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Magnesium in PDB 6dpu: Undecorated Gmpcpp Microtubule

Magnesium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Undecorated Gmpcpp Microtubule (pdb code 6dpu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Undecorated Gmpcpp Microtubule, PDB code: 6dpu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6dpu

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Magnesium binding site 1 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:6.9
occ:1.00
 O1B A:GTP501 2.0 7.0 1.0
O3G A:GTP501 2.1 7.0 1.0
PB A:GTP501 3.2 6.9 1.0
PG A:GTP501 3.3 7.0 1.0
O3B A:GTP501 3.7 7.0 1.0
O2G A:GTP501 3.7 7.0 1.0
O3A A:GTP501 3.8 7.0 1.0
CB A:GLN11 4.0 9.4 1.0
OE1 A:GLU71 4.0 23.6 1.0
OD1 A:ASP69 4.1 16.1 1.0
OD2 A:ASP69 4.1 15.8 1.0
OE1 A:GLN11 4.1 9.5 1.0
N A:GLN11 4.2 9.4 1.0
O1A A:GTP501 4.5 7.1 1.0
O2B A:GTP501 4.5 6.9 1.0
CG A:ASP69 4.5 15.9 1.0
O1G A:GTP501 4.6 7.0 1.0
NZ H:LYS254 4.6 22.6 1.0
CA A:GLN11 4.7 9.3 1.0
PA A:GTP501 4.7 7.0 1.0
CB A:ASP98 4.8 26.0 1.0
OD2 A:ASP98 4.9 26.9 1.0

Magnesium binding site 2 out of 12 in 6dpu

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Magnesium binding site 2 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:8.7
occ:1.00
 O2B B:G2P501 2.1 9.1 1.0
O2G B:G2P501 2.4 9.3 1.0
PG B:G2P501 3.4 9.3 1.0
PB B:G2P501 3.4 9.1 1.0
O1G B:G2P501 3.6 9.3 1.0
OE2 B:GLU71 3.7 23.1 1.0
O3B B:G2P501 3.7 9.2 1.0
CB B:GLN11 4.1 9.6 1.0
O2A B:G2P501 4.2 9.2 1.0
C3A B:G2P501 4.3 9.2 1.0
CD B:GLU71 4.4 22.9 1.0
OD1 B:ASP69 4.4 14.6 1.0
OE1 B:GLN11 4.4 10.2 1.0
N B:GLN11 4.4 9.3 1.0
O1B B:G2P501 4.6 9.2 1.0
OD2 B:ASP69 4.7 14.4 1.0
CG B:GLU71 4.7 22.1 1.0
O3G B:G2P501 4.8 9.3 1.0
PA B:G2P501 4.8 9.2 1.0
CA B:GLN11 4.9 9.4 1.0

Magnesium binding site 3 out of 12 in 6dpu

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Magnesium binding site 3 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:7.1
occ:1.00
 O1B C:GTP501 2.0 7.1 1.0
O3G C:GTP501 2.1 7.1 1.0
PB C:GTP501 3.2 7.1 1.0
PG C:GTP501 3.2 7.1 1.0
O3B C:GTP501 3.6 7.1 1.0
O2G C:GTP501 3.6 7.2 1.0
O3A C:GTP501 3.8 7.2 1.0
OD1 C:ASP69 4.0 17.5 1.0
CB C:GLN11 4.0 10.3 1.0
OE1 C:GLU71 4.1 25.0 1.0
OD2 C:ASP69 4.1 17.1 1.0
N C:GLN11 4.2 10.3 1.0
OE1 C:GLN11 4.2 10.4 1.0
O1A C:GTP501 4.4 7.2 1.0
O2B C:GTP501 4.4 7.1 1.0
CG C:ASP69 4.5 17.3 1.0
O1G C:GTP501 4.6 7.1 1.0
NZ I:LYS254 4.6 24.4 1.0
PA C:GTP501 4.7 7.2 1.0
CA C:GLN11 4.7 10.2 1.0
CB C:ASP98 4.8 26.9 1.0
OD2 C:ASP98 4.9 27.8 1.0
OG1 C:THR145 5.0 14.2 1.0

Magnesium binding site 4 out of 12 in 6dpu

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Magnesium binding site 4 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:9.1
occ:1.00
 O2B D:G2P501 2.0 9.3 1.0
O2G D:G2P501 2.3 9.6 1.0
PG D:G2P501 3.4 9.6 1.0
PB D:G2P501 3.4 9.3 1.0
O1G D:G2P501 3.7 9.6 1.0
O3B D:G2P501 3.7 9.5 1.0
OE2 D:GLU71 3.7 25.9 1.0
CB D:GLN11 4.0 10.7 1.0
O2A D:G2P501 4.2 9.3 1.0
OD1 D:ASP69 4.3 16.3 1.0
C3A D:G2P501 4.3 9.4 1.0
N D:GLN11 4.3 10.4 1.0
CD D:GLU71 4.4 25.6 1.0
OE1 D:GLN11 4.5 11.4 1.0
O1B D:G2P501 4.6 9.4 1.0
OD2 D:ASP69 4.6 16.2 1.0
O3G D:G2P501 4.7 9.6 1.0
CG D:GLU71 4.7 24.7 1.0
CA D:GLN11 4.8 10.4 1.0
PA D:G2P501 4.8 9.3 1.0
CG D:ASP69 4.9 16.2 1.0
CG2 D:THR74 5.0 26.1 1.0
OG1 D:THR145 5.0 12.0 1.0

Magnesium binding site 5 out of 12 in 6dpu

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Magnesium binding site 5 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:8.1
occ:1.00
 O1B E:GTP501 2.0 8.1 1.0
O3G E:GTP501 2.0 8.2 1.0
PB E:GTP501 3.1 8.1 1.0
PG E:GTP501 3.1 8.2 1.0
O3B E:GTP501 3.5 8.1 1.0
O2G E:GTP501 3.6 8.2 1.0
O3A E:GTP501 3.7 8.2 1.0
OE1 E:GLU71 4.1 25.5 1.0
OD1 E:ASP69 4.1 16.8 1.0
CB E:GLN11 4.2 9.9 1.0
OD2 E:ASP69 4.3 16.5 1.0
OE1 E:GLN11 4.3 10.0 1.0
N E:GLN11 4.3 9.9 1.0
O1A E:GTP501 4.4 8.2 1.0
O2B E:GTP501 4.4 8.1 1.0
O1G E:GTP501 4.4 8.2 1.0
NZ G:LYS254 4.5 25.1 1.0
PA E:GTP501 4.6 8.2 1.0
CG E:ASP69 4.7 16.6 1.0
CB E:ASP98 4.7 28.9 1.0
OD2 E:ASP98 4.8 30.0 1.0
CA E:GLN11 4.9 9.9 1.0
OG1 E:THR145 4.9 15.9 1.0

Magnesium binding site 6 out of 12 in 6dpu

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Magnesium binding site 6 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:10.2
occ:1.00
 O2B F:G2P501 2.0 10.7 1.0
O2G F:G2P501 2.4 10.9 1.0
PB F:G2P501 3.4 10.7 1.0
PG F:G2P501 3.4 10.8 1.0
OE2 F:GLU71 3.7 23.7 1.0
O3B F:G2P501 3.7 10.8 1.0
O1G F:G2P501 3.7 10.9 1.0
O2A F:G2P501 4.1 10.7 1.0
CB F:GLN11 4.1 10.3 1.0
C3A F:G2P501 4.3 10.7 1.0
OE1 F:GLN11 4.4 11.0 1.0
CD F:GLU71 4.4 23.4 1.0
N F:GLN11 4.5 9.9 1.0
OD1 F:ASP69 4.5 14.8 1.0
O1B F:G2P501 4.6 10.7 1.0
O3G F:G2P501 4.8 10.9 1.0
PA F:G2P501 4.8 10.7 1.0
CG F:GLU71 4.8 22.7 1.0
OD2 F:ASP69 4.8 14.7 1.0
CA F:GLN11 4.9 10.1 1.0
OE2 E:GLU254 5.0 26.4 1.0

Magnesium binding site 7 out of 12 in 6dpu

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Magnesium binding site 7 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:28.3
occ:1.00
 O2B G:G2P501 2.0 28.8 1.0
O2G G:G2P501 2.3 29.7 1.0
PG G:G2P501 3.3 29.6 1.0
PB G:G2P501 3.3 28.8 1.0
O1G G:G2P501 3.6 29.8 1.0
O3B G:G2P501 3.6 29.1 1.0
OE2 G:GLU71 3.6 41.4 1.0
O2A G:G2P501 4.1 28.2 1.0
CB G:GLN11 4.2 21.4 1.0
C3A G:G2P501 4.3 28.5 1.0
CD G:GLU71 4.4 41.2 1.0
OE1 G:GLN11 4.4 23.0 1.0
O1B G:G2P501 4.5 28.9 1.0
N G:GLN11 4.6 20.3 1.0
OD1 G:ASP69 4.6 27.4 1.0
O3G G:G2P501 4.7 29.7 1.0
PA G:G2P501 4.8 28.4 1.0
CG G:GLU71 4.8 39.8 1.0
OD2 G:ASP69 4.9 27.6 1.0
CA G:GLN11 5.0 20.8 1.0

Magnesium binding site 8 out of 12 in 6dpu

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Magnesium binding site 8 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:23.8
occ:1.00
 O2B H:G2P501 2.0 24.5 1.0
O2G H:G2P501 2.3 25.4 1.0
PG H:G2P501 3.3 25.3 1.0
PB H:G2P501 3.4 24.5 1.0
O1G H:G2P501 3.6 25.4 1.0
OE2 H:GLU71 3.6 40.1 1.0
O3B H:G2P501 3.7 24.9 1.0
CB H:GLN11 4.1 19.9 1.0
O2A H:G2P501 4.1 23.9 1.0
CD H:GLU71 4.3 40.0 1.0
OE1 H:GLN11 4.4 21.4 1.0
C3A H:G2P501 4.4 24.2 1.0
OD1 H:ASP69 4.5 26.8 1.0
N H:GLN11 4.5 19.0 1.0
O1B H:G2P501 4.6 24.6 1.0
O3G H:G2P501 4.7 25.4 1.0
CG H:GLU71 4.8 38.6 1.0
OD2 H:ASP69 4.8 26.8 1.0
PA H:G2P501 4.8 24.0 1.0
CA H:GLN11 4.9 19.3 1.0

Magnesium binding site 9 out of 12 in 6dpu

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Magnesium binding site 9 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg502

b:24.9
occ:1.00
 O2B I:G2P501 2.0 25.5 1.0
O2G I:G2P501 2.4 26.4 1.0
PG I:G2P501 3.4 26.4 1.0
PB I:G2P501 3.4 25.5 1.0
OE2 I:GLU71 3.6 42.5 1.0
O1G I:G2P501 3.6 26.6 1.0
O3B I:G2P501 3.7 25.9 1.0
CB I:GLN11 4.1 22.2 1.0
O2A I:G2P501 4.1 24.6 1.0
CD I:GLU71 4.3 42.4 1.0
OE1 I:GLN11 4.3 23.9 1.0
C3A I:G2P501 4.4 25.1 1.0
OD1 I:ASP69 4.5 29.0 1.0
N I:GLN11 4.5 21.3 1.0
O1B I:G2P501 4.6 25.5 1.0
O3G I:G2P501 4.7 26.4 1.0
CG I:GLU71 4.8 41.0 1.0
OD2 I:ASP69 4.8 29.1 1.0
PA I:G2P501 4.8 24.7 1.0
CA I:GLN11 4.9 21.6 1.0

Magnesium binding site 10 out of 12 in 6dpu

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Magnesium binding site 10 out of 12 in the Undecorated Gmpcpp Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Undecorated Gmpcpp Microtubule within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg502

b:5.7
occ:1.00
 O3G J:GTP501 1.9 5.7 1.0
O1B J:GTP501 2.0 5.7 1.0
PG J:GTP501 3.1 5.7 1.0
PB J:GTP501 3.1 5.7 1.0
O3B J:GTP501 3.5 5.7 1.0
O2G J:GTP501 3.5 5.7 1.0
O3A J:GTP501 3.6 5.7 1.0
CB J:GLN11 4.1 7.5 1.0
OE1 J:GLU71 4.1 19.0 1.0
OE1 J:GLN11 4.2 7.4 1.0
OD1 J:ASP69 4.3 12.7 1.0
O1A J:GTP501 4.4 5.8 1.0
N J:GLN11 4.4 7.6 1.0
NZ F:LYS254 4.4 18.0 1.0
O1G J:GTP501 4.4 5.7 1.0
OD2 J:ASP69 4.4 12.6 1.0
O2B J:GTP501 4.4 5.7 1.0
PA J:GTP501 4.6 5.8 1.0
CB J:ASP98 4.8 19.8 1.0
CG J:ASP69 4.8 12.6 1.0
OD2 J:ASP98 4.8 20.5 1.0
CA J:GLN11 4.9 7.5 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 23:26:58 2024

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