Magnesium in PDB 6dpv: Undecorated Gdp Microtubule

The binding sites of Magnesium atom in the Undecorated Gdp Microtubule (pdb code 6dpv). 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 Gdp Microtubule, PDB code: 6dpv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.6 occ:1.00 O1B A:GTP501 2.0 8.7 1.0 O1G A:GTP501 2.3 9.1 1.0 OD2 A:ASP98 3.0 36.8 1.0 PB A:GTP501 3.3 8.7 1.0 PG A:GTP501 3.4 8.9 1.0 OE1 A:GLU71 3.4 22.3 1.0 OD1 A:ASP98 3.6 37.6 1.0 CG A:ASP98 3.7 36.9 1.0 NZ H:LYS254 3.7 25.4 1.0 O3B A:GTP501 3.7 8.8 1.0 O2G A:GTP501 3.8 9.1 1.0 O3A A:GTP501 3.9 8.6 1.0 CB A:GLN11 4.0 8.9 1.0 OD2 A:ASP69 4.1 16.1 1.0 OE1 A:GLN11 4.2 9.1 1.0 OD1 A:ASP69 4.2 16.1 1.0 N A:GLN11 4.3 9.0 1.0 CD A:GLU71 4.4 22.1 1.0 O2B A:GTP501 4.5 8.7 1.0 O1A A:GTP501 4.5 8.5 1.0 CG A:ASP69 4.6 16.0 1.0 CG2 A:THR145 4.7 14.4 1.0 O3G A:GTP501 4.7 9.1 1.0 CA A:GLN11 4.7 8.9 1.0 PA A:GTP501 4.8 8.5 1.0 CG A:GLU71 4.8 21.6 1.0 CD A:GLN11 4.9 9.1 1.0 CE H:LYS254 5.0 25.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:9.1 occ:1.00 O1B C:GTP501 2.0 9.3 1.0 O1G C:GTP501 2.2 9.7 1.0 OD2 C:ASP98 2.9 40.0 1.0 PB C:GTP501 3.2 9.3 1.0 PG C:GTP501 3.3 9.5 1.0 OE1 C:GLU71 3.4 24.7 1.0 OD1 C:ASP98 3.5 40.9 1.0 CG C:ASP98 3.6 40.1 1.0 O3B C:GTP501 3.7 9.4 1.0 O2G C:GTP501 3.7 9.7 1.0 NZ I:LYS254 3.8 28.7 1.0 O3A C:GTP501 3.9 9.2 1.0 OD2 C:ASP69 4.0 18.1 1.0 CB C:GLN11 4.0 10.2 1.0 OD1 C:ASP69 4.1 18.2 1.0 N C:GLN11 4.2 10.3 1.0 OE1 C:GLN11 4.3 10.4 1.0 CD C:GLU71 4.4 24.5 1.0 O2B C:GTP501 4.5 9.2 1.0 CG C:ASP69 4.5 18.1 1.0 O1A C:GTP501 4.6 9.0 1.0 CG2 C:THR145 4.6 15.9 1.0 O3G C:GTP501 4.7 9.7 1.0 CA C:GLN11 4.7 10.1 1.0 PA C:GTP501 4.8 9.1 1.0 CG C:GLU71 4.8 23.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:10.3 occ:1.00 O1B E:GTP501 2.0 10.6 1.0 O1G E:GTP501 2.3 10.9 1.0 OD2 E:ASP98 3.0 39.7 1.0 PB E:GTP501 3.2 10.5 1.0 PG E:GTP501 3.4 10.8 1.0 OE1 E:GLU71 3.4 24.7 1.0 OD1 E:ASP98 3.6 40.8 1.0 CG E:ASP98 3.7 40.0 1.0 NZ G:LYS254 3.7 28.0 1.0 O3B E:GTP501 3.7 10.7 1.0 O2G E:GTP501 3.8 10.9 1.0 O3A E:GTP501 3.9 10.5 1.0 CB E:GLN11 4.0 9.9 1.0 OD2 E:ASP69 4.1 17.1 1.0 OE1 E:GLN11 4.2 10.1 1.0 OD1 E:ASP69 4.2 17.1 1.0 N E:GLN11 4.3 9.9 1.0 CD E:GLU71 4.4 24.3 1.0 O2B E:GTP501 4.5 10.5 1.0 O1A E:GTP501 4.5 10.4 1.0 CG E:ASP69 4.6 17.0 1.0 O3G E:GTP501 4.7 10.9 1.0 CG2 E:THR145 4.7 16.5 1.0 PA E:GTP501 4.7 10.4 1.0 CA E:GLN11 4.7 9.8 1.0 CG E:GLU71 4.8 23.7 1.0 CD E:GLN11 4.9 10.1 1.0 CE G:LYS254 4.9 27.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg502 b:7.4 occ:1.00 O1B J:GTP501 2.0 7.7 1.0 O1G J:GTP501 2.5 7.9 1.0 OD2 J:ASP98 2.9 27.8 1.0 OE1 J:GLU71 3.2 21.2 1.0 PB J:GTP501 3.4 7.7 1.0 OD1 J:ASP98 3.5 28.4 1.0 PG J:GTP501 3.6 7.8 1.0 CG J:ASP98 3.6 27.9 1.0 NZ F:LYS254 3.9 17.8 1.0 OD2 J:ASP69 3.9 14.0 1.0 O3B J:GTP501 3.9 7.7 1.0 O2G J:GTP501 3.9 7.9 1.0 CB J:GLN11 4.0 7.6 1.0 OD1 J:ASP69 4.0 14.0 1.0 O3A J:GTP501 4.1 7.7 1.0 OE1 J:GLN11 4.2 7.7 1.0 N J:GLN11 4.2 7.7 1.0 CD J:GLU71 4.2 20.8 1.0 CG J:ASP69 4.4 13.9 1.0 O2B J:GTP501 4.5 7.7 1.0 CG J:GLU71 4.6 20.1 1.0 O1A J:GTP501 4.7 7.6 1.0 CA J:GLN11 4.7 7.6 1.0 CG2 J:THR145 4.7 13.2 1.0 PA J:GTP501 4.9 7.6 1.0 O3G J:GTP501 4.9 7.9 1.0 CD J:GLN11 4.9 7.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg502 b:6.1 occ:1.00 O1B K:GTP501 2.0 6.3 1.0 O1G K:GTP501 2.4 6.5 1.0 OD2 K:ASP98 2.9 25.4 1.0 OE1 K:GLU71 3.2 19.3 1.0 PB K:GTP501 3.4 6.3 1.0 OD1 K:ASP98 3.5 26.0 1.0 PG K:GTP501 3.6 6.5 1.0 CG K:ASP98 3.6 25.5 1.0 NZ B:LYS254 3.9 15.8 1.0 OD2 K:ASP69 3.9 13.2 1.0 O3B K:GTP501 3.9 6.4 1.0 O2G K:GTP501 3.9 6.6 1.0 CB K:GLN11 4.0 6.8 1.0 OD1 K:ASP69 4.0 13.3 1.0 O3A K:GTP501 4.1 6.3 1.0 OE1 K:GLN11 4.2 6.9 1.0 N K:GLN11 4.2 7.0 1.0 CD K:GLU71 4.2 19.0 1.0 CG K:ASP69 4.4 13.2 1.0 O2B K:GTP501 4.5 6.3 1.0 CG K:GLU71 4.6 18.4 1.0 CA K:GLN11 4.7 6.8 1.0 O1A K:GTP501 4.7 6.2 1.0 CG2 K:THR145 4.7 11.5 1.0 O3G K:GTP501 4.9 6.5 1.0 PA K:GTP501 4.9 6.2 1.0 CD K:GLN11 4.9 6.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Undecorated Gdp Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:6.4 occ:1.00 O1B L:GTP501 2.0 6.7 1.0 O1G L:GTP501 2.4 6.9 1.0 OD2 L:ASP98 3.0 27.9 1.0 OE1 L:GLU71 3.3 21.2 1.0 PB L:GTP501 3.3 6.7 1.0 OD1 L:ASP98 3.5 28.5 1.0 PG L:GTP501 3.5 6.8 1.0 CG L:ASP98 3.6 27.9 1.0 O3B L:GTP501 3.8 6.8 1.0 O2G L:GTP501 3.9 6.9 1.0 OD2 L:ASP69 3.9 15.0 1.0 NZ D:LYS254 3.9 17.3 1.0 OD1 L:ASP69 4.0 15.2 1.0 CB L:GLN11 4.0 7.7 1.0 O3A L:GTP501 4.0 6.6 1.0 N L:GLN11 4.2 7.9 1.0 OE1 L:GLN11 4.3 7.8 1.0 CD L:GLU71 4.3 20.9 1.0 CG L:ASP69 4.4 15.0 1.0 O2B L:GTP501 4.5 6.6 1.0 CG2 L:THR145 4.6 12.5 1.0 CA L:GLN11 4.7 7.7 1.0 CG L:GLU71 4.7 20.3 1.0 O1A L:GTP501 4.7 6.5 1.0 O3G L:GTP501 4.8 6.9 1.0 PA L:GTP501 4.9 6.5 1.0 CD L:GLN11 5.0 7.8 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