Magnesium in PDB 5ubq: Cryo-Em Structure of Ciliary Microtubule Doublet

The binding sites of Magnesium atom in the Cryo-Em Structure of Ciliary Microtubule Doublet (pdb code 5ubq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of Ciliary Microtubule Doublet, PDB code: 5ubq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Ciliary Microtubule Doublet


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 Ciliary Microtubule Doublet within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:10.0 occ:1.00 O2G C:GTP501 1.4 10.0 1.0 O2B C:GTP501 1.5 10.0 1.0 CD C:GLU71 1.8 10.0 1.0 CG C:GLU71 1.8 10.0 1.0 OE2 C:GLU71 2.1 10.0 1.0 OD1 C:ASP69 2.3 10.0 1.0 OE1 C:GLU71 2.5 10.0 1.0 PG C:GTP501 2.7 10.0 1.0 CB C:GLU71 2.7 10.0 1.0 PB C:GTP501 2.8 10.0 1.0 CG C:ASP69 3.0 10.0 1.0 OD2 C:ASP69 3.0 10.0 1.0 H C:GLU71 3.1 10.0 1.0 HZ2 D:LYS252 3.1 10.0 1.0 O3B C:GTP501 3.2 10.0 1.0 N C:GLU71 3.4 10.0 1.0 CB C:ASP98 3.4 10.0 1.0 H C:THR145 3.4 10.0 1.0 H C:LEU70 3.5 10.0 1.0 HG1 C:THR145 3.5 10.0 1.0 CA C:GLU71 3.7 10.0 1.0 O1G C:GTP501 3.7 10.0 1.0 OD2 C:ASP98 3.8 10.0 1.0 O3A C:GTP501 3.8 10.0 1.0 O3G C:GTP501 3.8 10.0 1.0 O1B C:GTP501 3.8 10.0 1.0 OG1 C:THR145 3.9 10.0 1.0 NZ D:LYS252 4.0 10.0 1.0 N C:LEU70 4.0 10.0 1.0 CB C:THR145 4.1 10.0 1.0 H C:GLY144 4.1 10.0 1.0 CG C:ASP98 4.1 10.0 1.0 C C:LEU70 4.1 10.0 1.0 C C:GLY143 4.2 10.0 1.0 O C:GLY143 4.2 10.0 1.0 HZ3 D:LYS252 4.2 10.0 1.0 HZ1 D:LYS252 4.2 10.0 1.0 N C:THR145 4.3 10.0 1.0 N C:GLY144 4.3 10.0 1.0 H C:ALA99 4.3 10.0 1.0 CB C:ASP69 4.4 10.0 1.0 H C:GLY10 4.5 10.0 1.0 CA C:LEU70 4.5 10.0 1.0 CA C:GLY143 4.6 10.0 1.0 CA C:ASP98 4.6 10.0 1.0 C C:GLU71 4.7 10.0 1.0 O C:GLU71 4.7 10.0 1.0 C C:ASP69 4.8 10.0 1.0 H C:GLN11 4.8 10.0 1.0 CA C:GLY10 4.8 10.0 1.0 CA C:THR145 4.8 10.0 1.0 H C:GLY146 4.8 10.0 1.0 CB C:LEU70 4.9 10.0 1.0 O C:LEU70 4.9 10.0 1.0 CE D:LYS252 4.9 10.0 1.0 CA C:ASP69 5.0 10.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Ciliary Microtubule Doublet


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 Ciliary Microtubule Doublet within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:10.0 occ:1.00 O2G E:GTP501 1.4 10.0 1.0 O2B E:GTP501 1.5 10.0 1.0 CD E:GLU71 1.8 10.0 1.0 CG E:GLU71 1.8 10.0 1.0 OE2 E:GLU71 2.1 10.0 1.0 OD1 E:ASP69 2.3 10.0 1.0 OE1 E:GLU71 2.5 10.0 1.0 PG E:GTP501 2.7 10.0 1.0 CB E:GLU71 2.7 10.0 1.0 PB E:GTP501 2.8 10.0 1.0 CG E:ASP69 3.0 10.0 1.0 OD2 E:ASP69 3.0 10.0 1.0 H E:GLU71 3.0 10.0 1.0 HZ2 F:LYS252 3.1 10.0 1.0 O3B E:GTP501 3.2 10.0 1.0 N E:GLU71 3.4 10.0 1.0 CB E:ASP98 3.4 10.0 1.0 H E:THR145 3.4 10.0 1.0 H E:LEU70 3.5 10.0 1.0 HG1 E:THR145 3.5 10.0 1.0 CA E:GLU71 3.7 10.0 1.0 O1G E:GTP501 3.7 10.0 1.0 OD2 E:ASP98 3.8 10.0 1.0 O3A E:GTP501 3.8 10.0 1.0 O3G E:GTP501 3.8 10.0 1.0 O1B E:GTP501 3.8 10.0 1.0 OG1 E:THR145 3.9 10.0 1.0 NZ F:LYS252 4.0 10.0 1.0 N E:LEU70 4.0 10.0 1.0 CB E:THR145 4.1 10.0 1.0 H E:GLY144 4.1 10.0 1.0 CG E:ASP98 4.1 10.0 1.0 C E:LEU70 4.1 10.0 1.0 C E:GLY143 4.2 10.0 1.0 O E:GLY143 4.2 10.0 1.0 HZ3 F:LYS252 4.2 10.0 1.0 HZ1 F:LYS252 4.2 10.0 1.0 N E:THR145 4.3 10.0 1.0 N E:GLY144 4.3 10.0 1.0 H E:ALA99 4.3 10.0 1.0 CB E:ASP69 4.4 10.0 1.0 H E:GLY10 4.5 10.0 1.0 CA E:LEU70 4.5 10.0 1.0 CA E:ASP98 4.6 10.0 1.0 CA E:GLY143 4.6 10.0 1.0 C E:GLU71 4.7 10.0 1.0 O E:GLU71 4.7 10.0 1.0 C E:ASP69 4.8 10.0 1.0 H E:GLN11 4.8 10.0 1.0 CA E:GLY10 4.8 10.0 1.0 CA E:THR145 4.8 10.0 1.0 H E:GLY146 4.8 10.0 1.0 CB E:LEU70 4.9 10.0 1.0 O E:LEU70 4.9 10.0 1.0 CE F:LYS252 5.0 10.0 1.0 CA E:ASP69 5.0 10.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Ciliary Microtubule Doublet


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Ciliary Microtubule Doublet within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.0 occ:1.00 O2G A:GTP501 1.4 10.0 1.0 O2B A:GTP501 1.5 10.0 1.0 CD A:GLU71 1.8 10.0 1.0 CG A:GLU71 1.8 10.0 1.0 OE2 A:GLU71 2.1 10.0 1.0 OD1 A:ASP69 2.3 10.0 1.0 OE1 A:GLU71 2.5 10.0 1.0 PG A:GTP501 2.7 10.0 1.0 CB A:GLU71 2.7 10.0 1.0 PB A:GTP501 2.8 10.0 1.0 CG A:ASP69 3.0 10.0 1.0 OD2 A:ASP69 3.0 10.0 1.0 H A:GLU71 3.0 10.0 1.0 HZ2 B:LYS252 3.1 10.0 1.0 O3B A:GTP501 3.2 10.0 1.0 N A:GLU71 3.4 10.0 1.0 CB A:ASP98 3.4 10.0 1.0 H A:THR145 3.4 10.0 1.0 H A:LEU70 3.5 10.0 1.0 HG1 A:THR145 3.5 10.0 1.0 CA A:GLU71 3.7 10.0 1.0 O1G A:GTP501 3.7 10.0 1.0 OD2 A:ASP98 3.8 10.0 1.0 O3A A:GTP501 3.8 10.0 1.0 O3G A:GTP501 3.8 10.0 1.0 O1B A:GTP501 3.8 10.0 1.0 OG1 A:THR145 3.9 10.0 1.0 NZ B:LYS252 4.0 10.0 1.0 N A:LEU70 4.0 10.0 1.0 CB A:THR145 4.1 10.0 1.0 H A:GLY144 4.1 10.0 1.0 CG A:ASP98 4.1 10.0 1.0 C A:LEU70 4.1 10.0 1.0 C A:GLY143 4.2 10.0 1.0 O A:GLY143 4.2 10.0 1.0 HZ3 B:LYS252 4.2 10.0 1.0 HZ1 B:LYS252 4.2 10.0 1.0 N A:THR145 4.3 10.0 1.0 N A:GLY144 4.3 10.0 1.0 H A:ALA99 4.3 10.0 1.0 CB A:ASP69 4.4 10.0 1.0 H A:GLY10 4.5 10.0 1.0 CA A:LEU70 4.5 10.0 1.0 CA A:ASP98 4.6 10.0 1.0 CA A:GLY143 4.6 10.0 1.0 C A:GLU71 4.7 10.0 1.0 O A:GLU71 4.7 10.0 1.0 C A:ASP69 4.8 10.0 1.0 H A:GLN11 4.8 10.0 1.0 CA A:GLY10 4.8 10.0 1.0 CA A:THR145 4.8 10.0 1.0 H A:GLY146 4.8 10.0 1.0 CB A:LEU70 4.9 10.0 1.0 O A:LEU70 4.9 10.0 1.0 CE B:LYS252 4.9 10.0 1.0 CA A:ASP69 5.0 10.0 1.0

M.Ichikawa, D.Liu, P.L.Kastritis, K.Basu, T.C.Hsu, S.Yang, K.H.Bui. Subnanometre-Resolution Structure of the Doublet Microtubule Reveals New Classes of Microtubule-Associated Proteins. Nat Commun V. 8 15035 2017.
ISSN: ESSN 2041-1723
PubMed: 28462916
DOI: 10.1038/NCOMMS15035