Magnesium in PDB 7y5a: Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase

All present enzymatic activity of Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase:
7.1.2.2;

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase (pdb code 7y5a). 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 the Mycolicibacterium Smegmatis F1-Atpase, PDB code: 7y5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase


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 the Mycolicibacterium Smegmatis F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:140.2 occ:1.00 O2B A:ATP600 2.0 143.6 1.0 O1A A:ATP600 2.1 143.6 1.0 O3A A:ATP600 2.3 143.6 1.0 PB A:ATP600 2.4 143.6 1.0 O2G A:ATP600 2.4 143.6 1.0 O3B A:ATP600 2.5 143.6 1.0 PA A:ATP600 2.6 143.6 1.0 PG A:ATP600 3.0 143.6 1.0 O2A A:ATP600 3.6 143.6 1.0 O3G A:ATP600 3.7 143.6 1.0 O1B A:ATP600 3.8 143.6 1.0 O5' A:ATP600 3.9 143.6 1.0 OG1 A:THR179 4.0 128.2 1.0 CG2 A:THR179 4.2 128.2 1.0 O A:GLY177 4.2 131.3 1.0 O1G A:ATP600 4.3 143.6 1.0 NZ A:LYS175 4.4 141.7 1.0 CB A:THR179 4.8 128.2 1.0 CE A:LYS175 5.0 141.7 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase


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 the Mycolicibacterium Smegmatis F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:119.8 occ:1.00 O1A B:ATP600 2.0 125.5 1.0 O2B B:ATP600 2.0 125.5 1.0 O1G B:ATP600 2.1 125.5 1.0 PG B:ATP600 2.3 125.5 1.0 O3B B:ATP600 2.3 125.5 1.0 PB B:ATP600 2.4 125.5 1.0 O3A B:ATP600 2.5 125.5 1.0 PA B:ATP600 2.5 125.5 1.0 O2G B:ATP600 2.6 125.5 1.0 O2A B:ATP600 3.1 125.5 1.0 OG1 B:THR179 3.1 122.5 1.0 CG2 B:THR179 3.5 122.5 1.0 O3G B:ATP600 3.8 125.5 1.0 O1B B:ATP600 3.9 125.5 1.0 CB B:THR179 3.9 122.5 1.0 O5' B:ATP600 4.0 125.5 1.0 N B:THR179 4.5 122.5 1.0 CA B:THR179 4.9 122.5 1.0 C5' B:ATP600 4.9 125.5 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase


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 the Mycolicibacterium Smegmatis F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:134.5 occ:1.00 O2B C:ATP600 2.1 138.9 1.0 O2G C:ATP600 2.2 138.9 1.0 O1A C:ATP600 2.2 138.9 1.0 O3A C:ATP600 2.3 138.9 1.0 PB C:ATP600 2.3 138.9 1.0 O3B C:ATP600 2.4 138.9 1.0 PG C:ATP600 2.4 138.9 1.0 PA C:ATP600 2.4 138.9 1.0 O1G C:ATP600 2.6 138.9 1.0 O2A C:ATP600 2.9 138.9 1.0 OG1 C:THR179 3.3 127.3 1.0 CG2 C:THR179 3.6 127.3 1.0 O1B C:ATP600 3.8 138.9 1.0 O3G C:ATP600 3.9 138.9 1.0 O5' C:ATP600 4.0 138.9 1.0 CB C:THR179 4.1 127.3 1.0 NZ C:LYS175 4.5 138.2 1.0 N C:THR179 4.6 127.3 1.0 CE C:LYS175 4.8 138.2 1.0 N C:LYS178 5.0 128.9 1.0 CA C:THR179 5.0 127.3 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase


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 the Mycolicibacterium Smegmatis F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:173.0 occ:1.00 O3B D:ADP600 2.1 166.3 1.0 O1B D:ADP600 2.2 166.3 1.0 O2A D:ADP600 2.3 166.3 1.0 PB D:ADP600 2.4 166.3 1.0 PA D:ADP600 2.5 166.3 1.0 O1A D:ADP600 2.5 166.3 1.0 O3A D:ADP600 2.8 166.3 1.0 OG1 D:THR167 2.8 145.7 1.0 NH1 D:ARG193 3.4 128.4 1.0 NH2 D:ARG193 3.7 128.4 1.0 CB D:THR167 3.8 145.7 1.0 O2B D:ADP600 3.9 166.3 1.0 N D:THR167 3.9 145.7 1.0 CZ D:ARG193 4.0 128.4 1.0 O5' D:ADP600 4.1 166.3 1.0 CA D:THR167 4.5 145.7 1.0 N D:LYS166 4.5 142.1 1.0 CB D:LYS166 4.6 142.1 1.0 C5' D:ADP600 4.9 166.3 1.0 C D:LYS166 4.9 142.1 1.0 CA D:LYS166 4.9 142.1 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of the Mycolicibacterium Smegmatis F1-Atpase


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 the Mycolicibacterium Smegmatis F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:164.6 occ:1.00 O3B F:ADP600 2.1 166.1 1.0 O1B F:ADP600 2.2 166.1 1.0 O2A F:ADP600 2.3 166.1 1.0 O1A F:ADP600 2.4 166.1 1.0 PB F:ADP600 2.4 166.1 1.0 PA F:ADP600 2.4 166.1 1.0 CG F:LYS166 2.7 146.5 1.0 O3A F:ADP600 2.7 166.1 1.0 N F:LYS166 3.1 146.5 1.0 OG1 F:THR167 3.2 150.9 1.0 N F:THR167 3.2 150.9 1.0 CB F:LYS166 3.7 146.5 1.0 CA F:LYS166 3.7 146.5 1.0 CD F:LYS166 3.7 146.5 1.0 O2B F:ADP600 3.9 166.1 1.0 C F:LYS166 3.9 146.5 1.0 CB F:THR167 4.0 150.9 1.0 C F:GLY165 4.0 146.7 1.0 O5' F:ADP600 4.0 166.1 1.0 N F:GLY165 4.0 146.7 1.0 CA F:THR167 4.2 150.9 1.0 CA F:GLY165 4.3 146.7 1.0 CE F:LYS166 4.3 146.5 1.0 N F:VAL164 4.7 140.6 1.0 C5' F:ADP600 4.8 166.1 1.0 O F:GLY165 5.0 146.7 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