Magnesium in PDB 6tdy: Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1

The binding sites of Magnesium atom in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1 (pdb code 6tdy). 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 in Rotational State 1, PDB code: 6tdy:
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 in Rotational State 1


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 in Rotational State 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:37.2 occ:1.00 O2B A:ATP601 2.0 35.5 1.0 OG1 A:THR191 2.1 33.5 1.0 O3G A:ATP601 2.2 35.5 1.0 PB A:ATP601 3.3 35.5 1.0 OD1 A:ASP284 3.3 31.4 1.0 CB A:THR191 3.3 33.5 1.0 HB A:THR191 3.3 33.5 1.0 PG A:ATP601 3.4 35.5 1.0 O3B A:ATP601 3.5 35.5 1.0 OD2 A:ASP284 3.6 31.4 1.0 H A:THR191 3.7 33.5 1.0 HG21 A:THR191 3.8 33.5 1.0 CG A:ASP284 3.8 31.4 1.0 HE22 A:GLN223 3.8 34.2 1.0 O1A A:ATP601 3.9 35.5 1.0 CG2 A:THR191 4.1 33.5 1.0 NE2 A:GLN223 4.2 34.2 1.0 HE21 A:GLN223 4.3 34.2 1.0 O3A A:ATP601 4.3 35.5 1.0 N A:THR191 4.3 33.5 1.0 O1B A:ATP601 4.3 35.5 1.0 O2G A:ATP601 4.4 35.5 1.0 HE3 A:LYS190 4.4 33.0 1.0 CA A:THR191 4.4 33.5 1.0 PA A:ATP601 4.4 35.5 1.0 HG23 A:THR191 4.4 33.5 1.0 HB2 A:LYS190 4.4 33.0 1.0 O2A A:ATP601 4.5 35.5 1.0 O1G A:ATP601 4.5 35.5 1.0 HA A:THR191 4.7 33.5 1.0 HD13 A:ILE341 4.8 30.2 1.0 HG22 A:THR191 4.9 33.5 1.0 CD A:GLN223 5.0 34.2 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1


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 in Rotational State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:39.6 occ:1.00 O2B B:ATP601 2.0 39.0 1.0 O3G B:ATP601 2.0 39.0 1.0 OG1 B:THR191 2.0 35.2 1.0 HE22 B:GLN223 3.2 36.5 1.0 OD2 B:ASP284 3.2 33.4 1.0 CB B:THR191 3.3 35.2 1.0 PB B:ATP601 3.4 39.0 1.0 PG B:ATP601 3.4 39.0 1.0 HB B:THR191 3.4 35.2 1.0 NE2 B:GLN223 3.5 36.5 1.0 OD1 B:ASP284 3.5 33.4 1.0 HE21 B:GLN223 3.6 36.5 1.0 H B:THR191 3.7 35.2 1.0 HG21 B:THR191 3.8 35.2 1.0 CG B:ASP284 3.8 33.4 1.0 O3B B:ATP601 3.9 39.0 1.0 O2G B:ATP601 4.1 39.0 1.0 CG2 B:THR191 4.1 35.2 1.0 CD B:GLN223 4.3 36.5 1.0 O1B B:ATP601 4.3 39.0 1.0 N B:THR191 4.3 35.2 1.0 CA B:THR191 4.4 35.2 1.0 O1A B:ATP601 4.4 39.0 1.0 HB2 B:LYS190 4.5 34.1 1.0 O3A B:ATP601 4.5 39.0 1.0 HE2 B:LYS190 4.5 34.1 1.0 O1G B:ATP601 4.5 39.0 1.0 HG23 B:THR191 4.5 35.2 1.0 HA B:THR191 4.6 35.2 1.0 OE1 B:GLN223 4.7 36.5 1.0 HG3 B:GLN223 4.8 36.5 1.0 HG22 B:THR191 4.9 35.2 1.0 PA B:ATP601 4.9 39.0 1.0 HG21 B:ILE341 4.9 31.7 1.0 HD13 B:ILE341 4.9 31.7 1.0 HH B:TYR218 4.9 34.0 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1


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 in Rotational State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:31.6 occ:1.00 O2B C:ATP601 1.9 30.6 1.0 OG1 C:THR191 2.1 30.1 1.0 O1G C:ATP601 2.1 30.6 1.0 PB C:ATP601 3.2 30.6 1.0 PG C:ATP601 3.3 30.6 1.0 CB C:THR191 3.5 30.1 1.0 O3G C:ATP601 3.6 30.6 1.0 HB C:THR191 3.7 30.1 1.0 O3B C:ATP601 3.7 30.6 1.0 H C:THR191 3.8 30.1 1.0 OD1 C:ASP284 3.9 29.4 1.0 HG21 C:THR191 4.0 30.1 1.0 O1B C:ATP601 4.0 30.6 1.0 HB2 C:LYS190 4.2 29.1 1.0 OD2 C:ASP284 4.2 29.4 1.0 HE2 C:LYS190 4.2 29.1 1.0 CG2 C:THR191 4.3 30.1 1.0 N C:THR191 4.3 30.1 1.0 CA C:THR191 4.4 30.1 1.0 O3A C:ATP601 4.4 30.6 1.0 CG C:ASP284 4.5 29.4 1.0 HA C:THR191 4.5 30.1 1.0 HG23 C:THR191 4.5 30.1 1.0 OE1 C:GLN223 4.6 31.0 1.0 O1A C:ATP601 4.6 30.6 1.0 HE22 C:GLN223 4.6 31.0 1.0 O2G C:ATP601 4.6 30.6 1.0 PA C:ATP601 4.8 30.6 1.0 HG21 C:ILE341 4.9 26.0 1.0 O2A C:ATP601 4.9 30.6 1.0 OD2 C:ASP285 5.0 29.1 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1


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 in Rotational State 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:32.9 occ:1.00 OG1 D:THR174 2.1 35.7 1.0 O3B D:ADP601 2.1 36.0 1.0 PB D:ADP601 3.1 36.0 1.0 HB D:THR174 3.1 35.7 1.0 CB D:THR174 3.1 35.7 1.0 O2B D:ADP601 3.2 36.0 1.0 HG21 D:THR174 3.4 35.7 1.0 OE2 D:GLU203 3.7 37.6 1.0 HH12 D:ARG200 3.8 34.3 1.0 CG2 D:THR174 3.8 35.7 1.0 H D:THR174 3.9 35.7 1.0 O2A D:ADP601 3.9 36.0 1.0 HE3 D:LYS173 3.9 33.9 1.0 HH12 C:ARG388 4.0 33.1 1.0 HH11 C:ARG388 4.1 33.1 1.0 HH11 D:ARG200 4.1 34.3 1.0 O3A D:ADP601 4.1 36.0 1.0 HG3 D:LYS173 4.2 33.9 1.0 OE1 D:GLU203 4.2 37.6 1.0 OD1 D:ASP266 4.2 33.1 1.0 O1B D:ADP601 4.2 36.0 1.0 NH1 D:ARG200 4.3 34.3 1.0 NH1 C:ARG388 4.3 33.1 1.0 PA D:ADP601 4.3 36.0 1.0 HG23 D:THR174 4.3 35.7 1.0 CA D:THR174 4.3 35.7 1.0 CD D:GLU203 4.4 37.6 1.0 O1A D:ADP601 4.4 36.0 1.0 N D:THR174 4.4 35.7 1.0 OD2 D:ASP266 4.4 33.1 1.0 HG22 D:THR174 4.6 35.7 1.0 HE2 D:LYS173 4.6 33.9 1.0 HA D:THR174 4.7 35.7 1.0 CE D:LYS173 4.7 33.9 1.0 CG D:ASP266 4.8 33.1 1.0 HG2 D:LYS173 5.0 33.9 1.0 CG D:LYS173 5.0 33.9 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Euglena Gracilis Mitochondrial Atp Synthase, Oscp/F1/C-Ring in Rotational State 1


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 in Rotational State 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:40.1 occ:1.00 O2B F:ATP601 1.9 49.4 1.0 OG1 F:THR174 2.1 37.6 1.0 O3G F:ATP601 2.2 49.4 1.0 PB F:ATP601 3.3 49.4 1.0 PG F:ATP601 3.4 49.4 1.0 CB F:THR174 3.4 37.6 1.0 OE1 F:GLU199 3.5 35.5 1.0 HB F:THR174 3.6 37.6 1.0 HG21 F:THR174 3.7 37.6 1.0 HH12 F:ARG200 3.7 35.8 1.0 O1G F:ATP601 3.7 49.4 1.0 HE2 F:LYS173 3.8 35.5 1.0 O3B F:ATP601 3.8 49.4 1.0 HH11 F:ARG200 3.9 35.8 1.0 OE2 F:GLU203 3.9 40.3 1.0 CG2 F:THR174 4.0 37.6 1.0 H F:THR174 4.0 37.6 1.0 HG3 F:LYS173 4.1 35.5 1.0 NH1 F:ARG200 4.2 35.8 1.0 CD F:GLU199 4.2 35.5 1.0 OD2 F:ASP266 4.3 32.8 1.0 OD1 F:ASP266 4.3 32.8 1.0 HG23 F:THR174 4.3 37.6 1.0 O3A F:ATP601 4.3 49.4 1.0 O1B F:ATP601 4.4 49.4 1.0 CA F:THR174 4.5 37.6 1.0 HZ3 F:LYS173 4.5 35.5 1.0 N F:THR174 4.5 37.6 1.0 OE1 F:GLU203 4.6 40.3 1.0 HG2 F:LYS173 4.6 35.5 1.0 HG3 F:GLU199 4.6 35.5 1.0 HB3 F:GLU199 4.6 35.5 1.0 HA F:THR174 4.6 37.6 1.0 O1A F:ATP601 4.6 49.4 1.0 O2G F:ATP601 4.6 49.4 1.0 CE F:LYS173 4.7 35.5 1.0 CD F:GLU203 4.7 40.3 1.0 HZ1 F:LYS173 4.7 35.5 1.0 CG F:ASP266 4.7 32.8 1.0 CG F:LYS173 4.8 35.5 1.0 PA F:ATP601 4.8 49.4 1.0 O2A F:ATP601 4.8 49.4 1.0 OE2 F:GLU199 4.8 35.5 1.0 NZ F:LYS173 4.8 35.5 1.0 HG22 F:THR174 4.9 37.6 1.0 CG F:GLU199 4.9 35.5 1.0 HH22 B:ARG388 4.9 40.4 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