Magnesium in PDB 6j5i: Cryo-Em Structure of the Mammalian Dp-State Atp Synthase

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

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mammalian Dp-State Atp Synthase (pdb code 6j5i). 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 Dp-State Atp Synthase, PDB code: 6j5i:
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 Dp-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 Dp-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:10.2 occ:1.00 OG1 A:THR176 2.1 10.4 1.0 O2G A:ATP601 2.1 10.5 0.8 O2B A:ATP601 3.1 10.5 1.0 PG A:ATP601 3.3 10.5 0.8 CB A:THR176 3.3 10.4 1.0 O3G A:ATP601 3.6 10.5 0.8 CG2 A:THR176 3.6 10.4 1.0 O3B A:ATP601 4.1 10.5 1.0 PB A:ATP601 4.2 10.5 1.0 OD2 A:ASP269 4.2 9.7 1.0 NE2 A:GLN208 4.4 13.9 1.0 CA A:THR176 4.5 10.4 1.0 N A:THR176 4.5 10.4 1.0 O1G A:ATP601 4.5 10.5 0.8 O1A A:ATP601 4.8 10.5 1.0 OD1 A:ASP269 5.0 9.7 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of the Mammalian Dp-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 Dp-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:19.3 occ:1.00 OG1 B:THR176 2.2 23.9 1.0 O2B B:ATP601 2.8 32.8 1.0 OD1 B:ASP269 2.9 11.8 1.0 O3G B:ATP601 3.1 32.8 1.0 CB B:THR176 3.2 23.9 1.0 OD2 B:ASP269 3.3 11.8 1.0 CG B:ASP269 3.4 11.8 1.0 NE2 B:GLN208 3.7 18.3 1.0 CG2 B:THR176 3.9 23.9 1.0 PB B:ATP601 4.0 32.8 1.0 PG B:ATP601 4.2 32.8 1.0 O1B B:ATP601 4.4 32.8 1.0 O2G B:ATP601 4.4 32.8 1.0 CD B:GLN208 4.4 18.3 1.0 CA B:THR176 4.5 23.9 1.0 O3B B:ATP601 4.6 32.8 1.0 N B:THR176 4.7 23.9 1.0 CB B:ASP269 4.7 11.8 1.0 OE1 B:GLN208 4.9 18.3 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of the Mammalian Dp-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 Dp-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:8.6 occ:1.00 OG1 C:THR176 2.1 9.7 1.0 O3G C:ATP601 2.1 12.9 0.8 O2B C:ATP601 2.2 12.9 1.0 PB C:ATP601 3.3 12.9 1.0 PG C:ATP601 3.4 12.9 0.8 CB C:THR176 3.5 9.7 1.0 O3B C:ATP601 3.6 12.9 1.0 OD1 C:ASP269 3.7 15.5 1.0 OD2 C:ASP269 3.8 15.5 1.0 O1B C:ATP601 4.0 12.9 1.0 N C:THR176 4.0 9.7 1.0 CE C:LYS175 4.1 8.2 1.0 CG C:ASP269 4.2 15.5 1.0 CA C:THR176 4.2 9.7 1.0 CG2 C:THR176 4.3 9.7 1.0 O1G C:ATP601 4.3 12.9 0.8 O2G C:ATP601 4.4 12.9 0.8 CB C:LYS175 4.6 8.2 1.0 O3A C:ATP601 4.6 12.9 1.0 NZ C:LYS175 4.7 8.2 1.0 C C:LYS175 4.7 8.2 1.0 O2A C:ATP601 5.0 12.9 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of the Mammalian Dp-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 Dp-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:8.9 occ:1.00 O1B D:ADP501 2.0 16.3 1.0 OG1 D:THR165 2.2 11.5 1.0 O3A D:ADP501 3.1 16.3 1.0 PB D:ADP501 3.2 16.3 1.0 CB D:THR165 3.5 11.5 1.0 OE2 D:GLU194 3.6 14.8 1.0 OE1 D:GLU194 3.7 14.8 1.0 O2B D:ADP501 3.9 16.3 1.0 NH1 D:ARG191 4.0 12.5 1.0 CD D:GLU194 4.0 14.8 1.0 CG2 D:THR165 4.2 11.5 1.0 N D:THR165 4.3 11.5 1.0 O3B D:ADP501 4.4 16.3 1.0 PA D:ADP501 4.4 16.3 1.0 OE2 D:GLU190 4.5 13.8 1.0 CA D:THR165 4.5 11.5 1.0 CG D:GLU190 4.7 13.8 1.0 O1A D:ADP501 4.7 16.3 1.0 OD2 D:ASP258 4.8 11.2 1.0 CD D:GLU190 4.9 13.8 1.0 O2A D:ADP501 4.9 16.3 1.0 OD1 D:ASP258 4.9 11.2 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of the Mammalian Dp-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 Dp-State Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:9.8 occ:1.00 O1B F:ADP501 2.2 14.5 1.0 O3A F:ADP501 2.8 14.5 1.0 PB F:ADP501 3.1 14.5 1.0 CG2 F:THR165 3.7 12.9 1.0 CB F:THR165 3.8 12.9 1.0 O2B F:ADP501 4.0 14.5 1.0 PA F:ADP501 4.2 14.5 1.0 OE2 F:GLU190 4.3 17.8 1.0 O3B F:ADP501 4.3 14.5 1.0 CG F:GLU190 4.4 17.8 1.0 NZ F:LYS164 4.4 13.3 1.0 OD1 F:ASP258 4.5 15.8 1.0 O2A F:ADP501 4.5 14.5 1.0 CD F:GLU190 4.5 17.8 1.0 OE1 F:GLU194 4.6 15.9 1.0 OD2 F:ASP258 4.6 15.8 1.0 OG1 F:THR165 4.6 12.9 1.0 CE F:LYS164 4.7 13.3 1.0 OE2 F:GLU194 4.7 15.9 1.0 N F:THR165 4.8 12.9 1.0 O1A F:ADP501 4.8 14.5 1.0 CA F:THR165 5.0 12.9 1.0 CG F:ASP258 5.0 15.8 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