Magnesium in PDB 7y5c: 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;

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 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 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 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 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 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

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