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Magnesium in PDB 9io5: Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery

Enzymatic activity of Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery

All present enzymatic activity of Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery:
2.7.2.3; 3.6.3.14;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery (pdb code 9io5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery, PDB code: 9io5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 9io5

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Magnesium binding site 1 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:24.1
occ:1.00
 OG1 A:THR459 2.0 18.7 1.0
O2B A:ATP800 2.0 19.0 1.0
O2G A:ATP800 2.3 19.0 1.0
OE1 A:GLU484 3.2 17.7 1.0
CB A:THR459 3.3 18.7 1.0
PB A:ATP800 3.3 19.0 1.0
PG A:ATP800 3.6 19.0 1.0
O3B A:ATP800 3.6 19.0 1.0
N A:THR459 4.0 18.7 1.0
OE2 A:GLU488 4.0 22.2 1.0
NH1 A:ARG485 4.1 17.0 1.0
OE1 A:GLU488 4.1 22.2 1.0
CD A:GLU484 4.1 17.7 1.0
CA A:THR459 4.2 18.7 1.0
O1B A:ATP800 4.2 19.0 1.0
CG2 A:THR459 4.3 18.7 1.0
OD2 A:ASP546 4.4 13.9 1.0
O3A A:ATP800 4.4 19.0 1.0
CD A:GLU488 4.5 22.2 1.0
O3G A:ATP800 4.5 19.0 1.0
O1G A:ATP800 4.5 19.0 1.0
OD1 A:ASP546 4.6 13.9 1.0
CE A:LYS458 4.6 16.6 1.0
O1A A:ATP800 4.7 19.0 1.0
NZ A:LYS458 4.7 16.6 1.0
OE2 A:GLU484 4.7 17.7 1.0
CB A:LYS458 4.8 16.6 1.0
PA A:ATP800 4.9 19.0 1.0
CG A:ASP546 4.9 13.9 1.0
O2A A:ATP800 5.0 19.0 1.0
C A:LYS458 5.0 16.6 1.0

Magnesium binding site 2 out of 10 in 9io5

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Magnesium binding site 2 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg800

b:28.1
occ:1.00
 O1B B:ADP801 2.2 32.1 1.0
O2 B:PO4802 2.2 29.1 1.0
OG1 B:THR459 2.3 30.6 1.0
OD2 B:ASP546 3.5 14.4 1.0
P B:PO4802 3.5 29.1 1.0
PB B:ADP801 3.6 32.1 1.0
CB B:THR459 3.7 30.6 1.0
O3 B:PO4802 3.8 29.1 1.0
O2A B:ADP801 4.0 32.1 1.0
N B:THR459 4.0 30.6 1.0
O3B B:ADP801 4.3 32.1 1.0
CA B:THR459 4.3 30.6 1.0
O4 B:PO4802 4.3 29.1 1.0
O2B B:ADP801 4.3 32.1 1.0
CG B:ASP546 4.4 14.4 1.0
OD1 B:ASP546 4.4 14.4 1.0
CB B:LYS458 4.5 25.9 1.0
O1 B:PO4802 4.5 29.1 1.0
CG2 B:THR459 4.6 30.6 1.0
O3A B:ADP801 4.6 32.1 1.0
PA B:ADP801 4.7 32.1 1.0
OE1 B:GLU488 4.7 17.8 1.0
C B:LYS458 4.8 25.9 1.0
OE2 B:GLU488 5.0 17.8 1.0

Magnesium binding site 3 out of 10 in 9io5

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Magnesium binding site 3 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:11.4
occ:1.00
 OG1 D:THR155 2.1 10.5 1.0
O2B D:ATP600 2.2 15.7 1.0
O2G D:ATP600 2.4 15.7 1.0
CB D:THR155 3.3 10.5 1.0
PB D:ATP600 3.5 15.7 1.0
PG D:ATP600 3.7 15.7 1.0
O3B D:ATP600 3.7 15.7 1.0
CG2 D:THR155 4.0 10.5 1.0
OE2 D:GLU183 4.0 15.8 1.0
OD2 D:ASP240 4.0 12.1 1.0
OD1 D:ASP240 4.2 12.1 1.0
NZ D:LYS179 4.4 12.0 1.0
CA D:THR155 4.5 10.5 1.0
N D:THR155 4.5 10.5 1.0
O1B D:ATP600 4.5 15.7 1.0
O1G D:ATP600 4.5 15.7 1.0
CG D:ASP240 4.6 12.1 1.0
O3A D:ATP600 4.6 15.7 1.0
O1A D:ATP600 4.7 15.7 1.0
O3G D:ATP600 4.7 15.7 1.0
CD D:GLU183 4.9 15.8 1.0
OE1 D:GLU183 4.9 15.8 1.0
O2A D:ATP600 5.0 15.7 1.0
PA D:ATP600 5.0 15.7 1.0

Magnesium binding site 4 out of 10 in 9io5

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Magnesium binding site 4 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:11.1
occ:1.00
 O3G E:ATP600 2.0 15.1 1.0
OG1 E:THR155 2.2 11.0 1.0
O2B E:ATP600 2.3 15.1 1.0
PG E:ATP600 3.4 15.1 1.0
CB E:THR155 3.5 11.0 1.0
PB E:ATP600 3.5 15.1 1.0
O3B E:ATP600 3.6 15.1 1.0
OD2 E:ASP240 3.9 11.1 1.0
OE2 E:GLU183 4.0 14.0 1.0
NZ E:LYS179 4.0 11.1 1.0
OD1 E:ASP240 4.2 11.1 1.0
CG2 E:THR155 4.2 11.0 1.0
O2G E:ATP600 4.3 15.1 1.0
O1A E:ATP600 4.3 15.1 1.0
O1G E:ATP600 4.3 15.1 1.0
O3A E:ATP600 4.5 15.1 1.0
CG E:ASP240 4.5 11.1 1.0
N E:THR155 4.5 11.0 1.0
O1B E:ATP600 4.6 15.1 1.0
CA E:THR155 4.6 11.0 1.0
PA E:ATP600 4.9 15.1 1.0
CE E:LYS179 4.9 11.1 1.0
CD E:GLU183 5.0 14.0 1.0

Magnesium binding site 5 out of 10 in 9io5

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Magnesium binding site 5 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:11.3
occ:1.00
 OG1 F:THR155 2.1 10.8 1.0
O2B F:ATP600 2.1 15.2 1.0
O1G F:ATP600 2.3 15.2 1.0
CB F:THR155 3.3 10.8 1.0
PB F:ATP600 3.4 15.2 1.0
PG F:ATP600 3.4 15.2 1.0
O3B F:ATP600 3.5 15.2 1.0
OE2 F:GLU183 3.9 16.2 1.0
CG2 F:THR155 4.0 10.8 1.0
OD2 F:ASP240 4.2 10.6 1.0
OD1 F:ASP240 4.2 10.6 1.0
O1A F:ATP600 4.2 15.2 1.0
O3G F:ATP600 4.2 15.2 1.0
O3A F:ATP600 4.3 15.2 1.0
N F:THR155 4.4 10.8 1.0
CA F:THR155 4.4 10.8 1.0
O1B F:ATP600 4.4 15.2 1.0
CG F:ASP240 4.6 10.6 1.0
PA F:ATP600 4.6 15.2 1.0
O2G F:ATP600 4.7 15.2 1.0
NZ F:LYS179 4.7 11.1 1.0
O2A F:ATP600 4.8 15.2 1.0
CD F:GLU183 4.8 16.2 1.0
OE1 F:GLU183 4.8 16.2 1.0

Magnesium binding site 6 out of 10 in 9io5

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Magnesium binding site 6 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg801

b:34.0
occ:1.00
 O2G H:ATP800 2.0 52.0 1.0
O2B H:ATP800 2.1 52.0 1.0
OG1 H:THR459 2.5 19.5 1.0
OE1 H:GLU484 2.9 18.0 1.0
PB H:ATP800 3.4 52.0 1.0
PG H:ATP800 3.4 52.0 1.0
O3B H:ATP800 3.7 52.0 1.0
CD H:GLU484 3.9 18.0 1.0
CB H:THR459 4.0 19.5 1.0
NH1 H:ARG485 4.1 17.7 1.0
O1G H:ATP800 4.2 52.0 1.0
OE2 H:GLU484 4.3 18.0 1.0
N H:THR459 4.3 19.5 1.0
O1B H:ATP800 4.3 52.0 1.0
NZ H:LYS458 4.4 17.6 1.0
CE H:LYS458 4.5 17.6 1.0
O3A H:ATP800 4.5 52.0 1.0
O3G H:ATP800 4.5 52.0 1.0
CA H:THR459 4.6 19.5 1.0
OD1 H:ASP546 4.7 15.9 1.0
OE1 H:GLU488 4.7 21.4 1.0
CB H:LYS458 4.7 17.6 1.0
CG2 H:THR459 4.8 19.5 1.0
OD2 H:ASP546 4.8 15.9 1.0
O2A H:ATP800 4.9 52.0 1.0
NH2 K:ARG344 5.0 23.0 1.0

Magnesium binding site 7 out of 10 in 9io5

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Magnesium binding site 7 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg800

b:40.6
occ:1.00
 O1 I:PO4802 2.2 36.6 1.0
O1B I:ADP801 2.2 59.4 1.0
P I:PO4802 3.4 36.6 1.0
OE1 I:GLU488 3.5 18.4 1.0
O2 I:PO4802 3.6 36.6 1.0
PB I:ADP801 3.7 59.4 1.0
NZ I:LYS458 3.8 43.4 1.0
OE2 I:GLU488 3.8 18.4 1.0
CE I:LYS458 3.8 43.4 1.0
CD I:GLU488 4.0 18.4 1.0
NH1 I:ARG485 4.0 15.0 1.0
O3B I:ADP801 4.3 59.4 1.0
O4 I:PO4802 4.3 36.6 1.0
O1A I:ADP801 4.3 59.4 1.0
OD2 I:ASP546 4.3 16.4 1.0
OD1 I:ASP546 4.4 16.4 1.0
O3 I:PO4802 4.5 36.6 1.0
O3A I:ADP801 4.5 59.4 1.0
NE L:ARG344 4.6 21.6 1.0
O2B I:ADP801 4.6 59.4 1.0
NH2 L:ARG344 4.7 21.6 1.0
CG I:ASP546 4.8 16.4 1.0
NH2 I:ARG550 4.9 13.6 1.0

Magnesium binding site 8 out of 10 in 9io5

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Magnesium binding site 8 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:10.6
occ:1.00
 O2B K:ATP600 2.0 14.5 1.0
OG1 K:THR155 2.1 9.1 1.0
O2G K:ATP600 2.2 14.5 1.0
PB K:ATP600 3.3 14.5 1.0
CB K:THR155 3.4 9.1 1.0
PG K:ATP600 3.4 14.5 1.0
O3B K:ATP600 3.5 14.5 1.0
OD2 K:ASP240 3.8 11.9 1.0
O3G K:ATP600 4.1 14.5 1.0
N K:THR155 4.2 9.1 1.0
CG2 K:THR155 4.2 9.1 1.0
O1B K:ATP600 4.2 14.5 1.0
OD1 K:ASP240 4.2 11.9 1.0
OE2 K:GLU183 4.3 15.4 1.0
O3A K:ATP600 4.3 14.5 1.0
CA K:THR155 4.4 9.1 1.0
CG K:ASP240 4.4 11.9 1.0
O1A K:ATP600 4.5 14.5 1.0
O1G K:ATP600 4.6 14.5 1.0
NZ K:LYS179 4.8 12.9 1.0
PA K:ATP600 4.8 14.5 1.0
O2A K:ATP600 4.9 14.5 1.0

Magnesium binding site 9 out of 10 in 9io5

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Magnesium binding site 9 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:27.6
occ:1.00
 OG1 L:THR155 2.0 11.2 1.0
O1G L:ATP600 2.1 14.1 1.0
O2B L:ATP600 2.3 14.1 1.0
CB L:THR155 3.2 11.2 1.0
PG L:ATP600 3.3 14.1 1.0
PB L:ATP600 3.6 14.1 1.0
O3B L:ATP600 3.6 14.1 1.0
OD2 L:ASP240 4.0 12.7 1.0
CG2 L:THR155 4.0 11.2 1.0
OE2 L:GLU183 4.1 14.9 1.0
OD1 L:ASP240 4.1 12.7 1.0
O2G L:ATP600 4.3 14.1 1.0
N L:THR155 4.3 11.2 1.0
CA L:THR155 4.3 11.2 1.0
O3G L:ATP600 4.4 14.1 1.0
O1A L:ATP600 4.5 14.1 1.0
O3A L:ATP600 4.5 14.1 1.0
CG L:ASP240 4.5 12.7 1.0
O1B L:ATP600 4.6 14.1 1.0
NZ L:LYS179 4.6 13.0 1.0
PA L:ATP600 4.9 14.1 1.0
CD L:GLU183 4.9 14.9 1.0

Magnesium binding site 10 out of 10 in 9io5

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Magnesium binding site 10 out of 10 in the Cryo-Em Structure of G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery


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 G1-Atpase Dimer From Mycoplasma Mobile Gliding Machinery within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg601

b:11.2
occ:1.00
 OG1 M:THR155 2.1 15.2 1.0
O2G M:ATP600 2.2 20.1 1.0
O2B M:ATP600 2.4 20.1 1.0
CB M:THR155 3.4 15.2 1.0
PG M:ATP600 3.6 20.1 1.0
PB M:ATP600 3.6 20.1 1.0
OD1 M:ASP240 3.8 12.0 1.0
O3B M:ATP600 3.8 20.1 1.0
NZ M:LYS179 4.0 12.9 1.0
OD2 M:ASP240 4.1 12.0 1.0
N M:THR155 4.2 15.2 1.0
CG2 M:THR155 4.2 15.2 1.0
CA M:THR155 4.3 15.2 1.0
CG M:ASP240 4.4 12.0 1.0
O1B M:ATP600 4.4 20.1 1.0
O3G M:ATP600 4.5 20.1 1.0
O1G M:ATP600 4.5 20.1 1.0
OE2 M:GLU183 4.7 16.9 1.0
O3A M:ATP600 4.8 20.1 1.0
OE1 M:GLU183 4.9 16.9 1.0
O1A M:ATP600 4.9 20.1 1.0
CE M:LYS179 4.9 12.9 1.0

Reference:

T.Toyonaga, T.Kato, A.Kawamoto, T.Miyata, K.Kawakami, J.Fujita, T.Hamaguchi, K.Namba, M.Miyata. Dimeric Assembly of F 1 -Like Atpase For the Gliding Motility of Mycoplasma. Sci Adv V. 11 R9319 2025.
ISSN: ESSN 2375-2548
PubMed: 40009674
DOI: 10.1126/SCIADV.ADR9319
Page generated: Sat Aug 16 04:15:19 2025

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