Magnesium in PDB 3jar: Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3

The binding sites of Magnesium atom in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3 (pdb code 3jar). 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 Gdp-Microtubule Co-Polymerized with EB3, PDB code: 3jar:
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 Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:25.8 occ:1.00 O1B E:GTP501 2.0 26.7 1.0 O1G E:GTP501 2.0 28.1 1.0 OE2 E:GLU71 3.1 57.8 1.0 PB E:GTP501 3.1 26.6 1.0 PG E:GTP501 3.1 28.2 1.0 O3B E:GTP501 3.5 27.3 1.0 O2G E:GTP501 3.6 28.6 1.0 O3A E:GTP501 3.7 26.6 1.0 NZ G:LYS254 3.9 44.1 1.0 CD E:GLU71 4.1 55.8 1.0 OE1 E:GLN11 4.3 18.6 1.0 OD1 E:ASP69 4.3 31.0 1.0 OD2 E:ASP98 4.4 56.4 1.0 O2B E:GTP501 4.4 26.8 1.0 O1A E:GTP501 4.4 26.3 1.0 O3G E:GTP501 4.4 28.1 1.0 CB E:ASP98 4.5 53.1 1.0 CB E:GLN11 4.5 17.9 1.0 OD2 E:ASP69 4.6 30.9 1.0 PA E:GTP501 4.7 26.4 1.0 N E:GLN11 4.8 17.4 1.0 CG E:GLU71 4.8 52.6 1.0 O G:ASN249 4.9 43.1 1.0 OG1 E:THR145 4.9 26.3 1.0 CG E:ASP69 4.9 30.6 1.0 OE1 E:GLU71 5.0 56.8 1.0 CG E:ASP98 5.0 55.7 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:24.9 occ:1.00 O3G J:GTP501 1.9 25.6 1.0 O1B J:GTP501 2.0 24.3 1.0 PG J:GTP501 3.1 25.6 1.0 PB J:GTP501 3.2 24.0 1.0 OE2 J:GLU71 3.2 59.3 1.0 O3B J:GTP501 3.5 24.8 1.0 O2G J:GTP501 3.5 25.8 1.0 O3A J:GTP501 3.7 24.2 1.0 NZ F:LYS254 4.1 40.6 1.0 OD1 J:ASP69 4.1 30.7 1.0 CD J:GLU71 4.2 58.0 1.0 OE1 J:GLN11 4.3 18.8 1.0 O1G J:GTP501 4.4 25.6 1.0 O2B J:GTP501 4.4 24.1 1.0 CB J:GLN11 4.5 17.9 1.0 O1A J:GTP501 4.5 24.5 1.0 OD2 J:ASP69 4.5 30.2 1.0 OD2 J:ASP98 4.5 53.3 1.0 CB J:ASP98 4.5 52.0 1.0 N J:GLN11 4.6 17.3 1.0 PA J:GTP501 4.7 24.4 1.0 OG1 J:THR145 4.8 22.6 1.0 CG J:ASP69 4.8 30.0 1.0 CG J:GLU71 4.8 54.3 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:21.1 occ:1.00 O1B C:GTP501 2.0 22.5 1.0 O3G C:GTP501 2.1 23.7 1.0 OE2 C:GLU71 3.1 54.3 1.0 PB C:GTP501 3.2 22.5 1.0 PG C:GTP501 3.2 23.8 1.0 O3B C:GTP501 3.6 23.0 1.0 O2G C:GTP501 3.7 23.9 1.0 O3A C:GTP501 3.8 22.6 1.0 NZ I:LYS254 4.1 47.2 1.0 OD1 C:ASP69 4.1 31.3 1.0 CD C:GLU71 4.2 52.1 1.0 OE1 C:GLN11 4.3 20.3 1.0 O2B C:GTP501 4.4 22.6 1.0 O1A C:GTP501 4.4 22.6 1.0 CB C:GLN11 4.5 19.2 1.0 OD2 C:ASP69 4.5 31.4 1.0 OD2 C:ASP98 4.5 56.8 1.0 O1G C:GTP501 4.5 23.7 1.0 CB C:ASP98 4.5 53.5 1.0 N C:GLN11 4.6 18.7 1.0 PA C:GTP501 4.7 22.7 1.0 CG C:ASP69 4.8 31.0 1.0 CG C:GLU71 4.8 48.9 1.0 OG1 C:THR145 4.8 23.0 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:27.7 occ:1.00 O3G L:GTP501 2.0 29.8 1.0 O1B L:GTP501 2.0 28.4 1.0 OE2 L:GLU71 3.1 60.1 1.0 PG L:GTP501 3.2 29.6 1.0 PB L:GTP501 3.2 28.0 1.0 O3B L:GTP501 3.6 28.7 1.0 O2G L:GTP501 3.6 29.7 1.0 O3A L:GTP501 3.8 28.3 1.0 NZ D:LYS254 4.1 44.1 1.0 OD1 L:ASP69 4.1 34.2 1.0 CD L:GLU71 4.1 58.1 1.0 OE1 L:GLN11 4.3 23.0 1.0 O1G L:GTP501 4.5 29.4 1.0 O2B L:GTP501 4.5 28.2 1.0 OD2 L:ASP69 4.5 34.0 1.0 CB L:GLN11 4.5 21.6 1.0 O1A L:GTP501 4.5 28.8 1.0 OD2 L:ASP98 4.5 56.7 1.0 CB L:ASP98 4.5 54.6 1.0 N L:GLN11 4.7 21.1 1.0 PA L:GTP501 4.7 28.7 1.0 CG L:ASP69 4.8 33.7 1.0 CG L:GLU71 4.8 54.3 1.0 OG1 L:THR145 4.8 23.9 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.1 occ:1.00 O1B A:GTP501 1.9 22.9 1.0 O1G A:GTP501 2.0 24.4 1.0 PB A:GTP501 3.1 22.9 1.0 OE2 A:GLU71 3.1 53.3 1.0 PG A:GTP501 3.2 24.6 1.0 O3B A:GTP501 3.5 23.6 1.0 O2G A:GTP501 3.6 24.7 1.0 O3A A:GTP501 3.7 22.8 1.0 NZ H:LYS254 4.0 43.1 1.0 CD A:GLU71 4.2 51.4 1.0 OD1 A:ASP69 4.3 28.6 1.0 OE1 A:GLN11 4.3 18.0 1.0 O1A A:GTP501 4.4 22.6 1.0 O2B A:GTP501 4.4 23.0 1.0 O3G A:GTP501 4.5 24.4 1.0 OD2 A:ASP98 4.5 51.8 1.0 CB A:GLN11 4.5 17.2 1.0 CB A:ASP98 4.6 49.2 1.0 OD2 A:ASP69 4.6 28.6 1.0 PA A:GTP501 4.6 22.6 1.0 N A:GLN11 4.7 16.8 1.0 CG A:GLU71 4.8 48.4 1.0 CG A:ASP69 4.9 28.2 1.0 OG1 A:THR145 4.9 23.6 1.0 O H:ASN249 4.9 40.3 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerized with EB3


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 Gdp-Microtubule Co-Polymerized with EB3 within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:24.6 occ:1.00 O3G K:GTP501 1.9 26.2 1.0 O1B K:GTP501 2.0 24.6 1.0 PG K:GTP501 3.1 26.3 1.0 PB K:GTP501 3.1 24.3 1.0 OE2 K:GLU71 3.2 57.3 1.0 O3B K:GTP501 3.5 25.3 1.0 O2G K:GTP501 3.5 26.3 1.0 O3A K:GTP501 3.7 24.5 1.0 NZ B:LYS254 4.0 39.8 1.0 OD1 K:ASP69 4.2 29.9 1.0 CD K:GLU71 4.2 55.8 1.0 OE1 K:GLN11 4.3 19.9 1.0 O1G K:GTP501 4.4 26.2 1.0 O1A K:GTP501 4.4 24.8 1.0 O2B K:GTP501 4.4 24.4 1.0 CB K:GLN11 4.4 18.8 1.0 OD2 K:ASP98 4.5 50.9 1.0 OD2 K:ASP69 4.6 29.8 1.0 CB K:ASP98 4.6 49.7 1.0 N K:GLN11 4.6 18.4 1.0 PA K:GTP501 4.6 24.6 1.0 OG1 K:THR145 4.8 22.6 1.0 CG K:ASP69 4.8 29.5 1.0 CG K:GLU71 4.9 52.1 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