Magnesium in PDB 9dhz: Cryo-Em Structure of Hurp Bound to A Microtubule

The binding sites of Magnesium atom in the Cryo-Em Structure of Hurp Bound to A Microtubule (pdb code 9dhz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Hurp Bound to A Microtubule, PDB code: 9dhz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Hurp Bound to A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Hurp Bound to A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:56.8 occ:1.00 O1G B:GTP501 2.0 47.2 1.0 O1B B:GTP501 2.5 61.9 1.0 OE1 B:GLU71 2.6 63.6 1.0 PG B:GTP501 3.3 48.7 1.0 PB B:GTP501 3.6 43.9 1.0 NZ A:LYS252 3.7 44.8 1.0 O3B B:GTP501 3.7 32.3 1.0 CD B:GLU71 3.8 65.2 1.0 O3G B:GTP501 4.1 60.4 1.0 OD2 B:ASP98 4.2 72.6 1.0 CB B:ASP98 4.3 51.0 1.0 O2G B:GTP501 4.4 56.7 1.0 OE2 B:GLU71 4.5 73.4 1.0 OE1 B:GLN11 4.5 34.0 1.0 CB B:GLU71 4.5 61.6 1.0 OD2 B:ASP69 4.6 44.5 1.0 O2B B:GTP501 4.6 46.3 1.0 OD1 B:ASP69 4.6 58.5 1.0 CB B:GLN11 4.7 13.8 1.0 O3A B:GTP501 4.7 51.4 1.0 CG B:ASP98 4.7 60.0 1.0 CG B:GLU71 4.8 56.2 1.0 CE A:LYS252 4.8 46.4 1.0 OG1 B:THR145 4.9 66.2 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Hurp Bound to A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Hurp Bound to A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:55.8 occ:1.00 O1B L:GTP501 1.9 84.5 1.0 O1G L:GTP501 2.1 93.8 1.0 OE2 L:GLU71 2.5 67.8 1.0 PB L:GTP501 3.1 87.8 1.0 PG L:GTP501 3.1 105.4 1.0 O3B L:GTP501 3.3 88.8 1.0 CD L:GLU71 3.5 67.1 1.0 O2G L:GTP501 3.7 94.2 1.0 NZ K:LYS252 3.8 67.6 1.0 CG L:GLU71 3.9 66.9 1.0 O3A L:GTP501 4.1 99.0 1.0 CG2 L:THR145 4.1 52.2 1.0 O2B L:GTP501 4.2 87.7 1.0 OD1 L:ASP98 4.4 73.1 1.0 O3G L:GTP501 4.4 96.3 1.0 OD1 L:ASP69 4.4 62.6 1.0 OE1 L:GLN11 4.5 53.0 1.0 O1A L:GTP501 4.5 85.9 1.0 CB L:GLN11 4.5 24.4 1.0 CB L:ASP98 4.5 55.7 1.0 OE1 L:GLU71 4.5 62.5 1.0 N L:GLN11 4.7 34.9 1.0 OD2 L:ASP69 4.7 51.8 1.0 CE K:LYS252 4.9 68.2 1.0 PA L:GTP501 5.0 99.2 1.0 CG L:ASP98 5.0 63.7 1.0

J.M.Perez-Bertoldi, Y.Zhao, A.Thawani, A.Yildiz, E.Nogales. Hurp Regulates KIF18A Recruitment and Activity to Synergistically Control Microtubule Dynamics. Nat Commun V. 15 9687 2024.
ISSN: ESSN 2041-1723
PubMed: 39516196
DOI: 10.1038/S41467-024-53691-7