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Magnesium in PDB 3jal: Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 (pdb code 3jal). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3, PDB code: 3jal:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3jal

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:29.0
occ:1.00
 O1B E:GTP501 2.0 31.4 1.0
O3G E:GTP501 2.1 32.7 1.0
OE2 E:GLU71 3.0 59.6 1.0
PB E:GTP501 3.2 30.9 1.0
PG E:GTP501 3.2 32.8 1.0
O3B E:GTP501 3.6 31.6 1.0
O2G E:GTP501 3.7 32.9 1.0
O3A E:GTP501 3.7 31.2 1.0
CB E:GLN11 4.0 24.5 1.0
CD E:GLU71 4.0 57.8 1.0
OE1 E:GLN11 4.1 26.9 1.0
OD1 E:ASP69 4.1 38.8 1.0
N E:GLN11 4.2 23.1 1.0
OD2 E:ASP69 4.3 39.6 1.0
O1A E:GTP501 4.3 31.3 1.0
O2B E:GTP501 4.5 30.5 1.0
CG E:GLU71 4.5 54.2 1.0
O1G E:GTP501 4.5 32.6 1.0
PA E:GTP501 4.6 31.4 1.0
CG E:ASP69 4.6 38.4 1.0
NZ G:LYS254 4.7 52.7 1.0
CA E:GLN11 4.7 23.8 1.0
CD E:GLN11 4.9 26.1 1.0
CB E:ASP98 4.9 54.7 1.0
OD2 E:ASP98 4.9 56.5 1.0

Magnesium binding site 2 out of 6 in 3jal

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg502

b:23.3
occ:1.00
 O1B J:GTP501 2.0 25.8 1.0
O3G J:GTP501 2.1 26.7 1.0
OE2 J:GLU71 2.9 66.2 1.0
PB J:GTP501 3.2 25.5 1.0
PG J:GTP501 3.2 26.7 1.0
O3B J:GTP501 3.6 26.1 1.0
O2G J:GTP501 3.7 27.2 1.0
O3A J:GTP501 3.8 25.8 1.0
CD J:GLU71 3.9 63.6 1.0
OD1 J:ASP69 4.1 35.8 1.0
CB J:GLN11 4.3 22.9 1.0
OE1 J:GLN11 4.3 25.3 1.0
OD2 J:ASP69 4.3 36.2 1.0
CG J:GLU71 4.4 58.5 1.0
O1A J:GTP501 4.4 25.9 1.0
N J:GLN11 4.4 21.5 1.0
O2B J:GTP501 4.4 25.4 1.0
O1G J:GTP501 4.5 26.5 1.0
NZ F:LYS254 4.6 48.0 1.0
CG J:ASP69 4.6 35.6 1.0
PA J:GTP501 4.6 25.9 1.0
CB J:ASP98 4.7 50.1 1.0
OD2 J:ASP98 4.7 53.1 1.0
OG1 J:THR145 4.9 25.1 1.0
CA J:GLN11 4.9 22.1 1.0
OE1 J:GLU71 5.0 65.5 1.0

Magnesium binding site 3 out of 6 in 3jal

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.2
occ:1.00
 O1B C:GTP501 2.0 25.6 1.0
O3G C:GTP501 2.2 27.2 1.0
OE2 C:GLU71 2.9 55.2 1.0
PB C:GTP501 3.2 25.4 1.0
PG C:GTP501 3.3 27.3 1.0
O3B C:GTP501 3.7 26.2 1.0
O2G C:GTP501 3.7 27.5 1.0
O3A C:GTP501 3.7 25.8 1.0
CB C:GLN11 4.0 25.7 1.0
OE1 C:GLN11 4.0 28.5 1.0
CD C:GLU71 4.0 54.2 1.0
OD1 C:ASP69 4.2 39.4 1.0
N C:GLN11 4.3 23.8 1.0
OD2 C:ASP69 4.3 40.0 1.0
O1A C:GTP501 4.3 26.0 1.0
O2B C:GTP501 4.5 25.1 1.0
CG C:GLU71 4.5 51.6 1.0
PA C:GTP501 4.6 26.0 1.0
O1G C:GTP501 4.6 27.2 1.0
NZ I:LYS254 4.6 46.5 1.0
CG C:ASP69 4.7 39.2 1.0
CA C:GLN11 4.7 24.5 1.0
CD C:GLN11 4.8 27.6 1.0
OD2 C:ASP98 4.9 61.0 1.0
CB C:ASP98 5.0 57.3 1.0

Magnesium binding site 4 out of 6 in 3jal

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg502

b:24.7
occ:1.00
 O1B L:GTP501 2.0 26.4 1.0
O3G L:GTP501 2.2 27.2 1.0
OE2 L:GLU71 2.8 68.9 1.0
PB L:GTP501 3.2 26.2 1.0
PG L:GTP501 3.3 27.3 1.0
O3B L:GTP501 3.7 26.7 1.0
O2G L:GTP501 3.7 27.9 1.0
CD L:GLU71 3.8 67.0 1.0
O3A L:GTP501 3.8 26.6 1.0
OD1 L:ASP69 4.0 43.0 1.0
OD2 L:ASP69 4.2 43.6 1.0
OE1 L:GLN11 4.2 28.2 1.0
CG L:GLU71 4.3 62.2 1.0
CB L:GLN11 4.3 25.8 1.0
O2B L:GTP501 4.5 26.1 1.0
O1A L:GTP501 4.5 26.9 1.0
N L:GLN11 4.5 24.4 1.0
NZ D:LYS254 4.6 48.0 1.0
CG L:ASP69 4.6 42.7 1.0
O1G L:GTP501 4.6 27.0 1.0
CB L:ASP98 4.6 57.0 1.0
OD2 L:ASP98 4.7 61.4 1.0
PA L:GTP501 4.7 26.8 1.0
OE1 L:GLU71 4.9 69.3 1.0
CA L:GLN11 5.0 24.9 1.0
OG1 L:THR145 5.0 26.2 1.0

Magnesium binding site 5 out of 6 in 3jal

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:25.7
occ:1.00
 O1B A:GTP501 2.0 26.5 1.0
O3G A:GTP501 2.1 27.6 1.0
OE2 A:GLU71 3.0 52.2 1.0
PB A:GTP501 3.2 26.2 1.0
PG A:GTP501 3.2 27.7 1.0
O3B A:GTP501 3.6 26.8 1.0
O2G A:GTP501 3.6 27.8 1.0
O3A A:GTP501 3.7 26.5 1.0
CB A:GLN11 4.0 25.2 1.0
OE1 A:GLN11 4.0 27.6 1.0
CD A:GLU71 4.1 51.6 1.0
OD1 A:ASP69 4.1 38.7 1.0
N A:GLN11 4.2 23.6 1.0
O1A A:GTP501 4.2 26.6 1.0
OD2 A:ASP69 4.3 39.7 1.0
O2B A:GTP501 4.4 25.8 1.0
O1G A:GTP501 4.5 27.8 1.0
PA A:GTP501 4.5 26.7 1.0
CG A:GLU71 4.5 49.2 1.0
CG A:ASP69 4.7 38.5 1.0
CA A:GLN11 4.7 24.2 1.0
NZ H:LYS254 4.7 48.2 1.0
CD A:GLN11 4.8 26.8 1.0
OD2 A:ASP98 5.0 57.7 1.0
O2A A:GTP501 5.0 27.1 1.0
CB A:ASP98 5.0 55.3 1.0

Magnesium binding site 6 out of 6 in 3jal

Go back to Magnesium Binding Sites List in 3jal
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Gmpcpp-Microtubule Co-Polymerized with EB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg502

b:25.0
occ:1.00
 O1B K:GTP501 1.9 26.6 1.0
O3G K:GTP501 2.1 27.6 1.0
OE2 K:GLU71 2.9 63.9 1.0
PB K:GTP501 3.2 26.3 1.0
PG K:GTP501 3.2 27.7 1.0
O3B K:GTP501 3.6 26.9 1.0
O2G K:GTP501 3.6 28.3 1.0
O3A K:GTP501 3.7 26.4 1.0
CD K:GLU71 3.9 61.9 1.0
OD1 K:ASP69 4.1 39.5 1.0
CB K:GLN11 4.3 23.7 1.0
OE1 K:GLN11 4.3 25.9 1.0
OD2 K:ASP69 4.3 40.2 1.0
O1A K:GTP501 4.3 26.4 1.0
CG K:GLU71 4.4 57.4 1.0
O2B K:GTP501 4.4 26.2 1.0
N K:GLN11 4.5 22.3 1.0
O1G K:GTP501 4.5 27.5 1.0
NZ B:LYS254 4.5 47.0 1.0
PA K:GTP501 4.6 26.4 1.0
CG K:ASP69 4.7 39.3 1.0
CB K:ASP98 4.7 51.6 1.0
OD2 K:ASP98 4.7 54.8 1.0
OG1 K:THR145 4.9 26.4 1.0
OE1 K:GLU71 5.0 64.0 1.0
CA K:GLN11 5.0 22.8 1.0

Reference:

R.Zhang, G.M.Alushin, A.Brown, E.Nogales. Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation By Eb Proteins. Cell(Cambridge,Mass.) V. 162 849 2015.
ISSN: ISSN 0092-8674
PubMed: 26234155
DOI: 10.1016/J.CELL.2015.07.012
Page generated: Wed Aug 14 16:34:54 2024

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