Magnesium in PDB 7z2p: Tubulin-Nocodazole Complex

The structure of Tubulin-Nocodazole Complex, PDB code: 7z2p was solved by A.E.Prota, T.Muehlethaler, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.37 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.732, 158.09, 179.553, 90, 90, 90
R / Rfree (%)	17.8 / 20.9

The binding sites of Magnesium atom in the Tubulin-Nocodazole Complex (pdb code 7z2p). 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-Nocodazole Complex, PDB code: 7z2p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.0 occ:1.00 O A:HOH619 2.1 25.1 1.0 O1G A:GTP501 2.1 23.1 1.0 O1B A:GTP501 2.1 24.5 1.0 O A:HOH689 2.1 25.9 1.0 O A:HOH670 2.1 28.1 1.0 O A:HOH658 2.2 29.7 1.0 PG A:GTP501 3.2 28.3 1.0 PB A:GTP501 3.3 26.1 1.0 O3B A:GTP501 3.6 34.4 1.0 O2G A:GTP501 3.8 29.3 1.0 O3A A:GTP501 3.8 31.4 1.0 OE2 A:GLU71 4.0 44.3 1.0 NZ B:LYS254 4.0 34.8 1.0 OD1 A:ASP69 4.0 32.6 1.0 CB A:GLN11 4.1 26.1 1.0 OD2 A:ASP69 4.2 31.7 1.0 OD2 A:ASP98 4.2 40.7 1.0 N A:GLN11 4.3 28.7 1.0 CG A:GLU71 4.4 41.1 1.0 O1A A:GTP501 4.4 27.8 1.0 CB A:ASP98 4.5 33.1 1.0 O3G A:GTP501 4.5 27.2 1.0 O2B A:GTP501 4.6 30.3 1.0 OE1 A:GLN11 4.6 40.5 1.0 CG A:ASP69 4.6 35.8 1.0 CD A:GLU71 4.7 43.1 1.0 PA A:GTP501 4.7 29.4 1.0 CG A:ASP98 4.7 40.1 1.0 CA A:GLN11 4.8 27.4 1.0 O B:HOH614 4.8 52.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:18.4 occ:1.00 OE1 B:GLN11 2.2 31.9 1.0 O B:HOH646 2.2 30.6 1.0 O1A B:GDP501 2.3 26.8 1.0 O C:HOH704 2.3 36.4 1.0 O B:HOH613 2.4 33.5 1.0 O B:HOH677 2.5 28.3 1.0 O B:HOH748 2.7 54.1 1.0 CD B:GLN11 3.4 39.1 1.0 PA B:GDP501 3.6 26.2 1.0 O3A B:GDP501 3.8 29.4 1.0 OD2 B:ASP179 3.9 34.7 1.0 CB B:GLN11 4.1 28.1 1.0 CG B:GLN11 4.2 34.7 1.0 O C:HOH651 4.3 41.7 1.0 NE2 B:GLN11 4.4 37.8 1.0 C5' B:GDP501 4.4 29.9 1.0 OE1 C:GLU254 4.4 40.8 1.0 OD1 B:ASN101 4.5 33.0 1.0 O5' B:GDP501 4.5 29.5 1.0 O B:HOH747 4.5 53.3 1.0 O1B B:GDP501 4.6 24.1 1.0 O2A B:GDP501 4.7 28.1 1.0 C8 B:GDP501 4.8 30.2 1.0 PB B:GDP501 4.8 25.7 1.0 O B:HOH716 4.9 42.4 1.0 CG B:ASP179 4.9 38.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.0 occ:1.00 O1G C:GTP501 2.0 24.1 1.0 O C:HOH701 2.0 27.6 1.0 O C:HOH642 2.1 25.6 1.0 O1B C:GTP501 2.1 21.8 1.0 O C:HOH752 2.1 24.9 1.0 O C:HOH682 2.1 28.9 1.0 PG C:GTP501 3.1 26.4 1.0 PB C:GTP501 3.2 25.2 1.0 O3B C:GTP501 3.5 30.1 1.0 O2G C:GTP501 3.6 28.4 1.0 O3A C:GTP501 3.7 27.8 1.0 NZ D:LYS254 3.8 31.9 1.0 OE2 C:GLU71 4.0 46.8 1.0 OD1 C:ASP69 4.1 28.7 1.0 CB C:GLN11 4.2 22.6 1.0 OD2 C:ASP69 4.2 28.1 1.0 OD2 C:ASP98 4.2 40.1 1.0 CG C:GLU71 4.3 33.0 1.0 N C:GLN11 4.4 22.3 1.0 O3G C:GTP501 4.4 24.3 1.0 CB C:ASP98 4.5 32.9 1.0 O2B C:GTP501 4.5 26.6 1.0 O1A C:GTP501 4.6 27.1 1.0 CG C:ASP69 4.6 32.7 1.0 CD C:GLU71 4.7 42.6 1.0 CE D:LYS254 4.7 28.4 1.0 CG C:ASP98 4.7 36.9 1.0 PA C:GTP501 4.7 24.6 1.0 OE1 C:GLN11 4.8 37.0 1.0 O D:HOH601 4.9 66.4 1.0 CA C:GLN11 4.9 23.6 1.0 O D:HOH645 4.9 42.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:52.5 occ:1.00 O D:HOH619 1.9 52.2 1.0 OE1 D:GLN11 2.2 53.6 1.0 O D:HOH674 2.4 55.1 1.0 O1A D:GDP501 2.5 46.8 1.0 O D:HOH654 2.6 51.6 1.0 CD D:GLN11 3.4 60.0 1.0 PA D:GDP501 3.8 47.6 1.0 O3A D:GDP501 4.0 44.9 1.0 CB D:GLN11 4.2 52.4 1.0 NE2 D:GLN11 4.3 61.2 1.0 CG D:GLN11 4.3 52.3 1.0 C5' D:GDP501 4.4 49.5 1.0 OD1 D:ASN101 4.5 59.6 1.0 O5' D:GDP501 4.6 48.8 1.0 O1B D:GDP501 4.7 40.4 1.0 O2A D:GDP501 4.8 48.7 1.0 C8 D:GDP501 4.9 45.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:57.5 occ:1.00 OE2 F:GLU331 2.0 83.7 1.0 O3G F:ACP401 2.1 71.4 1.0 O2B F:ACP401 2.5 82.7 1.0 CD F:GLU331 2.8 71.9 1.0 OE1 F:GLU331 2.8 77.8 1.0 ND2 F:ASN333 3.2 77.8 1.0 PG F:ACP401 3.5 96.0 1.0 PB F:ACP401 3.7 74.8 1.0 NZ F:LYS74 3.7 83.1 1.0 C3B F:ACP401 3.9 79.5 1.0 O1B F:ACP401 4.1 90.1 1.0 CG F:ASN333 4.2 74.6 1.0 CG F:GLU331 4.2 62.6 1.0 O1G F:ACP401 4.4 93.0 1.0 O2G F:ACP401 4.5 82.3 1.0 CE F:LYS74 4.8 76.6 1.0 CB F:ASN333 4.9 55.3 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