Magnesium in PDB 6evy: Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerised with Doublecortin

The binding sites of Magnesium atom in the Cryo-Em Structure of Gtpgammas-Microtubule Co-Polymerised with Doublecortin (pdb code 6evy). 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-Polymerised with Doublecortin, PDB code: 6evy:
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-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:61.8 occ:1.00 O2B E:GTP501 2.1 61.8 1.0 O2G E:GTP501 2.2 61.8 1.0 O1G E:GTP501 2.2 61.8 1.0 PG E:GTP501 2.4 61.8 1.0 PB E:GTP501 2.5 61.8 1.0 O3A E:GTP501 2.6 61.8 1.0 OE2 E:GLU71 2.6 86.6 1.0 O3B E:GTP501 2.7 61.8 1.0 O2A E:GTP501 3.3 61.8 1.0 PA E:GTP501 3.5 61.8 1.0 CD E:GLU71 3.9 86.6 1.0 O3G E:GTP501 3.9 61.8 1.0 OE1 E:GLN11 4.0 82.4 1.0 O1A E:GTP501 4.0 61.8 1.0 O1B E:GTP501 4.0 61.8 1.0 CB E:GLN11 4.1 82.4 1.0 N E:GLN11 4.6 82.4 1.0 OE1 E:GLU71 4.7 86.6 1.0 CG E:GLU71 4.7 86.6 1.0 OG1 E:THR145 4.8 89.9 1.0 NZ G:LYS252 4.8 88.5 1.0 O5' E:GTP501 4.8 61.8 1.0 CD E:GLN11 5.0 82.4 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gtpgammas-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:67.5 occ:1.00 O2G J:GTP501 2.1 67.9 1.0 O2B J:GTP501 2.1 67.9 1.0 OE2 J:GLU71 2.6 0.4 1.0 PB J:GTP501 2.8 67.9 1.0 O3A J:GTP501 3.1 67.9 1.0 O3B J:GTP501 3.1 67.9 1.0 PG J:GTP501 3.2 67.9 1.0 OE1 J:GLN11 3.2 94.1 1.0 CB J:GLN11 3.3 94.1 1.0 O2A J:GTP501 3.3 67.9 1.0 PA J:GTP501 3.7 67.9 1.0 CD J:GLU71 3.8 0.4 1.0 N J:GLN11 4.0 94.1 1.0 O1G J:GTP501 4.1 67.9 1.0 CD J:GLN11 4.2 94.1 1.0 O3G J:GTP501 4.2 67.9 1.0 O1B J:GTP501 4.2 67.9 1.0 O1A J:GTP501 4.3 67.9 1.0 CA J:GLN11 4.3 94.1 1.0 CG J:GLN11 4.3 94.1 1.0 CG J:GLU71 4.5 0.4 1.0 OE1 J:GLU71 4.7 0.4 1.0 O F:ASN247 4.9 88.3 1.0 NZ F:LYS252 5.0 87.3 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gtpgammas-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:0.1 occ:1.00 O2B C:GTP501 2.1 0.1 1.0 O3G C:GTP501 2.2 0.1 1.0 O1G C:GTP501 2.2 0.1 1.0 PG C:GTP501 2.5 0.1 1.0 OE2 C:GLU71 2.5 0.6 1.0 PB C:GTP501 2.6 0.1 1.0 O3B C:GTP501 2.8 0.1 1.0 O3A C:GTP501 2.8 0.1 1.0 O2A C:GTP501 3.5 0.1 1.0 PA C:GTP501 3.7 0.1 1.0 CD C:GLU71 3.7 0.6 1.0 OE1 C:GLN11 3.9 93.5 1.0 O2G C:GTP501 3.9 0.1 1.0 CB C:GLN11 4.1 93.5 1.0 O1B C:GTP501 4.1 0.1 1.0 O1A C:GTP501 4.2 0.1 1.0 N C:GLN11 4.5 93.5 1.0 CG C:GLU71 4.6 0.6 1.0 OE1 C:GLU71 4.6 0.6 1.0 OG1 C:THR145 4.8 0.7 1.0 NZ I:LYS252 4.8 86.0 1.0 CD C:GLN11 4.9 93.5 1.0 CA C:GLN11 5.0 93.5 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gtpgammas-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:78.1 occ:1.00 O3G L:GTP501 2.0 78.1 1.0 O2B L:GTP501 2.1 78.1 1.0 OE2 L:GLU71 2.3 96.7 1.0 PB L:GTP501 2.8 78.1 1.0 O3B L:GTP501 2.9 78.1 1.0 PG L:GTP501 3.0 78.1 1.0 O3A L:GTP501 3.3 78.1 1.0 CD L:GLU71 3.5 96.7 1.0 CB L:GLN11 3.5 91.0 1.0 OE1 L:GLN11 3.5 91.0 1.0 O2G L:GTP501 3.7 78.1 1.0 O2A L:GTP501 3.8 78.1 1.0 N L:GLN11 4.0 91.0 1.0 CG L:GLU71 4.1 96.7 1.0 PA L:GTP501 4.2 78.1 1.0 O1B L:GTP501 4.2 78.1 1.0 O1G L:GTP501 4.3 78.1 1.0 CA L:GLN11 4.4 91.0 1.0 OE1 L:GLU71 4.4 96.7 1.0 CD L:GLN11 4.5 91.0 1.0 CG L:GLN11 4.6 91.0 1.0 OD1 L:ASP69 4.6 96.7 1.0 OG1 L:THR145 4.9 0.2 1.0 OD2 L:ASP69 4.9 96.7 1.0 O1A L:GTP501 4.9 78.1 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gtpgammas-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:77.4 occ:1.00 O1G A:GTP501 2.1 77.4 1.0 O2B A:GTP501 2.1 77.4 1.0 OE2 A:GLU71 2.2 89.3 1.0 PB A:GTP501 3.0 77.4 1.0 PG A:GTP501 3.3 77.4 1.0 O3B A:GTP501 3.3 77.4 1.0 OE1 A:GLN11 3.3 84.4 1.0 O3A A:GTP501 3.4 77.4 1.0 CB A:GLN11 3.4 84.4 1.0 CD A:GLU71 3.4 89.3 1.0 O2A A:GTP501 3.8 77.4 1.0 N A:GLN11 4.0 84.4 1.0 O3G A:GTP501 4.1 77.4 1.0 CG A:GLU71 4.2 89.3 1.0 PA A:GTP501 4.2 77.4 1.0 CD A:GLN11 4.2 84.4 1.0 O2G A:GTP501 4.4 77.4 1.0 CA A:GLN11 4.4 84.4 1.0 O1B A:GTP501 4.4 77.4 1.0 OE1 A:GLU71 4.4 89.3 1.0 CG A:GLN11 4.4 84.4 1.0 O1A A:GTP501 4.6 77.4 1.0 OD1 A:ASP69 4.8 89.1 1.0 OD2 A:ASP69 5.0 89.1 1.0 O H:ASN247 5.0 91.7 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gtpgammas-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 Gtpgammas-Microtubule Co-Polymerised with Doublecortin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:50.8 occ:1.00 O2B K:GTP501 2.1 53.0 1.0 O1G K:GTP501 2.1 53.0 1.0 O3G K:GTP501 2.1 53.0 1.0 OE2 K:GLU71 2.2 94.8 1.0 PG K:GTP501 2.5 53.0 1.0 PB K:GTP501 2.9 53.0 1.0 O3B K:GTP501 3.0 53.0 1.0 O3A K:GTP501 3.3 53.0 1.0 CD K:GLU71 3.5 94.8 1.0 O2A K:GTP501 3.7 53.0 1.0 OE1 K:GLN11 3.8 88.9 1.0 O2G K:GTP501 3.9 53.0 1.0 CB K:GLN11 4.0 88.9 1.0 PA K:GTP501 4.2 53.0 1.0 O1B K:GTP501 4.3 53.0 1.0 OE1 K:GLU71 4.3 94.8 1.0 CG K:GLU71 4.3 94.8 1.0 N K:GLN11 4.6 88.9 1.0 NZ B:LYS252 4.7 89.1 1.0 CD K:GLN11 4.8 88.9 1.0 O B:ASN247 4.8 89.0 1.0 OG1 K:THR145 4.9 0.3 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