Magnesium in PDB 3jas: Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin

The binding sites of Magnesium atom in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin (pdb code 3jas). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin, PDB code: 3jas:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


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 Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:19.4 occ:1.00 O1B E:GTP501 2.0 25.8 1.0 O1G E:GTP501 2.6 26.5 1.0 OD2 E:ASP98 2.8 57.8 1.0 OE1 E:GLU71 3.1 46.6 1.0 PB E:GTP501 3.3 25.9 1.0 PG E:GTP501 3.6 26.6 1.0 CG E:ASP98 3.7 56.2 1.0 OD1 E:ASP98 3.7 56.9 1.0 NZ G:LYS254 3.7 45.4 1.0 O3B E:GTP501 3.9 26.2 1.0 CB E:GLN11 3.9 20.4 1.0 O3A E:GTP501 4.0 25.9 1.0 OD2 E:ASP69 4.0 29.4 1.0 O2G E:GTP501 4.0 27.2 1.0 CD E:GLU71 4.1 45.5 1.0 OE1 E:GLN11 4.1 21.2 1.0 N E:GLN11 4.2 20.1 1.0 OD1 E:ASP69 4.2 29.4 1.0 O2B E:GTP501 4.5 26.1 1.0 CG E:ASP69 4.6 28.8 1.0 O1A E:GTP501 4.6 26.1 1.0 CG E:GLU71 4.6 43.4 1.0 CA E:GLN11 4.7 20.2 1.0 CG2 E:THR145 4.8 31.8 1.0 PA E:GTP501 4.8 26.2 1.0 CD E:GLN11 4.9 20.9 1.0 O3G E:GTP501 5.0 26.9 1.0 OE2 E:GLU71 5.0 46.0 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


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 Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:15.7 occ:1.00 O1B J:GTP501 1.9 18.0 1.0 O3G J:GTP501 2.5 18.6 1.0 OD2 J:ASP98 2.9 43.4 1.0 OE1 J:GLU71 3.2 38.7 1.0 PB J:GTP501 3.3 18.1 1.0 PG J:GTP501 3.6 18.5 1.0 CG J:ASP98 3.7 42.9 1.0 OD1 J:ASP98 3.7 43.0 1.0 NZ F:LYS254 3.7 30.1 1.0 O3B J:GTP501 3.8 18.3 1.0 CB J:GLN11 3.9 14.5 1.0 O2G J:GTP501 3.9 19.0 1.0 O3A J:GTP501 3.9 17.8 1.0 OD2 J:ASP69 4.0 22.0 1.0 N J:GLN11 4.1 14.2 1.0 CD J:GLU71 4.2 38.0 1.0 OE1 J:GLN11 4.2 15.1 1.0 OD1 J:ASP69 4.2 21.7 1.0 O2B J:GTP501 4.4 18.2 1.0 O1A J:GTP501 4.5 17.9 1.0 CG J:ASP69 4.6 21.5 1.0 CA J:GLN11 4.6 14.4 1.0 CG2 J:THR145 4.7 22.4 1.0 CG J:GLU71 4.7 35.8 1.0 PA J:GTP501 4.8 17.8 1.0 O1G J:GTP501 4.9 18.7 1.0 CD J:GLN11 5.0 15.1 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


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 Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:16.1 occ:1.00 O1B C:GTP501 1.9 19.5 1.0 O1G C:GTP501 2.3 20.1 1.0 OD2 C:ASP98 2.7 52.2 1.0 PB C:GTP501 3.1 19.7 1.0 OE1 C:GLU71 3.2 43.6 1.0 PG C:GTP501 3.4 20.1 1.0 CG C:ASP98 3.5 51.1 1.0 OD1 C:ASP98 3.5 51.5 1.0 O3B C:GTP501 3.7 19.9 1.0 NZ I:LYS254 3.7 42.5 1.0 O2G C:GTP501 3.7 20.6 1.0 O3A C:GTP501 3.8 19.5 1.0 OD2 C:ASP69 4.1 29.8 1.0 CB C:GLN11 4.1 19.6 1.0 CD C:GLU71 4.2 43.0 1.0 OD1 C:ASP69 4.2 29.9 1.0 N C:GLN11 4.3 19.2 1.0 O2B C:GTP501 4.3 19.8 1.0 OE1 C:GLN11 4.4 20.9 1.0 CG2 C:THR145 4.6 26.6 1.0 O1A C:GTP501 4.6 19.4 1.0 CG C:ASP69 4.6 29.4 1.0 O3G C:GTP501 4.7 20.2 1.0 PA C:GTP501 4.7 19.5 1.0 CG C:GLU71 4.7 41.2 1.0 CA C:GLN11 4.8 19.2 1.0 CB C:ASP98 5.0 48.9 1.0 CE I:LYS254 5.0 41.8 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:12.5 occ:1.00 O1B L:GTP501 1.8 13.9 1.0 O3G L:GTP501 2.3 14.6 1.0 OD2 L:ASP98 2.7 44.6 1.0 PB L:GTP501 3.1 14.0 1.0 OE1 L:GLU71 3.2 40.1 1.0 PG L:GTP501 3.4 14.5 1.0 CG L:ASP98 3.5 44.2 1.0 OD1 L:ASP98 3.5 44.4 1.0 O3B L:GTP501 3.7 14.3 1.0 NZ D:LYS254 3.7 29.5 1.0 O2G L:GTP501 3.8 14.8 1.0 O3A L:GTP501 3.9 13.8 1.0 OD2 L:ASP69 4.0 25.5 1.0 CB L:GLN11 4.1 14.9 1.0 CD L:GLU71 4.2 39.5 1.0 OD1 L:ASP69 4.2 25.7 1.0 N L:GLN11 4.3 14.9 1.0 O2B L:GTP501 4.3 14.1 1.0 OE1 L:GLN11 4.4 15.6 1.0 CG2 L:THR145 4.5 20.9 1.0 CG L:ASP69 4.5 25.3 1.0 O1A L:GTP501 4.6 13.6 1.0 CG L:GLU71 4.7 37.1 1.0 O1G L:GTP501 4.7 14.6 1.0 PA L:GTP501 4.7 13.6 1.0 CA L:GLN11 4.8 14.7 1.0 CB L:ASP98 5.0 42.9 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.7 occ:1.00 O1B A:GTP501 1.9 21.9 1.0 O1G A:GTP501 2.4 22.6 1.0 OD2 A:ASP98 2.7 51.0 1.0 OE1 A:GLU71 3.2 41.6 1.0 PB A:GTP501 3.2 22.1 1.0 PG A:GTP501 3.4 22.7 1.0 CG A:ASP98 3.6 49.4 1.0 OD1 A:ASP98 3.6 49.9 1.0 NZ H:LYS254 3.7 42.4 1.0 O3B A:GTP501 3.7 22.4 1.0 O2G A:GTP501 3.8 23.3 1.0 O3A A:GTP501 3.9 21.9 1.0 CB A:GLN11 4.0 19.0 1.0 OD2 A:ASP69 4.1 27.6 1.0 CD A:GLU71 4.2 41.0 1.0 N A:GLN11 4.3 18.8 1.0 OD1 A:ASP69 4.3 27.7 1.0 OE1 A:GLN11 4.3 19.9 1.0 O2B A:GTP501 4.4 22.2 1.0 O1A A:GTP501 4.6 22.0 1.0 CG A:ASP69 4.6 27.2 1.0 CG2 A:THR145 4.7 28.7 1.0 CG A:GLU71 4.7 39.5 1.0 PA A:GTP501 4.7 22.0 1.0 CA A:GLN11 4.8 18.8 1.0 O3G A:GTP501 4.8 22.8 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Dynamic Gdp-Microtubule (14 Protofilaments) Decorated with Kinesin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:12.8 occ:1.00 O1B K:GTP501 1.9 14.7 1.0 O3G K:GTP501 2.3 15.3 1.0 OD2 K:ASP98 2.7 42.8 1.0 PB K:GTP501 3.2 14.8 1.0 OE1 K:GLU71 3.2 37.9 1.0 PG K:GTP501 3.5 15.2 1.0 CG K:ASP98 3.6 42.2 1.0 OD1 K:ASP98 3.6 42.5 1.0 NZ B:LYS254 3.7 27.9 1.0 O3B K:GTP501 3.7 15.1 1.0 O2G K:GTP501 3.8 15.6 1.0 O3A K:GTP501 3.9 14.6 1.0 OD2 K:ASP69 4.1 22.7 1.0 CB K:GLN11 4.1 14.9 1.0 CD K:GLU71 4.2 37.4 1.0 N K:GLN11 4.2 14.8 1.0 OD1 K:ASP69 4.3 22.7 1.0 OE1 K:GLN11 4.3 15.6 1.0 O2B K:GTP501 4.4 14.9 1.0 O1A K:GTP501 4.6 14.4 1.0 CG K:ASP69 4.6 22.3 1.0 CG2 K:THR145 4.6 21.6 1.0 CG K:GLU71 4.7 35.4 1.0 PA K:GTP501 4.8 14.4 1.0 CA K:GLN11 4.8 14.8 1.0 O1G K:GTP501 4.8 15.4 1.0 CE B:LYS254 5.0 27.7 1.0

R.Zhang, G.M.Alushin, A.Brown, E.Nogales. Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation By Eb Proteins. Cell(Cambridge,Mass.) V. 162 849 2015.
ISSN: ISSN 0092-8674
PubMed: 26234155
DOI: 10.1016/J.CELL.2015.07.012