Magnesium in PDB 6dpw: Undecorated Gtpgammas Microtubule

Magnesium Binding Sites:

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 6dpw

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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 6dpw

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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 6dpw

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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 6dpw

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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 6dpw

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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 6dpw

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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

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 Dec 14 22:36:35 2020

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