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Magnesium in PDB 6dpv: Undecorated Gdp Microtubule

Magnesium Binding Sites:

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 6dpv

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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 6dpv

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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 6dpv

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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 6dpv

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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 6dpv

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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 6dpv

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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

Reference:

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
Page generated: Mon Sep 30 23:27:02 2024

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