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Magnesium in PDB 8yh8: F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition

Enzymatic activity of F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition

All present enzymatic activity of F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition:
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition (pdb code 8yh8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition, PDB code: 8yh8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8yh8

Go back to Magnesium Binding Sites List in 8yh8
Magnesium binding site 1 out of 3 in the F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:28.3
occ:1.00
O1B D:ADP502 1.9 41.4 1.0
OG1 D:THR165 2.2 42.2 1.0
PB D:ADP502 3.2 27.3 1.0
CB D:THR165 3.4 28.0 1.0
O3B D:ADP502 3.6 32.1 1.0
NH2 D:ARG191 3.9 26.9 1.0
OE1 D:GLU190 4.1 30.0 1.0
O1A D:ADP502 4.1 47.5 1.0
N D:THR165 4.1 12.3 1.0
OE2 D:GLU194 4.2 40.2 1.0
O2B D:ADP502 4.2 30.3 1.0
O3A D:ADP502 4.2 39.2 1.0
CA D:THR165 4.3 18.0 1.0
OE1 D:GLU194 4.3 40.3 1.0
CG2 D:THR165 4.3 25.9 1.0
PA D:ADP502 4.5 19.1 1.0
NH2 C:ARG365 4.5 24.4 1.0
O2A D:ADP502 4.6 30.2 1.0
CD D:GLU194 4.7 39.5 1.0
CD D:GLU190 4.8 30.0 1.0
OD1 D:ASP252 5.0 43.1 1.0

Magnesium binding site 2 out of 3 in 8yh8

Go back to Magnesium Binding Sites List in 8yh8
Magnesium binding site 2 out of 3 in the F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:63.5
occ:1.00
O3B E:ADP501 1.8 51.3 1.0
O1B E:ADP501 1.9 58.1 1.0
PB E:ADP501 2.4 61.3 1.0
O2B E:ADP501 3.3 50.8 1.0
O3A E:ADP501 3.6 59.1 1.0
OG1 E:THR165 3.8 48.1 1.0
O1A E:ADP501 4.4 58.3 1.0
CB E:LYS164 4.4 40.7 1.0
PA E:ADP501 4.5 73.2 1.0
N E:GLY161 4.7 53.1 1.0
N E:THR165 4.9 36.0 1.0

Magnesium binding site 3 out of 3 in 8yh8

Go back to Magnesium Binding Sites List in 8yh8
Magnesium binding site 3 out of 3 in the F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F1 Domain of Non-Catalytic Site Depleted and Epsilon C-Terminal Domain Deleted FOF1-Atpase From Bacillus PS3,Under Atp Saturated Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:32.3
occ:1.00
O1G F:ATP500 1.9 40.7 1.0
OG1 F:THR165 2.1 42.1 1.0
O2B F:ATP500 2.3 37.3 1.0
PG F:ATP500 3.0 52.9 1.0
O3B F:ATP500 3.4 37.5 1.0
O3G F:ATP500 3.4 41.3 1.0
PB F:ATP500 3.5 23.4 1.0
CB F:THR165 3.5 30.8 1.0
NH2 F:ARG191 4.1 20.4 1.0
NZ F:LYS164 4.2 22.7 1.0
CG2 F:THR165 4.2 27.4 1.0
N F:THR165 4.3 23.4 1.0
O2A F:ATP500 4.3 37.6 1.0
O2G F:ATP500 4.3 38.4 1.0
O1B F:ATP500 4.4 27.8 1.0
OE1 F:GLU194 4.4 43.6 1.0
CA F:THR165 4.4 25.0 1.0
OD1 F:ASP252 4.5 35.5 1.0
O3A F:ATP500 4.6 36.9 1.0
NH1 B:ARG365 4.9 24.3 1.0

Reference:

R.Kobayashi, A.Nakano, K.Mitsuoka, K.Yokoyama. Adp-Inhibited Structure of Non-Catalytic Site-Depleted F O F 1 -Atpase From Thermophilic Bacillus Sp. Ps-3. Biochim Biophys Acta V.1866 49536 2025BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 39788275
DOI: 10.1016/J.BBABIO.2025.149536
Page generated: Fri Aug 15 21:27:28 2025

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