Magnesium in PDB 6ew0: Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol

The binding sites of Magnesium atom in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol (pdb code 6ew0). 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-Polymerised with Doublecortin and Supplemented with Taxol, PDB code: 6ew0:
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-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:49.4 occ:1.00 O1G E:GTP501 2.1 49.9 1.0 O3A E:GTP501 2.1 49.9 1.0 O2B E:GTP501 2.3 49.9 1.0 PB E:GTP501 2.4 49.9 1.0 PG E:GTP501 2.5 49.9 1.0 O2G E:GTP501 2.6 49.9 1.0 O3B E:GTP501 2.7 49.9 1.0 O2A E:GTP501 2.8 49.9 1.0 PA E:GTP501 2.9 49.9 1.0 OE2 E:GLU71 3.4 0.5 1.0 OE1 E:GLN11 3.6 93.8 1.0 O1A E:GTP501 3.6 49.9 1.0 CB E:GLN11 3.8 93.8 1.0 O1B E:GTP501 3.9 49.9 1.0 O3G E:GTP501 4.0 49.9 1.0 CD E:GLU71 4.3 0.5 1.0 O5' E:GTP501 4.3 49.9 1.0 N E:GLN11 4.5 93.8 1.0 NZ G:LYS252 4.5 0.5 1.0 CD E:GLN11 4.6 93.8 1.0 CA E:GLN11 4.8 93.8 1.0 CG E:GLN11 4.8 93.8 1.0 OE1 E:GLU71 4.9 0.5 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:0.4 occ:1.00 O1G J:GTP501 2.1 0.1 1.0 O3A J:GTP501 2.1 0.1 1.0 O2B J:GTP501 2.4 0.1 1.0 PB J:GTP501 2.4 0.1 1.0 O3G J:GTP501 2.5 0.1 1.0 PG J:GTP501 2.5 0.1 1.0 O3B J:GTP501 2.7 0.1 1.0 O2A J:GTP501 2.7 0.1 1.0 PA J:GTP501 2.9 0.1 1.0 OE2 J:GLU71 3.3 0.0 1.0 OE1 J:GLN11 3.4 96.4 1.0 O1A J:GTP501 3.8 0.1 1.0 CB J:GLN11 3.9 96.4 1.0 O1B J:GTP501 3.9 0.1 1.0 O2G J:GTP501 4.0 0.1 1.0 O5' J:GTP501 4.2 0.1 1.0 CD J:GLU71 4.2 0.0 1.0 NZ F:LYS252 4.2 0.4 1.0 CD J:GLN11 4.4 96.4 1.0 N J:GLN11 4.7 96.4 1.0 OE1 J:GLU71 4.8 0.0 1.0 CG J:GLN11 4.8 96.4 1.0 CA J:GLN11 4.9 96.4 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:76.9 occ:1.00 O2G C:GTP501 2.1 76.8 1.0 O2B C:GTP501 2.2 76.8 1.0 O1G C:GTP501 2.3 76.8 1.0 PG C:GTP501 2.4 76.8 1.0 PB C:GTP501 2.4 76.8 1.0 O3A C:GTP501 2.5 76.8 1.0 O3B C:GTP501 2.6 76.8 1.0 O2A C:GTP501 3.1 76.8 1.0 OE2 C:GLU71 3.2 0.9 1.0 PA C:GTP501 3.3 76.8 1.0 OE1 C:GLN11 3.6 92.0 1.0 CB C:GLN11 3.6 92.0 1.0 O1A C:GTP501 3.8 76.8 1.0 O3G C:GTP501 3.9 76.8 1.0 O1B C:GTP501 4.0 76.8 1.0 CD C:GLU71 4.0 0.9 1.0 N C:GLN11 4.1 92.0 1.0 CA C:GLN11 4.5 92.0 1.0 CD C:GLN11 4.5 92.0 1.0 CG C:GLN11 4.7 92.0 1.0 O5' C:GTP501 4.7 76.8 1.0 OE1 C:GLU71 4.7 0.9 1.0 OD1 C:ASP69 4.7 1.0 1.0 CG C:GLU71 4.7 0.9 1.0 OG1 C:THR145 4.9 0.8 1.0 NZ I:LYS252 4.9 0.5 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:0.9 occ:1.00 O3G L:GTP501 2.1 0.1 1.0 O3B L:GTP501 2.1 0.1 1.0 O2B L:GTP501 2.2 0.1 1.0 PB L:GTP501 2.4 0.1 1.0 PG L:GTP501 2.6 0.1 1.0 OE2 L:GLU71 3.0 0.2 1.0 O3A L:GTP501 3.0 0.1 1.0 CD L:GLU71 3.6 0.2 1.0 O2G L:GTP501 3.6 0.1 1.0 O1G L:GTP501 3.7 0.1 1.0 O1B L:GTP501 3.9 0.1 1.0 OD1 L:ASP69 3.9 0.0 1.0 CB L:GLN11 4.0 93.5 1.0 CG L:GLU71 4.0 0.2 1.0 O2A L:GTP501 4.1 0.1 1.0 PA L:GTP501 4.1 0.1 1.0 OG1 L:THR145 4.2 0.6 1.0 OE1 L:GLN11 4.2 93.5 1.0 N L:GLN11 4.2 93.5 1.0 OE1 L:GLU71 4.3 0.2 1.0 OD2 L:ASP69 4.5 0.0 1.0 O1A L:GTP501 4.7 0.1 1.0 CG L:ASP69 4.7 0.0 1.0 CB L:THR145 4.7 0.6 1.0 CB L:ASP98 4.7 0.7 1.0 CA L:GLN11 4.7 93.5 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:94.3 occ:1.00 O2G A:GTP501 2.1 94.0 1.0 O3B A:GTP501 2.2 94.0 1.0 O2B A:GTP501 2.3 94.0 1.0 PB A:GTP501 2.4 94.0 1.0 PG A:GTP501 2.6 94.0 1.0 O3A A:GTP501 2.8 94.0 1.0 OE2 A:GLU71 2.9 0.6 1.0 CD A:GLU71 3.6 0.6 1.0 O1G A:GTP501 3.7 94.0 1.0 O3G A:GTP501 3.7 94.0 1.0 O2A A:GTP501 3.8 94.0 1.0 CB A:GLN11 3.9 95.1 1.0 PA A:GTP501 3.9 94.0 1.0 O1B A:GTP501 3.9 94.0 1.0 OE1 A:GLN11 3.9 95.1 1.0 N A:GLN11 4.2 95.1 1.0 CG A:GLU71 4.2 0.6 1.0 OD1 A:ASP69 4.2 0.2 1.0 OE1 A:GLU71 4.3 0.6 1.0 OG1 A:THR145 4.4 0.6 1.0 O1A A:GTP501 4.6 94.0 1.0 CA A:GLN11 4.7 95.1 1.0 OD2 A:ASP69 4.7 0.2 1.0 CD A:GLN11 4.9 95.1 1.0 CG A:ASP69 4.9 0.2 1.0 CB A:THR145 4.9 0.6 1.0 CB A:ASP98 4.9 0.0 1.0 CG A:GLN11 5.0 95.1 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin and Supplemented with Taxol


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-Polymerised with Doublecortin and Supplemented with Taxol within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:88.0 occ:1.00 O2B K:GTP501 2.1 87.6 1.0 O1G K:GTP501 2.1 87.6 1.0 O3G K:GTP501 2.2 87.6 1.0 PG K:GTP501 2.4 87.6 1.0 PB K:GTP501 2.6 87.6 1.0 O3B K:GTP501 2.7 87.6 1.0 O3A K:GTP501 2.9 87.6 1.0 OE2 K:GLU71 3.1 0.1 1.0 O2A K:GTP501 3.3 87.6 1.0 OE1 K:GLN11 3.6 0.4 1.0 PA K:GTP501 3.7 87.6 1.0 CB K:GLN11 3.8 0.4 1.0 CD K:GLU71 3.9 0.1 1.0 O2G K:GTP501 3.9 87.6 1.0 O1B K:GTP501 4.1 87.6 1.0 N K:GLN11 4.4 0.4 1.0 OE1 K:GLU71 4.5 0.1 1.0 O1A K:GTP501 4.5 87.6 1.0 CG K:GLU71 4.6 0.1 1.0 CD K:GLN11 4.6 0.4 1.0 NZ B:LYS252 4.7 0.0 1.0 CA K:GLN11 4.8 0.4 1.0 OD1 K:ASP69 4.8 0.4 1.0 CG K:GLN11 4.8 0.4 1.0 OG1 K:THR145 4.9 0.2 1.0 O5' K:GTP501 5.0 87.6 1.0

S.W.Manka, C.A.Moores. The Role of Tubulin-Tubulin Lattice Contacts in the Mechanism of Microtubule Dynamic Instability. Nat. Struct. Mol. Biol. V. 25 607 2018.
ISSN: ESSN 1545-9985
PubMed: 29967541
DOI: 10.1038/S41594-018-0087-8