Magnesium in PDB 5s4r: Tubulin-Z117233350-Complex

The structure of Tubulin-Z117233350-Complex, PDB code: 5s4r 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)	62.92 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 159.89, 180.03, 90, 90, 90
R / Rfree (%)	21.4 / 25.1

The structure of Tubulin-Z117233350-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z117233350-Complex (pdb code 5s4r). 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-Z117233350-Complex, PDB code: 5s4r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:66.3 occ:1.00 O A:HOH617 1.9 61.4 1.0 O1G A:GTP501 2.0 57.2 1.0 O A:HOH619 2.2 60.3 1.0 O1B A:GTP501 2.2 54.6 1.0 O A:HOH604 2.3 68.5 1.0 O A:HOH629 2.3 59.0 1.0 PG A:GTP501 3.2 60.9 1.0 PB A:GTP501 3.3 57.3 1.0 O3B A:GTP501 3.6 65.4 1.0 OE1 A:GLU71 3.6 81.6 1.0 O3A A:GTP501 3.7 61.1 1.0 O2G A:GTP501 3.8 60.4 1.0 CB A:GLN11 3.9 58.6 1.0 OD1 A:ASP69 4.0 65.2 1.0 OD2 A:ASP69 4.1 62.4 1.0 NE2 A:GLN11 4.1 69.6 1.0 OD2 A:ASP98 4.3 68.3 1.0 NZ B:LYS254 4.3 76.3 1.0 N A:GLN11 4.3 58.0 1.0 O3G A:GTP501 4.5 58.2 1.0 CG A:ASP69 4.5 64.2 1.0 O2B A:GTP501 4.6 62.4 1.0 CB A:ASP98 4.6 66.7 1.0 O1A A:GTP501 4.6 58.0 1.0 CA A:GLN11 4.7 60.7 1.0 PA A:GTP501 4.7 55.0 1.0 CG A:ASP98 4.8 63.0 1.0 CD A:GLU71 4.8 86.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.8 occ:1.00 O B:HOH636 2.0 54.6 1.0 OE1 B:GLN11 2.0 69.0 1.0 O B:HOH612 2.1 61.9 1.0 O C:HOH656 2.1 51.6 1.0 O1A B:GDP501 2.3 53.1 1.0 O B:HOH637 2.4 52.8 1.0 CD B:GLN11 3.2 67.2 1.0 PA B:GDP501 3.6 48.9 1.0 CB B:GLN11 3.9 59.2 1.0 OD2 B:ASP179 4.0 51.2 1.0 O3A B:GDP501 4.0 50.8 1.0 CG B:GLN11 4.1 62.1 1.0 NE2 B:GLN11 4.1 70.2 1.0 O1B B:GDP501 4.3 52.2 1.0 OE1 C:GLU254 4.4 59.0 1.0 OD1 B:ASN101 4.5 53.5 1.0 O2A B:GDP501 4.5 47.4 1.0 C5' B:GDP501 4.6 51.1 1.0 O5' B:GDP501 4.6 49.2 1.0 PB B:GDP501 4.8 47.9 1.0 C8 B:GDP501 5.0 54.3 1.0 ND2 B:ASN101 5.0 52.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:56.2 occ:1.00 O C:HOH623 2.0 52.2 1.0 O C:HOH679 2.0 52.6 1.0 O C:HOH617 2.0 53.7 1.0 O1B C:GTP501 2.1 51.2 1.0 O C:HOH642 2.1 53.7 1.0 O1G C:GTP501 2.1 50.1 1.0 PB C:GTP501 3.2 47.1 1.0 PG C:GTP501 3.2 47.6 1.0 O3B C:GTP501 3.5 59.3 1.0 O3A C:GTP501 3.6 54.6 1.0 O2G C:GTP501 3.8 52.2 1.0 NZ D:LYS254 3.8 55.8 1.0 OE2 C:GLU71 4.0 63.8 1.0 OD2 C:ASP98 4.1 59.4 1.0 OD1 C:ASP69 4.1 55.6 1.0 OD2 C:ASP69 4.2 56.2 1.0 CB C:GLN11 4.2 54.4 1.0 CG C:GLU71 4.4 62.5 1.0 N C:GLN11 4.5 51.6 1.0 O2B C:GTP501 4.5 54.5 1.0 O3G C:GTP501 4.5 48.3 1.0 CB C:ASP98 4.5 57.4 1.0 CG C:ASP69 4.6 55.2 1.0 CD C:GLU71 4.7 65.8 1.0 O1A C:GTP501 4.7 58.4 1.0 OE1 C:GLN11 4.7 67.0 1.0 CG C:ASP98 4.7 57.7 1.0 PA C:GTP501 4.7 47.7 1.0 O C:HOH721 4.8 75.3 1.0 OG1 C:THR145 4.9 55.0 1.0 CA C:GLN11 5.0 54.4 1.0 CE D:LYS254 5.0 55.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:80.0 occ:1.00 O D:HOH603 2.1 78.6 1.0 O1A D:GDP501 2.2 96.5 1.0 OE1 D:GLN11 2.2 87.8 1.0 CD D:GLN11 3.3 88.9 1.0 PA D:GDP501 3.6 83.2 1.0 CB D:GLN11 3.7 87.3 1.0 O2A D:GDP501 4.0 80.1 1.0 O1B D:GDP501 4.1 80.5 1.0 CG D:GLN11 4.1 89.3 1.0 O3B D:GDP501 4.3 91.9 1.0 NE2 D:GLN11 4.3 90.9 1.0 O3A D:GDP501 4.4 85.7 1.0 PB D:GDP501 4.5 80.6 1.0 OD1 D:ASN101 4.5 84.9 1.0 O5' D:GDP501 4.7 83.1 1.0 C5' D:GDP501 4.8 85.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z117233350-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z117233350-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:115.4 occ:1.00 OE2 F:GLU331 2.3 116.4 1.0 O3G F:ACP401 2.3 121.0 1.0 O1B F:ACP401 2.3 125.4 1.0 OD1 F:ASN333 3.1 117.5 1.0 CD F:GLU331 3.2 115.0 1.0 OE1 F:GLU331 3.3 117.8 1.0 NZ F:LYS74 3.5 125.6 1.0 PB F:ACP401 3.6 127.9 1.0 PG F:ACP401 3.8 128.7 1.0 O2B F:ACP401 3.9 129.6 1.0 CG F:ASN333 4.1 112.2 1.0 C3B F:ACP401 4.4 128.0 1.0 O1G F:ACP401 4.5 121.8 1.0 ND2 F:ASN333 4.6 109.6 1.0 CG F:GLU331 4.6 104.5 1.0 CE F:LYS74 4.8 124.2 1.0 O3A F:ACP401 4.8 127.0 1.0 O1A F:ACP401 4.9 120.2 1.0 O2G F:ACP401 4.9 114.8 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