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Magnesium in PDB 8gpv: Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium

Protein crystallography data

The structure of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium, PDB code: 8gpv was solved by M.Wang, Y.Zhao, M.Hattori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.06 / 1.82
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.063, 81.063, 104.565, 90, 90, 90
R / Rfree (%) 22.5 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium (pdb code 8gpv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium, PDB code: 8gpv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8gpv

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Magnesium binding site 1 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:49.1
occ:1.00
 O A:HOH437 2.2 42.2 1.0
O A:HOH471 2.2 51.3 1.0
O A:HOH495 2.2 52.2 1.0
O A:HOH405 4.1 57.1 1.0
O A:HOH443 4.1 52.1 1.0
O A:HOH439 4.1 53.0 1.0
OD1 A:ASP136 4.2 38.0 1.0
OE2 A:GLU117 4.2 51.9 1.0
OD2 A:ASP136 4.3 41.4 1.0
OE1 A:GLU117 4.3 48.8 1.0
OD1 A:ASP114 4.6 62.2 1.0
CG A:ASP136 4.6 38.8 1.0
CD A:GLU117 4.7 53.4 1.0
CG A:PRO88 4.8 39.8 1.0
O A:HOH548 5.0 62.7 1.0

Magnesium binding site 2 out of 6 in 8gpv

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Magnesium binding site 2 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:52.2
occ:1.00
 O A:HOH491 1.9 59.9 1.0
O A:HOH506 2.1 62.6 1.0
O A:HOH430 2.1 64.6 1.0
O A:HOH451 2.2 59.8 1.0
OD1 A:ASP127 3.7 73.7 1.0
OD1 A:ASP209 4.0 50.8 1.0
OE1 A:GLU250 4.1 74.0 1.0
O A:HOH436 4.1 71.5 1.0
OD2 A:ASP209 4.2 55.6 1.0
CG A:ASP127 4.3 73.0 1.0
CB A:ASP127 4.4 59.9 1.0
OE2 A:GLU250 4.4 64.3 1.0
OE1 A:GLU211 4.4 69.8 1.0
CG A:ASP209 4.5 50.9 1.0
CD A:GLU250 4.6 70.7 1.0
OE1 A:GLU253 4.9 72.0 1.0

Magnesium binding site 3 out of 6 in 8gpv

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Magnesium binding site 3 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:45.7
occ:1.00
 OD1 A:ASP221 2.0 43.0 1.0
O A:GLN218 2.0 39.8 1.0
O A:HOH500 2.1 46.6 1.0
CG A:ASP221 3.1 46.4 1.0
C A:GLN218 3.1 42.0 1.0
OD2 A:ASP221 3.5 46.5 1.0
CA A:GLN218 3.6 42.2 1.0
CB A:GLN218 4.1 46.8 1.0
N A:ARG219 4.3 40.9 1.0
CB A:ASP221 4.3 42.9 1.0
O A:HOH416 4.4 46.9 1.0
N A:ASP221 4.5 37.8 1.0
CA A:ASP221 4.5 42.1 1.0
CG A:GLN218 4.5 64.0 1.0
C A:ARG219 4.7 47.8 1.0
CA A:ARG219 4.7 46.6 1.0
O A:MET217 4.7 41.0 1.0
O A:ARG219 4.7 44.5 1.0
N A:GLN218 4.9 40.2 1.0

Magnesium binding site 4 out of 6 in 8gpv

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Magnesium binding site 4 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:33.9
occ:1.00
 OD2 A:ASP242 2.0 35.2 1.0
O A:HOH498 2.0 34.0 1.0
O A:HOH428 2.0 38.0 1.0
O A:HOH454 2.1 35.4 1.0
OD2 A:ASP89 2.1 37.2 1.0
O A:HOH448 2.1 34.3 1.0
CG A:ASP242 3.0 35.5 1.0
CG A:ASP89 3.1 38.2 1.0
OD1 A:ASP242 3.4 39.9 1.0
OD1 A:ASP89 3.4 34.0 1.0
O A:HOH525 3.9 38.8 1.0
OG1 A:THR239 3.9 33.3 1.0
O A:HOH574 3.9 48.5 1.0
OE2 A:GLU161 3.9 42.4 1.0
MG A:MG307 4.0 47.6 1.0
OE1 A:GLU161 4.1 38.6 1.0
O A:HOH435 4.1 37.0 1.0
CD A:GLU161 4.2 45.7 1.0
OD1 A:ASP241 4.3 40.1 1.0
OD1 A:ASP90 4.4 38.9 1.0
CB A:ASP242 4.4 31.6 1.0
CB A:ASP89 4.5 33.6 1.0
O A:HOH472 4.6 45.2 1.0
OD2 A:ASP241 4.8 40.3 1.0
OD2 A:ASP90 4.8 37.7 1.0
O A:HOH475 4.8 42.3 1.0
CG A:ASP90 4.9 39.9 1.0
CG A:ASP241 4.9 45.7 1.0

Magnesium binding site 5 out of 6 in 8gpv

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Magnesium binding site 5 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:68.5
occ:1.00
 O A:HOH425 2.0 67.6 1.0
O A:HOH459 2.3 67.3 1.0
O A:HOH408 2.3 71.1 1.0
OD1 A:ASP254 2.3 73.7 1.0
O A:HOH436 2.4 71.5 1.0
CG A:ASP254 3.5 79.0 1.0
OE1 A:GLU253 3.7 72.0 1.0
OD2 A:ASP254 3.9 78.9 1.0
OE1 A:GLU211 4.1 69.8 1.0
OE1 A:GLU250 4.3 74.0 1.0
O A:HOH506 4.4 62.6 1.0
O A:GLU250 4.5 75.0 1.0
CB A:ASP254 4.7 79.2 1.0
CD A:GLU253 4.8 71.5 1.0
CA A:ASP254 4.8 79.7 1.0
OE2 A:GLU211 4.9 65.0 1.0
N A:ASP254 4.9 76.0 1.0
CD A:GLU211 4.9 67.3 1.0

Magnesium binding site 6 out of 6 in 8gpv

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Magnesium binding site 6 out of 6 in the Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cytoplasmic Domain Structure of the Mgte MG2+ Channel From Clostridiales Bacterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:47.6
occ:1.00
 OD2 A:ASP90 2.3 37.7 1.0
O A:HOH574 2.3 48.5 1.0
O A:HOH517 2.4 60.9 1.0
OD2 A:ASP87 2.5 46.2 1.0
O A:HOH448 2.8 34.3 1.0
O A:HOH472 2.9 45.2 1.0
O A:HOH419 3.3 57.9 1.0
CG A:ASP90 3.3 39.9 1.0
O A:HOH428 3.4 38.0 1.0
O A:HOH577 3.5 69.6 1.0
CG A:ASP87 3.5 35.8 1.0
O A:HOH454 3.8 35.4 1.0
OD1 A:ASP90 3.8 38.9 1.0
CB A:ASP87 3.8 30.9 1.0
O A:HOH485 3.9 42.4 1.0
MG A:MG305 4.0 33.9 1.0
OE1 A:GLU161 4.4 38.6 1.0
O A:HOH535 4.6 58.0 1.0
OD1 A:ASP87 4.6 42.7 1.0
CB A:ASP90 4.6 35.5 1.0
OD1 A:ASP89 4.7 34.0 1.0
OE2 A:GLU161 4.7 42.4 1.0
O A:HOH499 4.7 48.3 1.0
O A:HOH547 4.8 57.5 1.0

Reference:

M.Wang, Y.Zhao, Y.Hayashi, K.Ito, M.Hattori. Novel MG2+ Binding Sites in the Cytoplasmic Domain of the Mgte MG2+ Channels Revealed By X-Ray Crystal Structures Acta Biochim.Biophys.Sinica 2023.
ISSN: ISSN 0582-9879
DOI: 10.3724/ABBS.2023067
Page generated: Fri Oct 4 03:53:56 2024

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