Magnesium in PDB 7z2n: Tubulin-18-Complex

The structure of Tubulin-18-Complex, PDB code: 7z2n was solved by T.Muehlethaler, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.016, 157.703, 180.154, 90, 90, 90
R / Rfree (%)	18.9 / 22.4

The structure of Tubulin-18-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-18-Complex (pdb code 7z2n). 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-18-Complex, PDB code: 7z2n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.2 occ:1.00 O A:HOH636 2.0 37.8 1.0 O1G A:GTP501 2.1 33.0 1.0 O A:HOH673 2.1 39.4 1.0 O A:HOH694 2.1 39.5 1.0 O A:HOH631 2.2 38.5 1.0 O1B A:GTP501 2.2 34.6 1.0 PG A:GTP501 3.3 41.3 1.0 PB A:GTP501 3.3 36.3 1.0 O3B A:GTP501 3.6 45.7 1.0 O3A A:GTP501 3.7 43.5 1.0 OE1 A:GLU71 3.7 57.9 1.0 O2G A:GTP501 3.8 41.5 1.0 NZ B:LYS254 3.9 44.7 1.0 CB A:GLN11 4.1 37.4 1.0 OD1 A:ASP69 4.1 40.1 1.0 OD2 A:ASP98 4.2 46.2 1.0 OD2 A:ASP69 4.2 43.4 1.0 N A:GLN11 4.4 40.4 1.0 CB A:ASP98 4.4 43.9 1.0 OE1 A:GLN11 4.5 49.9 1.0 O3G A:GTP501 4.5 38.9 1.0 O1A A:GTP501 4.6 41.6 1.0 O2B A:GTP501 4.6 42.7 1.0 CG A:ASP69 4.6 47.6 1.0 CG A:ASP98 4.7 48.9 1.0 PA A:GTP501 4.7 41.2 1.0 CA A:GLN11 4.8 42.9 1.0 O B:HOH635 4.8 57.4 1.0 CD A:GLU71 4.9 55.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.9 occ:1.00 O B:HOH625 2.0 44.0 1.0 OE1 B:GLN11 2.2 50.2 1.0 O1A B:GDP501 2.3 40.6 1.0 O B:HOH605 2.3 48.1 1.0 O C:HOH676 2.3 52.2 1.0 O B:HOH697 2.4 46.5 1.0 O C:HOH788 3.3 61.7 1.0 CD B:GLN11 3.4 54.7 1.0 PA B:GDP501 3.5 39.6 1.0 OD2 B:ASP179 3.7 53.5 1.0 O3A B:GDP501 3.8 43.9 1.0 OD1 B:ASN101 4.2 47.4 1.0 CB B:GLN11 4.2 42.2 1.0 C5' B:GDP501 4.2 42.7 1.0 CG B:GLN11 4.3 49.3 1.0 O5' B:GDP501 4.3 38.3 1.0 NE2 B:GLN11 4.4 54.5 1.0 OE1 C:GLU254 4.6 58.0 1.0 O1B B:GDP501 4.6 38.2 1.0 O2A B:GDP501 4.7 41.0 1.0 CG B:ASP179 4.8 52.5 1.0 ND2 B:ASN101 4.8 45.1 1.0 C8 B:GDP501 4.8 41.2 1.0 PB B:GDP501 4.9 38.3 1.0 CG B:ASN101 4.9 49.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:35.8 occ:1.00 O1G C:GTP501 2.0 33.6 1.0 O C:HOH658 2.0 33.5 1.0 O C:HOH713 2.1 35.4 1.0 O C:HOH649 2.1 36.0 1.0 O1B C:GTP501 2.1 33.3 1.0 O C:HOH623 2.1 34.6 1.0 PG C:GTP501 3.2 35.4 1.0 PB C:GTP501 3.2 34.5 1.0 O3B C:GTP501 3.6 40.3 1.0 O2G C:GTP501 3.6 39.0 1.0 O3A C:GTP501 3.7 39.4 1.0 NZ D:LYS254 3.8 39.5 1.0 OD1 C:ASP69 4.1 41.7 1.0 OD2 C:ASP98 4.2 45.9 1.0 CB C:GLN11 4.2 33.3 1.0 OE2 C:GLU71 4.2 53.0 1.0 CG C:GLU71 4.2 43.3 1.0 OD2 C:ASP69 4.3 37.6 1.0 N C:GLN11 4.4 31.9 1.0 O3G C:GTP501 4.4 34.5 1.0 CB C:ASP98 4.4 37.0 1.0 O2B C:GTP501 4.5 38.5 1.0 O1A C:GTP501 4.6 36.2 1.0 CG C:ASP69 4.6 40.6 1.0 CD C:GLU71 4.7 44.9 1.0 PA C:GTP501 4.7 36.1 1.0 CG C:ASP98 4.7 41.1 1.0 NE2 C:GLN11 4.8 45.9 1.0 CA C:GLN11 4.9 34.2 1.0 CE D:LYS254 4.9 37.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.6 occ:1.00 O D:HOH611 2.3 67.9 1.0 O1A D:GDP501 2.3 76.7 1.0 OE1 D:GLN11 2.3 72.7 1.0 O D:HOH636 2.4 66.8 1.0 O D:HOH608 2.5 75.1 1.0 CD D:GLN11 3.4 76.2 1.0 PA D:GDP501 3.7 62.6 1.0 CB D:GLN11 3.9 67.9 1.0 O1B D:GDP501 4.0 62.0 1.0 CG D:GLN11 4.2 67.8 1.0 O3A D:GDP501 4.3 60.0 1.0 NE2 D:GLN11 4.3 71.1 1.0 O2A D:GDP501 4.4 64.5 1.0 PB D:GDP501 4.7 59.5 1.0 OD1 D:ASN101 4.7 74.4 1.0 O5' D:GDP501 4.8 62.4 1.0 C5' D:GDP501 4.9 65.5 1.0 O3B D:GDP501 5.0 71.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-18-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:85.8 occ:1.00 OE2 F:GLU331 2.3 93.4 1.0 O1B F:ACP401 2.4 102.5 1.0 O3G F:ACP401 2.5 93.1 1.0 OE1 F:GLU331 2.7 91.3 1.0 CD F:GLU331 2.8 89.2 1.0 NZ F:LYS74 3.3 97.0 1.0 OD1 F:ASN333 3.5 87.7 1.0 PB F:ACP401 3.6 100.2 1.0 O2B F:ACP401 3.9 104.6 1.0 PG F:ACP401 4.0 105.7 1.0 ND2 F:ASN333 4.0 87.9 1.0 CG F:ASN333 4.1 84.0 1.0 CG F:GLU331 4.3 75.4 1.0 C3B F:ACP401 4.5 98.4 1.0 CE F:LYS74 4.6 92.3 1.0 O1G F:ACP401 4.7 106.2 1.0 O3A F:ACP401 4.9 94.9 1.0 O2G F:ACP401 5.0 90.2 1.0

N.M.De La Roche, T.Muhlethaler, R.M.C.Di Martino, J.A.Ortega, D.Gioia, B.Roy, A.E.Prota, M.O.Steinmetz, A.Cavalli. Novel Fragment-Derived Colchicine-Site Binders As Microtubule-Destabilizing Agents. Eur.J.Med.Chem. V. 241 14614 2022.
ISSN: ISSN 0223-5234
PubMed: 35939994
DOI: 10.1016/J.EJMECH.2022.114614