Magnesium in PDB 6tdz: Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2

The binding sites of Magnesium atom in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 (pdb code 6tdz). 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2, PDB code: 6tdz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:35.7 occ:1.00 O3G B:ATP601 1.9 39.2 1.0 OG1 B:THR191 2.0 34.8 1.0 O2B B:ATP601 2.2 39.2 1.0 PG B:ATP601 3.1 39.2 1.0 CB B:THR191 3.3 34.8 1.0 PB B:ATP601 3.3 39.2 1.0 O3B B:ATP601 3.3 39.2 1.0 HB B:THR191 3.4 34.8 1.0 OD1 B:ASP284 3.4 35.4 1.0 OD2 B:ASP284 3.6 35.4 1.0 H B:THR191 3.6 34.8 1.0 HG21 B:THR191 3.7 34.8 1.0 O2G B:ATP601 3.9 39.2 1.0 CG B:ASP284 3.9 35.4 1.0 CG2 B:THR191 4.0 34.8 1.0 O1A B:ATP601 4.2 39.2 1.0 N B:THR191 4.3 34.8 1.0 O1G B:ATP601 4.3 39.2 1.0 O1B B:ATP601 4.3 39.2 1.0 CA B:THR191 4.3 34.8 1.0 HG23 B:THR191 4.4 34.8 1.0 HE3 B:LYS190 4.4 35.8 1.0 HB2 B:LYS190 4.4 35.8 1.0 O3A B:ATP601 4.5 39.2 1.0 PA B:ATP601 4.7 39.2 1.0 HA B:THR191 4.7 34.8 1.0 HE22 B:GLN223 4.7 37.2 1.0 HD13 B:ILE341 4.8 33.5 1.0 O2A B:ATP601 4.8 39.2 1.0 HG22 B:THR191 4.9 34.8 1.0 NE2 B:GLN223 4.9 37.2 1.0 OE1 B:GLN223 4.9 37.2 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:33.7 occ:1.00 O2B C:ATP601 1.8 33.8 1.0 OG1 C:THR191 2.2 29.1 1.0 O3G C:ATP601 2.3 33.8 1.0 PB C:ATP601 2.9 33.8 1.0 PG C:ATP601 3.2 33.8 1.0 OD2 C:ASP284 3.4 28.4 1.0 HB C:THR191 3.4 29.1 1.0 O1G C:ATP601 3.4 33.8 1.0 CB C:THR191 3.4 29.1 1.0 O3B C:ATP601 3.5 33.8 1.0 H C:THR191 3.5 29.1 1.0 OD1 C:ASP284 3.6 28.4 1.0 O1B C:ATP601 3.6 33.8 1.0 CG C:ASP284 3.9 28.4 1.0 HE2 C:LYS190 3.9 33.5 1.0 HB2 C:LYS190 4.1 33.5 1.0 HG21 C:THR191 4.1 29.1 1.0 N C:THR191 4.1 29.1 1.0 O3A C:ATP601 4.3 33.8 1.0 CA C:THR191 4.3 29.1 1.0 CG2 C:THR191 4.4 29.1 1.0 HE22 C:GLN223 4.5 29.2 1.0 OE1 C:GLN223 4.5 29.2 1.0 O1A C:ATP601 4.6 33.8 1.0 HG21 C:ILE341 4.6 31.6 1.0 HA C:THR191 4.6 29.1 1.0 O2G C:ATP601 4.6 33.8 1.0 NE2 C:GLN223 4.8 29.2 1.0 HZ1 C:LYS190 4.8 33.5 1.0 CD C:GLN223 4.8 29.2 1.0 PA C:ATP601 4.8 33.8 1.0 CE C:LYS190 4.8 33.5 1.0 HD13 C:ILE341 4.8 31.6 1.0 HG23 C:THR191 4.9 29.1 1.0 HZ3 C:LYS190 5.0 33.5 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:29.3 occ:1.00 O2B A:ATP601 1.7 31.6 1.0 OG1 A:THR191 2.2 27.8 1.0 O3G A:ATP601 2.4 31.6 1.0 PB A:ATP601 2.9 31.6 1.0 PG A:ATP601 3.3 31.6 1.0 O3B A:ATP601 3.5 31.6 1.0 CB A:THR191 3.5 27.8 1.0 O1B A:ATP601 3.5 31.6 1.0 H A:THR191 3.5 27.8 1.0 O1G A:ATP601 3.6 31.6 1.0 HB A:THR191 3.6 27.8 1.0 HB2 A:LYS190 3.8 27.6 1.0 OD1 A:ASP284 4.0 29.2 1.0 HE2 A:LYS190 4.0 27.6 1.0 N A:THR191 4.1 27.8 1.0 O3A A:ATP601 4.2 31.6 1.0 HG21 A:THR191 4.3 27.8 1.0 CA A:THR191 4.4 27.8 1.0 HG21 A:ILE341 4.5 26.2 1.0 CG2 A:THR191 4.5 27.8 1.0 OD2 A:ASP284 4.5 29.2 1.0 HA A:THR191 4.7 27.8 1.0 O1A A:ATP601 4.7 31.6 1.0 CG A:ASP284 4.7 29.2 1.0 O2G A:ATP601 4.7 31.6 1.0 PA A:ATP601 4.8 31.6 1.0 HE22 A:GLN223 4.8 32.3 1.0 CB A:LYS190 4.8 27.6 1.0 OE1 A:GLN223 4.8 32.3 1.0 O2A A:ATP601 4.8 31.6 1.0 HD13 A:ILE341 4.8 26.2 1.0 HG23 A:THR191 4.9 27.8 1.0 HZ1 A:LYS190 4.9 27.6 1.0 CE A:LYS190 4.9 27.6 1.0 OD2 A:ASP285 4.9 31.9 1.0 HZ3 A:LYS190 4.9 27.6 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:34.0 occ:1.00 O3B E:ADP601 1.7 40.0 1.0 OG1 E:THR174 2.0 41.2 1.0 PB E:ADP601 2.8 40.0 1.0 O1B E:ADP601 3.0 40.0 1.0 CB E:THR174 3.3 41.2 1.0 HB E:THR174 3.4 41.2 1.0 HE3 E:LYS173 3.8 38.6 1.0 HG21 E:THR174 3.8 41.2 1.0 H E:THR174 3.8 41.2 1.0 O2A E:ADP601 3.8 40.0 1.0 O2B E:ADP601 3.9 40.0 1.0 O3A E:ADP601 3.9 40.0 1.0 OE2 E:GLU203 3.9 38.7 1.0 HH12 E:ARG200 4.0 35.3 1.0 HG3 E:LYS173 4.1 38.6 1.0 CG2 E:THR174 4.1 41.2 1.0 OD1 E:ASP266 4.1 39.6 1.0 PA E:ADP601 4.2 40.0 1.0 HH11 E:ARG200 4.3 35.3 1.0 OD2 E:ASP266 4.3 39.6 1.0 HH11 A:ARG388 4.3 36.4 1.0 HH12 A:ARG388 4.3 36.4 1.0 CA E:THR174 4.3 41.2 1.0 N E:THR174 4.3 41.2 1.0 HG2 E:LYS173 4.4 38.6 1.0 NH1 E:ARG200 4.4 35.3 1.0 HA E:THR174 4.5 41.2 1.0 OE1 E:GLU203 4.5 38.7 1.0 HG23 E:THR174 4.5 41.2 1.0 NH1 A:ARG388 4.6 36.4 1.0 CE E:LYS173 4.6 38.6 1.0 HE2 E:LYS173 4.6 38.6 1.0 O1A E:ADP601 4.6 40.0 1.0 CG E:ASP266 4.6 39.6 1.0 CD E:GLU203 4.7 38.7 1.0 CG E:LYS173 4.7 38.6 1.0 HG22 E:THR174 4.9 41.2 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, 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 Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring, Rotational State 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:34.4 occ:1.00 O2B D:ATP601 1.9 48.7 1.0 OG1 D:THR174 2.1 33.3 1.0 O1G D:ATP601 2.3 48.7 1.0 OE1 D:GLU199 3.2 33.5 1.0 CB D:THR174 3.4 33.3 1.0 PB D:ATP601 3.4 48.7 1.0 HH12 D:ARG200 3.4 30.7 1.0 HB D:THR174 3.5 33.3 1.0 HG21 D:THR174 3.6 33.3 1.0 PG D:ATP601 3.6 48.7 1.0 OE2 D:GLU203 3.7 30.0 1.0 HH11 D:ARG200 3.7 30.7 1.0 NH1 D:ARG200 3.9 30.7 1.0 O3B D:ATP601 3.9 48.7 1.0 CG2 D:THR174 4.0 33.3 1.0 CD D:GLU199 4.0 33.5 1.0 H D:THR174 4.1 33.3 1.0 HE2 D:LYS173 4.2 32.2 1.0 OD2 D:ASP266 4.2 30.9 1.0 OD1 D:ASP266 4.2 30.9 1.0 OE1 D:GLU203 4.3 30.0 1.0 O3G D:ATP601 4.3 48.7 1.0 O3A D:ATP601 4.4 48.7 1.0 HG3 D:LYS173 4.4 32.2 1.0 HG23 D:THR174 4.4 33.3 1.0 CD D:GLU203 4.4 30.0 1.0 O1B D:ATP601 4.4 48.7 1.0 OE2 D:GLU199 4.5 33.5 1.0 CA D:THR174 4.5 33.3 1.0 O1A D:ATP601 4.5 48.7 1.0 HH22 C:ARG388 4.6 37.1 1.0 N D:THR174 4.6 33.3 1.0 CG D:ASP266 4.6 30.9 1.0 HG3 D:GLU199 4.7 33.5 1.0 HZ3 D:LYS173 4.7 32.2 1.0 HA D:THR174 4.7 33.3 1.0 O2G D:ATP601 4.7 48.7 1.0 PA D:ATP601 4.8 48.7 1.0 HG22 D:THR174 4.8 33.3 1.0 O2A D:ATP601 4.8 48.7 1.0 HG2 D:LYS173 4.9 32.2 1.0 CG D:GLU199 4.9 33.5 1.0 HB3 D:GLU199 5.0 33.5 1.0

A.Muhleip, S.E.Mccomas, A.Amunts. Structure of A Mitochondrial Atp Synthase with Bound Native Cardiolipin. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31738165
DOI: 10.7554/ELIFE.51179