Magnesium in PDB 6evz: Cryo-Em Structure of Gdp-Microtubule Co-Polymerised with Doublecortin

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:75.0 occ:1.00 O2G A:GTP501 2.1 75.5 1.0 O2B A:GTP501 2.3 75.5 1.0 O3A A:GTP501 2.4 75.5 1.0 PB A:GTP501 2.4 75.5 1.0 O3B A:GTP501 2.6 75.5 1.0 O2A A:GTP501 2.7 75.5 1.0 PG A:GTP501 2.8 75.5 1.0 PA A:GTP501 3.1 75.5 1.0 OE2 A:GLU71 3.3 56.0 1.0 O1G A:GTP501 3.3 75.5 1.0 OE1 A:GLN11 3.6 44.6 1.0 CB A:GLN11 3.7 44.6 1.0 O1B A:GTP501 4.0 75.5 1.0 O1A A:GTP501 4.0 75.5 1.0 O3G A:GTP501 4.1 75.5 1.0 CD A:GLU71 4.3 56.0 1.0 N A:GLN11 4.3 44.6 1.0 O5' A:GTP501 4.3 75.5 1.0 CD A:GLN11 4.5 44.6 1.0 NZ H:LYS252 4.5 52.0 1.0 CA A:GLN11 4.6 44.6 1.0 CG A:GLN11 4.7 44.6 1.0 OE1 A:GLU71 4.9 56.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:67.3 occ:1.00 O2G E:GTP501 2.1 67.3 1.0 O2B E:GTP501 2.2 67.3 1.0 O3A E:GTP501 2.3 67.3 1.0 PB E:GTP501 2.4 67.3 1.0 O2A E:GTP501 2.7 67.3 1.0 O3B E:GTP501 2.8 67.3 1.0 PG E:GTP501 2.8 67.3 1.0 PA E:GTP501 3.1 67.3 1.0 O1G E:GTP501 3.3 67.3 1.0 OE2 E:GLU71 3.3 55.5 1.0 OE1 E:GLN11 3.5 44.0 1.0 CB E:GLN11 3.6 44.0 1.0 O1A E:GTP501 3.9 67.3 1.0 O1B E:GTP501 3.9 67.3 1.0 O3G E:GTP501 4.2 67.3 1.0 N E:GLN11 4.3 44.0 1.0 CD E:GLU71 4.3 55.5 1.0 O5' E:GTP501 4.4 67.3 1.0 CD E:GLN11 4.5 44.0 1.0 NZ G:LYS252 4.5 48.1 1.0 CA E:GLN11 4.6 44.0 1.0 CG E:GLN11 4.7 44.0 1.0 OE1 E:GLU71 4.9 55.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:69.0 occ:1.00 O2G J:GTP501 2.1 69.1 1.0 O2B J:GTP501 2.3 69.1 1.0 O3A J:GTP501 2.4 69.1 1.0 PB J:GTP501 2.4 69.1 1.0 O3B J:GTP501 2.6 69.1 1.0 O2A J:GTP501 2.7 69.1 1.0 PG J:GTP501 2.8 69.1 1.0 PA J:GTP501 3.1 69.1 1.0 OE2 J:GLU71 3.3 57.5 1.0 O1G J:GTP501 3.3 69.1 1.0 OE1 J:GLN11 3.6 45.6 1.0 CB J:GLN11 3.7 45.6 1.0 O1B J:GTP501 3.9 69.1 1.0 O1A J:GTP501 3.9 69.1 1.0 O3G J:GTP501 4.1 69.1 1.0 CD J:GLU71 4.2 57.5 1.0 N J:GLN11 4.3 45.6 1.0 O5' J:GTP501 4.4 69.1 1.0 NZ F:LYS252 4.5 45.8 1.0 CD J:GLN11 4.5 45.6 1.0 CA J:GLN11 4.6 45.6 1.0 CG J:GLN11 4.7 45.6 1.0 OE1 J:GLU71 4.9 57.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:60.4 occ:1.00 O2G C:GTP501 2.1 60.4 1.0 O2B C:GTP501 2.1 60.4 1.0 PB C:GTP501 2.4 60.4 1.0 O3A C:GTP501 2.5 60.4 1.0 O3B C:GTP501 2.7 60.4 1.0 PG C:GTP501 2.8 60.4 1.0 O2A C:GTP501 3.0 60.4 1.0 OE2 C:GLU71 3.1 58.0 1.0 PA C:GTP501 3.3 60.4 1.0 O1G C:GTP501 3.4 60.4 1.0 OE1 C:GLN11 3.6 45.6 1.0 CB C:GLN11 3.6 45.6 1.0 O1B C:GTP501 3.9 60.4 1.0 CD C:GLU71 4.0 58.0 1.0 O3G C:GTP501 4.2 60.4 1.0 O1A C:GTP501 4.2 60.4 1.0 N C:GLN11 4.2 45.6 1.0 CD C:GLN11 4.6 45.6 1.0 CA C:GLN11 4.6 45.6 1.0 NZ I:LYS252 4.6 48.4 1.0 O5' C:GTP501 4.6 60.4 1.0 OE1 C:GLU71 4.7 58.0 1.0 CG C:GLN11 4.7 45.6 1.0 CG C:GLU71 4.8 58.0 1.0 OD1 C:ASP69 5.0 51.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:70.9 occ:1.00 O2G L:GTP501 2.1 71.0 1.0 O2B L:GTP501 2.1 71.0 1.0 O3A L:GTP501 2.4 71.0 1.0 PB L:GTP501 2.4 71.0 1.0 O3B L:GTP501 2.7 71.0 1.0 PG L:GTP501 2.8 71.0 1.0 O2A L:GTP501 2.8 71.0 1.0 PA L:GTP501 3.2 71.0 1.0 OE2 L:GLU71 3.2 61.9 1.0 O1G L:GTP501 3.3 71.0 1.0 OE1 L:GLN11 3.6 49.8 1.0 CB L:GLN11 3.8 49.8 1.0 O1B L:GTP501 3.9 71.0 1.0 CD L:GLU71 4.1 61.9 1.0 O1A L:GTP501 4.1 71.0 1.0 O3G L:GTP501 4.2 71.0 1.0 N L:GLN11 4.3 49.8 1.0 O5' L:GTP501 4.4 71.0 1.0 NZ D:LYS252 4.5 51.0 1.0 CD L:GLN11 4.6 49.8 1.0 CA L:GLN11 4.7 49.8 1.0 OE1 L:GLU71 4.7 61.9 1.0 CG L:GLN11 4.8 49.8 1.0 CG L:GLU71 4.9 61.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:71.9 occ:1.00 O2G K:GTP501 2.1 72.2 1.0 O3A K:GTP501 2.3 72.2 1.0 O2B K:GTP501 2.3 72.2 1.0 PB K:GTP501 2.4 72.2 1.0 O2A K:GTP501 2.6 72.2 1.0 O3B K:GTP501 2.6 72.2 1.0 PG K:GTP501 2.8 72.2 1.0 PA K:GTP501 3.0 72.2 1.0 O1G K:GTP501 3.3 72.2 1.0 OE2 K:GLU71 3.4 62.6 1.0 OE1 K:GLN11 3.5 50.4 1.0 CB K:GLN11 3.8 50.4 1.0 O1B K:GTP501 4.0 72.2 1.0 O1A K:GTP501 4.0 72.2 1.0 O3G K:GTP501 4.1 72.2 1.0 O5' K:GTP501 4.2 72.2 1.0 CD K:GLU71 4.3 62.6 1.0 NZ B:LYS252 4.3 51.3 1.0 N K:GLN11 4.4 50.4 1.0 CD K:GLN11 4.5 50.4 1.0 CA K:GLN11 4.7 50.4 1.0 CG K:GLN11 4.8 50.4 1.0 OE1 K:GLU71 4.9 62.6 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