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Magnesium in PDB 7y5c: Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)

Enzymatic activity of Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)

All present enzymatic activity of Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2):
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) (pdb code 7y5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2), PDB code: 7y5c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7y5c

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Magnesium binding site 1 out of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)


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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:86.0
occ:1.00
O1G A:ATP601 2.0 112.8 1.0
O3A A:ATP601 2.1 112.8 1.0
O3B A:ATP601 2.2 112.8 1.0
O1A A:ATP601 2.2 112.8 1.0
PB A:ATP601 2.2 112.8 1.0
PG A:ATP601 2.3 112.8 1.0
PA A:ATP601 2.3 112.8 1.0
O1B A:ATP601 2.3 112.8 1.0
O3G A:ATP601 2.7 112.8 1.0
O2A A:ATP601 2.8 112.8 1.0
OG1 A:THR179 3.5 60.0 1.0
O2B A:ATP601 3.7 112.8 1.0
O2G A:ATP601 3.8 112.8 1.0
O5' A:ATP601 3.8 112.8 1.0
CB A:THR179 4.0 60.0 1.0
N A:THR179 4.5 60.0 1.0
C5' A:ATP601 4.8 112.8 1.0
CA A:GLY177 4.9 83.0 1.0
N A:LYS178 4.9 75.1 1.0
CA A:THR179 4.9 60.0 1.0
N A:GLY177 5.0 83.0 1.0

Magnesium binding site 2 out of 5 in 7y5c

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Magnesium binding site 2 out of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)


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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg600

b:125.0
occ:1.00
O1A B:ATP601 2.0 114.4 1.0
O3A B:ATP601 2.1 114.4 1.0
O3G B:ATP601 2.1 114.4 1.0
PG B:ATP601 2.3 114.4 1.0
O3B B:ATP601 2.3 114.4 1.0
PA B:ATP601 2.3 114.4 1.0
PB B:ATP601 2.3 114.4 1.0
O1G B:ATP601 2.4 114.4 1.0
O1B B:ATP601 2.5 114.4 1.0
O2A B:ATP601 2.9 114.4 1.0
OG1 B:THR179 3.3 103.6 1.0
CB B:THR179 3.7 103.6 1.0
O5' B:ATP601 3.8 114.4 1.0
O2G B:ATP601 3.8 114.4 1.0
O2B B:ATP601 3.8 114.4 1.0
N B:THR179 4.6 103.6 1.0
CG2 B:THR179 4.7 103.6 1.0
C5' B:ATP601 4.8 114.4 1.0
CA B:THR179 4.8 103.6 1.0

Magnesium binding site 3 out of 5 in 7y5c

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Magnesium binding site 3 out of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)


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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg600

b:98.8
occ:1.00
O1A C:ATP601 2.1 115.1 1.0
O1B C:ATP601 2.1 115.1 1.0
O3A C:ATP601 2.2 115.1 1.0
O3G C:ATP601 2.3 115.1 1.0
PB C:ATP601 2.3 115.1 1.0
O3B C:ATP601 2.5 115.1 1.0
PA C:ATP601 2.6 115.1 1.0
PG C:ATP601 2.6 115.1 1.0
OG1 C:THR179 2.9 104.6 1.0
O1G C:ATP601 2.9 115.1 1.0
O2A C:ATP601 3.6 115.1 1.0
CG2 C:THR179 3.6 104.6 1.0
O2B C:ATP601 3.8 115.1 1.0
O5' C:ATP601 3.8 115.1 1.0
CB C:THR179 3.8 104.6 1.0
O2G C:ATP601 4.1 115.1 1.0
NZ C:LYS175 4.2 119.2 1.0
N C:THR179 4.6 104.6 1.0
CA C:THR179 4.9 104.6 1.0

Magnesium binding site 4 out of 5 in 7y5c

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Magnesium binding site 4 out of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)


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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg500

b:82.4
occ:1.00
O2A D:ATP501 1.9 86.3 1.0
O1B D:ATP501 1.9 86.3 1.0
N D:THR167 2.1 71.3 1.0
PA D:ATP501 2.3 86.3 1.0
O3A D:ATP501 2.3 86.3 1.0
PB D:ATP501 2.4 86.3 1.0
CB D:THR167 2.6 71.3 1.0
OG1 D:THR167 2.8 71.3 1.0
O1A D:ATP501 2.8 86.3 1.0
CA D:THR167 2.8 71.3 1.0
N D:LYS166 2.9 75.8 1.0
C D:LYS166 3.2 75.8 1.0
O2B D:ATP501 3.2 86.3 1.0
C D:GLY165 3.3 78.0 1.0
CA D:LYS166 3.5 75.8 1.0
CG D:LYS166 3.7 75.8 1.0
CA D:GLY165 3.7 78.0 1.0
N D:VAL168 3.8 77.4 1.0
O5' D:ATP501 3.8 86.3 1.0
C D:THR167 3.8 71.3 1.0
O3B D:ATP501 3.9 86.3 1.0
CG2 D:THR167 4.0 71.3 1.0
N D:GLY165 4.0 78.0 1.0
O D:GLY165 4.1 78.0 1.0
CB D:LYS166 4.2 75.8 1.0
O D:LYS166 4.3 75.8 1.0
C5' D:ATP501 4.5 86.3 1.0
NZ D:LYS166 4.7 75.8 1.0
PG D:ATP501 4.9 86.3 1.0
CD D:LYS166 5.0 75.8 1.0
O3G D:ATP501 5.0 86.3 1.0

Magnesium binding site 5 out of 5 in 7y5c

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Magnesium binding site 5 out of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)


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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg500

b:53.9
occ:1.00
O3B F:ATP501 2.0 64.3 1.0
O1B F:ATP501 2.0 64.3 1.0
OG1 F:THR167 2.1 46.7 1.0
PB F:ATP501 2.4 64.3 1.0
O2G F:ATP501 2.7 64.3 1.0
PG F:ATP501 2.9 64.3 1.0
CB F:THR167 3.1 46.7 1.0
O3A F:ATP501 3.4 64.3 1.0
N F:THR167 3.5 46.7 1.0
O3G F:ATP501 3.5 64.3 1.0
O2B F:ATP501 3.7 64.3 1.0
O1A F:ATP501 3.9 64.3 1.0
CA F:THR167 3.9 46.7 1.0
PA F:ATP501 4.0 64.3 1.0
O2A F:ATP501 4.1 64.3 1.0
O1G F:ATP501 4.1 64.3 1.0
CG2 F:THR167 4.2 46.7 1.0
N F:LYS166 4.5 52.3 1.0
C F:LYS166 4.6 52.3 1.0
CB F:LYS166 4.8 52.3 1.0
CA F:LYS166 4.9 52.3 1.0

Reference:

C.F.Wong, W.G.Saw, S.Basak, M.Sano, H.Ueno, H.W.Kerk, D.Litty, P.Ragunathan, T.Dick, V.Muller, H.Noji, G.Gruber. Structural Elements Involved in Atp Hydrolysis Inhibition and Atp Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-Atp Synthase Decipher New Targets For Inhibitors. Antimicrob.Agents Chemother. V. 66 2022.
ISSN: ESSN 1098-6596
PubMed: 36445139
DOI: 10.1128/AAC.01056-22
Page generated: Thu Oct 3 13:29:44 2024

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