Magnesium in PDB 5jyg: Cryo-Em Structure of the Mamk Filament at 6.5 A

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mamk Filament at 6.5 A (pdb code 5jyg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Cryo-Em Structure of the Mamk Filament at 6.5 A, PDB code: 5jyg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 5jyg

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Magnesium binding site 1 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:0.0
occ:1.00
O3B A:ADP402 2.5 0.0 1.0
O2A A:ADP402 3.4 0.0 1.0
OD2 A:ASP161 3.6 0.0 1.0
PB A:ADP402 3.7 0.0 1.0
OE1 A:GLU143 3.7 0.0 1.0
O1B A:ADP402 3.8 0.0 1.0
CD A:GLU143 4.1 0.0 1.0
OE2 A:GLU143 4.1 0.0 1.0
OD1 A:ASP17 4.2 0.0 1.0
CG A:ASP161 4.4 0.0 1.0
PA A:ADP402 4.4 0.0 1.0
OD1 A:ASP161 4.4 0.0 1.0
O3A A:ADP402 4.5 0.0 1.0
O A:LEU18 4.9 0.0 1.0
O2B A:ADP402 5.0 0.0 1.0

Magnesium binding site 2 out of 14 in 5jyg

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Magnesium binding site 2 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:0.0
occ:1.00
OE1 B:GLU143 3.1 0.0 1.0
O2B B:ADP402 3.2 0.0 1.0
OE2 B:GLU143 3.2 0.0 1.0
O3B B:ADP402 3.2 0.0 1.0
CD B:GLU143 3.3 0.0 1.0
OD2 B:ASP161 3.7 0.0 1.0
PB B:ADP402 3.7 0.0 1.0
OD1 B:ASP17 4.0 0.0 1.0
O2A B:ADP402 4.2 0.0 1.0
OD1 B:ASP161 4.3 0.0 1.0
CG B:ASP161 4.4 0.0 1.0
CG B:GLU143 4.4 0.0 1.0
CA B:GLY19 4.4 0.0 1.0
OD2 B:ASP17 4.8 0.0 1.0
O1B B:ADP402 4.8 0.0 1.0
CG B:ASP17 4.8 0.0 1.0
O3A B:ADP402 4.9 0.0 1.0
CB B:GLU143 5.0 0.0 1.0

Magnesium binding site 3 out of 14 in 5jyg

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Magnesium binding site 3 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:0.0
occ:1.00
O3B C:ADP402 2.6 0.0 1.0
OE1 C:GLU143 3.3 0.0 1.0
PB C:ADP402 3.7 0.0 1.0
CD C:GLU143 3.9 0.0 1.0
O2B C:ADP402 4.0 0.0 1.0
OD1 C:ASP17 4.1 0.0 1.0
O3A C:ADP402 4.1 0.0 1.0
OE2 C:GLU143 4.2 0.0 1.0
O2A C:ADP402 4.3 0.0 1.0
OG1 C:THR166 4.5 0.0 1.0
OD2 C:ASP17 4.7 0.0 1.0
PA C:ADP402 4.7 0.0 1.0
OD2 C:ASP161 4.8 0.0 1.0
CG C:ASP17 4.8 0.0 1.0
CG C:GLU143 5.0 0.0 1.0

Magnesium binding site 4 out of 14 in 5jyg

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Magnesium binding site 4 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:0.0
occ:1.00
O3B D:ADP402 2.5 0.0 1.0
OE1 D:GLU143 3.2 0.0 1.0
OE2 D:GLU143 3.3 0.0 1.0
O2A D:ADP402 3.4 0.0 1.0
CD D:GLU143 3.4 0.0 1.0
OD2 D:ASP161 3.5 0.0 1.0
O D:LEU18 3.7 0.0 1.0
PB D:ADP402 4.0 0.0 1.0
OD1 D:ASP17 4.3 0.0 1.0
CG D:ASP161 4.4 0.0 1.0
PA D:ADP402 4.4 0.0 1.0
OD1 D:ASP161 4.5 0.0 1.0
CG D:GLU143 4.5 0.0 1.0
O3A D:ADP402 4.6 0.0 1.0
O2B D:ADP402 4.8 0.0 1.0
O1A D:ADP402 4.8 0.0 1.0
C D:LEU18 4.9 0.0 1.0
CA D:GLY19 5.0 0.0 1.0
O1B D:ADP402 5.0 0.0 1.0

Magnesium binding site 5 out of 14 in 5jyg

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Magnesium binding site 5 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:0.0
occ:1.00
O3B E:ADP402 2.5 0.0 1.0
O2A E:ADP402 3.4 0.0 1.0
OD2 E:ASP161 3.6 0.0 1.0
PB E:ADP402 3.7 0.0 1.0
OE1 E:GLU143 3.7 0.0 1.0
O1B E:ADP402 3.8 0.0 1.0
CD E:GLU143 4.1 0.0 1.0
OE2 E:GLU143 4.1 0.0 1.0
OD1 E:ASP17 4.2 0.0 1.0
CG E:ASP161 4.4 0.0 1.0
PA E:ADP402 4.4 0.0 1.0
OD1 E:ASP161 4.4 0.0 1.0
O3A E:ADP402 4.5 0.0 1.0
O E:LEU18 4.9 0.0 1.0
O2B E:ADP402 5.0 0.0 1.0

Magnesium binding site 6 out of 14 in 5jyg

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Magnesium binding site 6 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


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 the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:0.0
occ:1.00
OE1 F:GLU143 3.1 0.0 1.0
O2B F:ADP402 3.2 0.0 1.0
OE2 F:GLU143 3.2 0.0 1.0
O3B F:ADP402 3.2 0.0 1.0
CD F:GLU143 3.3 0.0 1.0
OD2 F:ASP161 3.7 0.0 1.0
PB F:ADP402 3.7 0.0 1.0
OD1 F:ASP17 4.0 0.0 1.0
O2A F:ADP402 4.2 0.0 1.0
OD1 F:ASP161 4.3 0.0 1.0
CG F:ASP161 4.4 0.0 1.0
CG F:GLU143 4.4 0.0 1.0
CA F:GLY19 4.4 0.0 1.0
OD2 F:ASP17 4.8 0.0 1.0
O1B F:ADP402 4.8 0.0 1.0
CG F:ASP17 4.8 0.0 1.0
O3A F:ADP402 4.9 0.0 1.0
CB F:GLU143 5.0 0.0 1.0

Magnesium binding site 7 out of 14 in 5jyg

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Magnesium binding site 7 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:0.0
occ:1.00
O3B G:ADP402 2.6 0.0 1.0
OE1 G:GLU143 3.3 0.0 1.0
PB G:ADP402 3.7 0.0 1.0
CD G:GLU143 3.9 0.0 1.0
O2B G:ADP402 4.0 0.0 1.0
OD1 G:ASP17 4.1 0.0 1.0
O3A G:ADP402 4.1 0.0 1.0
OE2 G:GLU143 4.2 0.0 1.0
O2A G:ADP402 4.3 0.0 1.0
OG1 G:THR166 4.5 0.0 1.0
OD2 G:ASP17 4.7 0.0 1.0
PA G:ADP402 4.7 0.0 1.0
OD2 G:ASP161 4.8 0.0 1.0
CG G:ASP17 4.8 0.0 1.0
CG G:GLU143 5.0 0.0 1.0

Magnesium binding site 8 out of 14 in 5jyg

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Magnesium binding site 8 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:0.0
occ:1.00
O3B H:ADP402 2.6 0.0 1.0
OE1 H:GLU143 3.3 0.0 1.0
PB H:ADP402 3.7 0.0 1.0
CD H:GLU143 3.9 0.0 1.0
O2B H:ADP402 4.0 0.0 1.0
OD1 H:ASP17 4.1 0.0 1.0
O3A H:ADP402 4.1 0.0 1.0
OE2 H:GLU143 4.2 0.0 1.0
O2A H:ADP402 4.3 0.0 1.0
OG1 H:THR166 4.5 0.0 1.0
OD2 H:ASP17 4.7 0.0 1.0
PA H:ADP402 4.7 0.0 1.0
OD2 H:ASP161 4.8 0.0 1.0
CG H:ASP17 4.8 0.0 1.0
CG H:GLU143 5.0 0.0 1.0

Magnesium binding site 9 out of 14 in 5jyg

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Magnesium binding site 9 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:0.0
occ:1.00
O3B I:ADP402 2.5 0.0 1.0
OE1 I:GLU143 3.2 0.0 1.0
OE2 I:GLU143 3.3 0.0 1.0
O2A I:ADP402 3.4 0.0 1.0
CD I:GLU143 3.4 0.0 1.0
OD2 I:ASP161 3.5 0.0 1.0
O I:LEU18 3.7 0.0 1.0
PB I:ADP402 4.0 0.0 1.0
OD1 I:ASP76 4.2 0.0 1.0
OD1 I:ASP17 4.3 0.0 1.0
CG I:ASP161 4.4 0.0 1.0
PA I:ADP402 4.4 0.0 1.0
OD1 I:ASP161 4.5 0.0 1.0
CG I:GLU143 4.5 0.0 1.0
O3A I:ADP402 4.6 0.0 1.0
O2B I:ADP402 4.8 0.0 1.0
O1A I:ADP402 4.8 0.0 1.0
C I:LEU18 4.9 0.0 1.0
CA I:GLY19 5.0 0.0 1.0
O1B I:ADP402 5.0 0.0 1.0

Magnesium binding site 10 out of 14 in 5jyg

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Magnesium binding site 10 out of 14 in the Cryo-Em Structure of the Mamk Filament at 6.5 A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Mamk Filament at 6.5 A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:0.0
occ:1.00
O3B J:ADP402 2.5 0.0 1.0
O2A J:ADP402 3.4 0.0 1.0
OD2 J:ASP161 3.6 0.0 1.0
PB J:ADP402 3.7 0.0 1.0
OE1 J:GLU143 3.7 0.0 1.0
O1B J:ADP402 3.8 0.0 1.0
CD J:GLU143 4.1 0.0 1.0
OE2 J:GLU143 4.1 0.0 1.0
OD1 J:ASP17 4.2 0.0 1.0
CG J:ASP161 4.4 0.0 1.0
PA J:ADP402 4.4 0.0 1.0
OD1 J:ASP161 4.4 0.0 1.0
O3A J:ADP402 4.5 0.0 1.0
O J:LEU18 4.9 0.0 1.0
O2B J:ADP402 5.0 0.0 1.0

Reference:

J.R.Bergeron, R.Hutto, E.Ozyamak, N.Hom, J.Hansen, O.Draper, M.E.Byrne, S.Keyhani, A.Komeili, J.M.Kollman. Structure of the Magnetosome-Associated Actin-Like Mamk Filament at Subnanometer Resolution. Protein Sci. V. 26 93 2017.
ISSN: ESSN 1469-896X
PubMed: 27391173
DOI: 10.1002/PRO.2979
Page generated: Mon Dec 14 20:36:35 2020

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