN11 4.1 78.5 1.0 C5' D:GDP501 4.4 82.6 1.0 O5' D:GDP501 4.6 82.2 1.0 O1B D:GDP501 4.6 76.5 1.0 C8 D:GDP501 4.6 74.7 1.0 OD1 D:ASN101 4.7 83.7 1.0 O3A D:GDP501 4.8 83.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434816-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434816-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:122.1 occ:1.00 OD1 F:ASN333 2.9 111.0 1.0 O1B F:ACP401 2.9 146.3 1.0 OE2 F:GLU331 2.9 121.7 1.0 O3G F:ACP401 3.1 140.1 1.0 OE1 F:GLU331 3.3 120.6 1.0 CD F:GLU331 3.5 117.3 1.0 NZ F:LYS74 3.6 119.5 1.0 CG F:ASN333 4.0 104.8 1.0 PB F:ACP401 4.2 151.1 1.0 O2B F:ACP401 4.4 156.0 1.0 PG F:ACP401 4.6 156.5 1.0 ND2 F:ASN333 4.7 105.3 1.0 CE F:LYS74 4.8 115.5 1.0 CG F:GLU331 4.9 103.8 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