Magnesium in PDB 6j5j: Cryo-Em Structure of the Mammalian E-State Atp Synthase

All present enzymatic activity of Cryo-Em Structure of the Mammalian E-State Atp Synthase:
7.1.2.2;

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mammalian E-State Atp Synthase (pdb code 6j5j). 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 Mammalian E-State Atp Synthase, PDB code: 6j5j:
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 Mammalian E-State Atp Synthase


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 Mammalian E-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:22.1 occ:1.00 O2G A:ATP601 2.1 24.9 0.8 O2B A:ATP601 2.1 24.9 1.0 OG1 A:THR176 2.1 20.0 1.0 O3B A:ATP601 2.1 24.9 1.0 PG A:ATP601 2.5 24.9 0.8 PB A:ATP601 2.6 24.9 1.0 O1G A:ATP601 3.0 24.9 0.8 CB A:THR176 3.2 20.0 1.0 O1A A:ATP601 3.5 24.9 1.0 O3A A:ATP601 3.7 24.9 1.0 O1B A:ATP601 3.8 24.9 1.0 O3G A:ATP601 3.9 24.9 0.8 PA A:ATP601 4.0 24.9 1.0 N A:THR176 4.1 20.0 1.0 CG2 A:THR176 4.2 20.0 1.0 CA A:THR176 4.3 20.0 1.0 O2A A:ATP601 4.3 24.9 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of the Mammalian E-State Atp Synthase


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 Mammalian E-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:29.7 occ:1.00 O2B B:ATP601 2.2 40.7 1.0 OG1 B:THR176 2.5 32.9 1.0 O2G B:ATP601 2.5 40.7 1.0 O3G B:ATP601 2.8 40.7 1.0 PG B:ATP601 3.1 40.7 1.0 PB B:ATP601 3.3 40.7 1.0 O3B B:ATP601 3.4 40.7 1.0 CB B:THR176 3.7 32.9 1.0 O1B B:ATP601 4.3 40.7 1.0 NE2 B:GLN208 4.3 27.1 1.0 O1A B:ATP601 4.3 40.7 1.0 CG2 B:THR176 4.5 32.9 1.0 O1G B:ATP601 4.5 40.7 1.0 O3A B:ATP601 4.5 40.7 1.0 OD1 B:ASP269 4.7 31.7 1.0 N B:THR176 4.7 32.9 1.0 PA B:ATP601 4.8 40.7 1.0 CA B:THR176 4.8 32.9 1.0 CD B:GLN208 4.9 27.1 1.0 O2A B:ATP601 5.0 40.7 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of the Mammalian E-State Atp Synthase


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 Mammalian E-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:27.9 occ:1.00 O2B C:ATP601 2.1 40.3 1.0 O3G C:ATP601 2.1 40.3 0.8 OG1 C:THR176 2.5 31.4 1.0 PB C:ATP601 3.1 40.3 1.0 PG C:ATP601 3.3 40.3 0.8 O3B C:ATP601 3.5 40.3 1.0 O1B C:ATP601 3.5 40.3 1.0 CB C:THR176 3.7 31.4 1.0 OD2 C:ASP269 3.7 33.1 1.0 O1G C:ATP601 3.8 40.3 0.8 OD1 C:ASP269 4.0 33.1 1.0 CG C:ASP269 4.3 33.1 1.0 N C:THR176 4.5 31.4 1.0 O3A C:ATP601 4.5 40.3 1.0 NE2 C:GLN208 4.5 24.7 1.0 CG2 C:THR176 4.5 31.4 1.0 O2G C:ATP601 4.6 40.3 0.8 O1A C:ATP601 4.7 40.3 1.0 CA C:THR176 4.7 31.4 1.0 NZ C:LYS175 4.9 32.1 1.0 CE C:LYS175 5.0 32.1 1.0 PA C:ATP601 5.0 40.3 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of the Mammalian E-State Atp Synthase


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 Mammalian E-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:39.4 occ:1.00 O1B D:ADP501 2.1 29.6 1.0 OG1 D:THR165 2.1 22.0 1.0 OE1 D:GLU190 2.6 25.1 1.0 CD D:GLU190 3.4 25.1 1.0 CB D:THR165 3.5 22.0 1.0 PB D:ADP501 3.6 29.6 1.0 OE2 D:GLU190 3.8 25.1 1.0 OE1 D:GLU194 4.0 30.9 1.0 NH1 D:ARG191 4.0 24.7 1.0 CG2 D:THR165 4.0 22.0 1.0 OD2 D:ASP258 4.1 29.5 1.0 O3A D:ADP501 4.2 29.6 1.0 O2B D:ADP501 4.3 29.6 1.0 OD1 D:ASP258 4.4 29.5 1.0 CG D:GLU190 4.5 25.1 1.0 CA D:THR165 4.5 22.0 1.0 O3B D:ADP501 4.5 29.6 1.0 N D:THR165 4.6 22.0 1.0 CG D:ASP258 4.7 29.5 1.0 OE2 D:GLU194 4.7 30.9 1.0 CD D:GLU194 4.8 30.9 1.0 O1A D:ADP501 4.9 29.6 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of the Mammalian E-State Atp Synthase


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 Mammalian E-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:22.3 occ:1.00 OG1 F:THR165 2.1 31.4 1.0 O1B F:ADP501 2.2 39.7 1.0 O3A F:ADP501 2.9 39.7 1.0 CB F:THR165 3.2 31.4 1.0 PB F:ADP501 3.2 39.7 1.0 CG2 F:THR165 3.9 31.4 1.0 PA F:ADP501 4.1 39.7 1.0 O2B F:ADP501 4.2 39.7 1.0 O3B F:ADP501 4.2 39.7 1.0 N F:THR165 4.4 31.4 1.0 NH1 F:ARG191 4.4 29.6 1.0 CA F:THR165 4.4 31.4 1.0 O1A F:ADP501 4.4 39.7 1.0 O2A F:ADP501 4.4 39.7 1.0 OE2 F:GLU194 4.4 40.4 1.0 OE1 F:GLU194 4.5 40.4 1.0 OD1 F:ASP258 4.9 18.7 1.0 CD F:GLU194 4.9 40.4 1.0 C F:LYS164 4.9 26.3 1.0

J.Gu, L.Zhang, S.Zong, R.Guo, T.Liu, J.Yi, P.Wang, W.Zhuo, M.Yang. Cryo-Em Structure of the Mammalian Atp Synthase Tetramer Bound with Inhibitory Protein IF1. Science V. 364 1068 2019.
ISSN: ESSN 1095-9203
PubMed: 31197009
DOI: 10.1126/SCIENCE.AAW4852