Magnesium in PDB 6dpw: Undecorated Gtpgammas Microtubule

The binding sites of Magnesium atom in the Undecorated Gtpgammas Microtubule (pdb code 6dpw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Undecorated Gtpgammas Microtubule, PDB code: 6dpw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.1 occ:1.00 O1G A:GTP501 2.1 13.8 1.0 O1B A:GTP501 2.1 13.6 1.0 OE2 A:GLU71 2.6 36.1 1.0 PG A:GTP501 3.2 13.9 1.0 PB A:GTP501 3.3 13.4 1.0 O2G A:GTP501 3.6 14.0 1.0 O3B A:GTP501 3.6 13.7 1.0 CD A:GLU71 3.8 35.7 1.0 O3A A:GTP501 3.8 13.5 1.0 OD1 A:ASP69 4.1 22.4 1.0 OD2 A:ASP69 4.3 22.4 1.0 CB A:ASP98 4.4 34.1 1.0 OE1 A:GLN11 4.5 20.1 1.0 O1A A:GTP501 4.5 13.6 1.0 CB A:GLN11 4.5 17.9 1.0 O2B A:GTP501 4.6 13.4 1.0 O3G A:GTP501 4.6 13.9 1.0 OE1 A:GLU71 4.6 35.8 1.0 CG A:GLU71 4.6 34.6 1.0 CG A:ASP69 4.6 22.2 1.0 N A:GLN11 4.7 16.8 1.0 NZ H:LYS254 4.7 33.0 1.0 OD2 A:ASP98 4.7 34.5 1.0 PA A:GTP501 4.8 13.5 1.0 OG1 A:THR145 4.8 20.7 1.0 CG A:ASP98 5.0 34.8 1.0

Magnesium binding site 2 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:13.7 occ:1.00 O1B C:GTP501 2.0 14.5 1.0 O1G C:GTP501 2.1 14.6 1.0 OE2 C:GLU71 2.6 39.0 1.0 PG C:GTP501 3.2 14.7 1.0 PB C:GTP501 3.2 14.4 1.0 O2G C:GTP501 3.6 14.9 1.0 O3B C:GTP501 3.6 14.6 1.0 CD C:GLU71 3.7 38.7 1.0 O3A C:GTP501 3.8 14.5 1.0 OD1 C:ASP69 4.0 26.0 1.0 OD2 C:ASP69 4.2 25.8 1.0 CB C:ASP98 4.3 40.4 1.0 O2B C:GTP501 4.5 14.4 1.0 O1A C:GTP501 4.5 14.5 1.0 CG C:GLU71 4.5 37.5 1.0 CG C:ASP69 4.5 25.8 1.0 O3G C:GTP501 4.6 14.7 1.0 OE1 C:GLU71 4.6 38.7 1.0 OE1 C:GLN11 4.6 23.0 1.0 CB C:GLN11 4.6 20.2 1.0 OD2 C:ASP98 4.7 41.7 1.0 OG1 C:THR145 4.7 20.5 1.0 N C:GLN11 4.7 19.2 1.0 NZ I:LYS254 4.7 37.9 1.0 PA C:GTP501 4.8 14.6 1.0 CG C:ASP98 4.9 41.8 1.0

Magnesium binding site 3 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:16.8 occ:1.00 O1G E:GTP501 2.0 17.8 1.0 O1B E:GTP501 2.1 17.4 1.0 OE2 E:GLU71 2.7 41.9 1.0 PG E:GTP501 3.2 17.8 1.0 PB E:GTP501 3.2 17.2 1.0 O3B E:GTP501 3.6 17.5 1.0 O2G E:GTP501 3.6 18.0 1.0 O3A E:GTP501 3.8 17.3 1.0 CD E:GLU71 3.8 41.2 1.0 OD1 E:ASP69 4.1 24.6 1.0 OD2 E:ASP69 4.3 24.7 1.0 O1A E:GTP501 4.4 17.4 1.0 CB E:ASP98 4.4 38.3 1.0 O3G E:GTP501 4.5 17.8 1.0 O2B E:GTP501 4.5 17.2 1.0 OE1 E:GLN11 4.5 22.6 1.0 CB E:GLN11 4.6 20.0 1.0 OE1 E:GLU71 4.6 41.5 1.0 NZ G:LYS254 4.6 35.4 1.0 CG E:GLU71 4.7 39.7 1.0 PA E:GTP501 4.7 17.4 1.0 OD2 E:ASP98 4.7 38.4 1.0 CG E:ASP69 4.7 24.2 1.0 N E:GLN11 4.7 18.4 1.0 OG1 E:THR145 4.8 26.0 1.0 CG E:ASP98 5.0 38.7 1.0

Magnesium binding site 4 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:30.6 occ:1.00 O1B J:GTP501 2.1 31.1 1.0 O1G J:GTP501 2.3 31.6 1.0 OE2 J:GLU71 2.6 62.5 1.0 PB J:GTP501 3.3 30.5 1.0 PG J:GTP501 3.4 31.6 1.0 CD J:GLU71 3.7 61.9 1.0 O3B J:GTP501 3.8 30.8 1.0 O2G J:GTP501 3.8 32.3 1.0 O3A J:GTP501 3.9 30.4 1.0 OD1 J:ASP69 3.9 38.5 1.0 OD2 J:ASP69 4.1 38.1 1.0 OE1 J:GLN11 4.3 34.5 1.0 CB J:GLN11 4.4 31.1 1.0 CG J:ASP69 4.5 37.7 1.0 O1A J:GTP501 4.5 30.3 1.0 N J:GLN11 4.5 29.1 1.0 CG J:GLU71 4.5 59.4 1.0 CB J:ASP98 4.5 57.1 1.0 O2B J:GTP501 4.6 30.8 1.0 OE1 J:GLU71 4.6 62.6 1.0 O3G J:GTP501 4.7 31.4 1.0 PA J:GTP501 4.8 30.4 1.0 OD2 J:ASP98 4.8 59.0 1.0 NZ F:LYS254 4.8 47.4 1.0 OG1 J:THR145 4.9 40.7 1.0

Magnesium binding site 5 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:25.3 occ:1.00 O1B K:GTP501 2.1 25.2 1.0 O1G K:GTP501 2.4 25.6 1.0 OE2 K:GLU71 2.5 58.6 1.0 PB K:GTP501 3.4 24.7 1.0 PG K:GTP501 3.5 25.5 1.0 CD K:GLU71 3.6 58.2 1.0 O2G K:GTP501 3.8 26.0 1.0 O3B K:GTP501 3.8 25.0 1.0 OD1 K:ASP69 3.8 36.9 1.0 OD2 K:ASP69 4.0 36.4 1.0 O3A K:GTP501 4.0 24.7 1.0 OE1 K:GLN11 4.3 32.6 1.0 CB K:GLN11 4.3 29.3 1.0 CG K:ASP69 4.4 36.3 1.0 CG K:GLU71 4.4 55.8 1.0 N K:GLN11 4.4 27.6 1.0 OE1 K:GLU71 4.5 59.1 1.0 CB K:ASP98 4.5 53.0 1.0 O1A K:GTP501 4.6 24.8 1.0 O2B K:GTP501 4.6 24.9 1.0 O3G K:GTP501 4.8 25.5 1.0 PA K:GTP501 4.8 24.8 1.0 OD2 K:ASP98 4.9 55.2 1.0 OG1 K:THR145 4.9 34.6 1.0 NZ B:LYS254 4.9 44.2 1.0 CA K:GLN11 5.0 28.2 1.0

Magnesium binding site 6 out of 6 in the Undecorated Gtpgammas Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Undecorated Gtpgammas Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:26.6 occ:1.00 O1B L:GTP501 2.1 26.9 1.0 O1G L:GTP501 2.3 26.9 1.0 OE2 L:GLU71 2.5 60.2 1.0 PB L:GTP501 3.3 26.6 1.0 PG L:GTP501 3.4 26.7 1.0 CD L:GLU71 3.7 60.0 1.0 O2G L:GTP501 3.7 27.5 1.0 O3B L:GTP501 3.7 26.5 1.0 OD1 L:ASP69 3.8 41.3 1.0 O3A L:GTP501 4.0 26.7 1.0 OD2 L:ASP69 4.0 40.4 1.0 CG L:ASP69 4.3 40.6 1.0 CG L:GLU71 4.4 57.7 1.0 OE1 L:GLN11 4.4 36.5 1.0 CB L:GLN11 4.4 32.6 1.0 CB L:ASP98 4.4 59.7 1.0 N L:GLN11 4.5 31.2 1.0 OE1 L:GLU71 4.5 60.8 1.0 O2B L:GTP501 4.6 26.7 1.0 O1A L:GTP501 4.7 26.6 1.0 O3G L:GTP501 4.7 26.7 1.0 OG1 L:THR145 4.7 34.0 1.0 OD2 L:ASP98 4.8 63.1 1.0 PA L:GTP501 4.9 26.8 1.0 NZ D:LYS254 4.9 48.4 1.0

R.Zhang, B.Lafrance, E.Nogales. Separating the Effects of Nucleotide and Eb Binding on Microtubule Structure. Proc. Natl. Acad. Sci. V. 115 E6191 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29915050
DOI: 10.1073/PNAS.1802637115