Magnesium in PDB 3jak: Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)

The binding sites of Magnesium atom in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) (pdb code 3jak). 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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound), PDB code: 3jak:
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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:9.3 occ:1.00 O1B E:GTP501 2.1 9.2 1.0 O1G E:GTP501 2.2 9.4 1.0 OE2 E:GLU71 2.6 24.2 1.0 PB E:GTP501 3.3 9.1 1.0 PG E:GTP501 3.3 9.4 1.0 CD E:GLU71 3.7 24.3 1.0 O3B E:GTP501 3.7 9.2 1.0 O2G E:GTP501 3.7 9.5 1.0 O3A E:GTP501 3.9 9.1 1.0 OD2 E:ASP69 4.2 17.3 1.0 OD1 E:ASP69 4.3 17.2 1.0 OE1 E:GLN11 4.3 11.7 1.0 OE1 E:GLU71 4.4 24.8 1.0 CB E:GLN11 4.4 11.3 1.0 O1A E:GTP501 4.5 9.1 1.0 O2B E:GTP501 4.5 9.1 1.0 NZ G:LYS254 4.6 19.6 1.0 CB E:ASP98 4.6 23.2 1.0 CG E:GLU71 4.6 23.5 1.0 O3G E:GTP501 4.6 9.4 1.0 N E:GLN11 4.7 11.2 1.0 CG E:ASP69 4.7 17.1 1.0 PA E:GTP501 4.8 9.1 1.0 OD2 E:ASP98 4.8 23.2 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:9.7 occ:1.00 O1G J:GTP501 2.0 10.1 1.0 O1B J:GTP501 2.1 9.9 1.0 OE2 J:GLU71 2.6 22.5 1.0 PG J:GTP501 3.2 10.2 1.0 PB J:GTP501 3.2 9.9 1.0 O3B J:GTP501 3.6 10.0 1.0 O2G J:GTP501 3.6 10.2 1.0 CD J:GLU71 3.7 22.5 1.0 O3A J:GTP501 3.8 9.9 1.0 OD1 J:ASP69 4.2 17.3 1.0 OD2 J:ASP69 4.3 17.4 1.0 OE1 J:GLN11 4.4 11.5 1.0 OE1 J:GLU71 4.5 22.8 1.0 O3G J:GTP501 4.5 10.2 1.0 CB J:GLN11 4.5 11.2 1.0 O2B J:GTP501 4.5 9.9 1.0 CB J:ASP98 4.5 22.8 1.0 O1A J:GTP501 4.6 10.0 1.0 NZ F:LYS254 4.6 18.9 1.0 CG J:GLU71 4.7 22.0 1.0 N J:GLN11 4.7 11.1 1.0 CG J:ASP69 4.7 17.3 1.0 PA J:GTP501 4.8 9.9 1.0 OD2 J:ASP98 4.8 22.9 1.0 OG1 J:THR145 5.0 13.1 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:8.3 occ:1.00 O1B C:GTP501 2.1 8.4 1.0 O1G C:GTP501 2.2 8.6 1.0 OE2 C:GLU71 2.6 24.6 1.0 PB C:GTP501 3.3 8.4 1.0 PG C:GTP501 3.3 8.6 1.0 CD C:GLU71 3.7 24.6 1.0 O3B C:GTP501 3.7 8.5 1.0 O2G C:GTP501 3.7 8.7 1.0 O3A C:GTP501 3.9 8.4 1.0 OD2 C:ASP69 4.2 16.8 1.0 OD1 C:ASP69 4.2 16.7 1.0 OE1 C:GLN11 4.3 10.8 1.0 CB C:GLN11 4.4 10.5 1.0 OE1 C:GLU71 4.4 25.1 1.0 O1A C:GTP501 4.5 8.5 1.0 O2B C:GTP501 4.5 8.4 1.0 N C:GLN11 4.6 10.4 1.0 CG C:GLU71 4.6 23.8 1.0 CB C:ASP98 4.6 24.4 1.0 CG C:ASP69 4.6 16.7 1.0 NZ I:LYS254 4.7 19.0 1.0 O3G C:GTP501 4.7 8.7 1.0 PA C:GTP501 4.8 8.4 1.0 OD2 C:ASP98 4.9 24.7 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:10.9 occ:1.00 O1B L:GTP501 2.1 11.3 1.0 O1G L:GTP501 2.2 11.5 1.0 OE2 L:GLU71 2.5 27.8 1.0 PB L:GTP501 3.3 11.3 1.0 PG L:GTP501 3.3 11.5 1.0 CD L:GLU71 3.6 27.7 1.0 O3B L:GTP501 3.7 11.4 1.0 O2G L:GTP501 3.7 11.7 1.0 O3A L:GTP501 3.9 11.4 1.0 OD2 L:ASP69 4.1 20.2 1.0 OD1 L:ASP69 4.1 20.2 1.0 OE1 L:GLN11 4.3 13.1 1.0 OE1 L:GLU71 4.3 28.1 1.0 CB L:GLN11 4.4 12.7 1.0 CG L:GLU71 4.5 26.8 1.0 O2B L:GTP501 4.6 11.4 1.0 CB L:ASP98 4.6 25.8 1.0 CG L:ASP69 4.6 20.1 1.0 N L:GLN11 4.6 12.6 1.0 O3G L:GTP501 4.6 11.6 1.0 O1A L:GTP501 4.6 11.4 1.0 NZ D:LYS254 4.7 20.6 1.0 OD2 L:ASP98 4.8 26.4 1.0 PA L:GTP501 4.9 11.4 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.2 occ:1.00 O1B A:GTP501 2.1 8.2 1.0 O1G A:GTP501 2.2 8.3 1.0 OE2 A:GLU71 2.5 24.2 1.0 PB A:GTP501 3.3 8.2 1.0 PG A:GTP501 3.4 8.3 1.0 CD A:GLU71 3.7 24.2 1.0 O3B A:GTP501 3.7 8.2 1.0 O2G A:GTP501 3.7 8.4 1.0 O3A A:GTP501 3.9 8.2 1.0 OD2 A:ASP69 4.1 16.6 1.0 OD1 A:ASP69 4.2 16.6 1.0 OE1 A:GLN11 4.3 10.9 1.0 CB A:GLN11 4.3 10.6 1.0 OE1 A:GLU71 4.4 24.8 1.0 O1A A:GTP501 4.5 8.2 1.0 O2B A:GTP501 4.5 8.2 1.0 N A:GLN11 4.6 10.4 1.0 CG A:GLU71 4.6 23.4 1.0 CG A:ASP69 4.6 16.5 1.0 CB A:ASP98 4.6 21.7 1.0 O3G A:GTP501 4.7 8.4 1.0 NZ H:LYS254 4.7 18.2 1.0 PA A:GTP501 4.8 8.2 1.0 OD2 A:ASP98 4.9 21.7 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound)


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 Gtpgammas-Microtubule Co-Polymerized with EB3 (Merged Dataset with and Without Kinesin Bound) within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:9.8 occ:1.00 O1B K:GTP501 2.1 10.1 1.0 O1G K:GTP501 2.1 10.2 1.0 OE2 K:GLU71 2.5 23.9 1.0 PG K:GTP501 3.3 10.2 1.0 PB K:GTP501 3.3 10.1 1.0 CD K:GLU71 3.7 23.9 1.0 O3B K:GTP501 3.7 10.2 1.0 O2G K:GTP501 3.7 10.4 1.0 O3A K:GTP501 3.9 10.1 1.0 OD1 K:ASP69 4.2 17.8 1.0 OD2 K:ASP69 4.2 17.8 1.0 OE1 K:GLN11 4.3 11.8 1.0 OE1 K:GLU71 4.4 24.2 1.0 CB K:GLN11 4.4 11.5 1.0 CB K:ASP98 4.5 22.8 1.0 CG K:GLU71 4.6 23.2 1.0 O3G K:GTP501 4.6 10.3 1.0 O2B K:GTP501 4.6 10.1 1.0 O1A K:GTP501 4.6 10.2 1.0 N K:GLN11 4.6 11.3 1.0 CG K:ASP69 4.6 17.7 1.0 NZ B:LYS254 4.6 18.0 1.0 OD2 K:ASP98 4.8 23.1 1.0 PA K:GTP501 4.8 10.2 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