Magnesium in PDB 8eff: Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane

The structure of Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Fluorine	(F)	16 atoms
Aluminium	(Al)	4 atoms

The binding sites of Magnesium atom in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane (pdb code 8eff). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane, PDB code: 8eff:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:7.9 occ:1.00 O3B A:GDP1001 2.2 9.7 1.0 HG21 A:THR302 2.5 134.1 1.0 HB2 A:MET322 2.7 33.6 1.0 HG1 A:THR323 2.7 32.5 1.0 HE2 A:PHE314 2.8 35.8 1.0 OG1 A:THR323 3.0 32.5 1.0 HG23 A:THR302 3.2 134.1 1.0 OG1 A:THR302 3.2 134.1 1.0 O1B A:GDP1001 3.2 7.1 1.0 CG2 A:THR302 3.2 134.1 1.0 PB A:GDP1001 3.2 7.8 1.0 H A:THR323 3.3 25.9 1.0 F4 A:ALF1002 3.6 16.1 1.0 CB A:MET322 3.6 33.6 1.0 O1A A:GDP1001 3.6 6.8 1.0 AL A:ALF1002 3.6 14.3 1.0 HB3 A:MET322 3.6 33.6 1.0 CE2 A:PHE314 3.7 35.8 1.0 CB A:THR302 3.8 134.1 1.0 N A:THR323 3.9 25.9 1.0 HG1 A:THR302 3.9 134.1 1.0 F1 A:ALF1002 4.0 15.2 1.0 HG22 A:THR302 4.1 134.1 1.0 HG3 A:MET322 4.1 33.6 1.0 F2 A:ALF1002 4.1 15.3 1.0 HZ A:PHE314 4.1 35.8 1.0 HB A:THR302 4.2 134.1 1.0 O3A A:GDP1001 4.2 9.1 1.0 CB A:THR323 4.3 32.5 1.0 H A:MET322 4.4 24.4 1.0 O2B A:GDP1001 4.4 6.3 1.0 CZ A:PHE314 4.4 35.8 1.0 CG A:MET322 4.4 33.6 1.0 PA A:GDP1001 4.4 8.3 1.0 H A:THR302 4.4 89.8 1.0 F3 A:ALF1002 4.5 15.9 1.0 HB A:THR323 4.6 32.5 1.0 CA A:MET322 4.6 22.5 1.0 HD2 A:PHE314 4.6 35.8 1.0 CA A:THR323 4.6 22.2 1.0 C A:MET322 4.6 27.9 1.0 CD2 A:PHE314 4.7 35.8 1.0 HG2 A:MET322 4.7 33.6 1.0 HZ3 A:LYS301 4.7 134.2 1.0 HA A:THR323 4.8 22.2 1.0 HA A:ARG316 4.9 23.5 1.0 O2A A:GDP1001 4.9 8.8 1.0 N A:MET322 4.9 24.4 1.0 O A:PRO315 5.0 27.0 1.0

Magnesium binding site 2 out of 4 in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:8.2 occ:1.00 O2B B:GDP1001 2.0 8.5 1.0 HB B:THR323 2.1 34.1 1.0 F4 B:ALF1002 2.2 13.6 1.0 OG1 B:THR323 2.2 34.1 1.0 F1 B:ALF1002 2.2 11.9 1.0 AL B:ALF1002 2.4 10.9 1.0 O3B B:GDP1001 2.4 8.0 1.0 HE3 B:LYS301 2.6 134.2 1.0 CB B:THR323 2.6 34.1 1.0 PB B:GDP1001 2.6 7.9 1.0 HE2 B:LYS301 2.7 134.2 1.0 H B:THR323 2.8 25.9 1.0 CE B:LYS301 3.0 134.2 1.0 HD3 B:LYS301 3.2 134.2 1.0 O1B B:GDP1001 3.3 5.6 1.0 HB3 B:LYS301 3.3 134.2 1.0 N B:THR323 3.5 25.9 1.0 HG21 B:THR323 3.6 34.1 1.0 F2 B:ALF1002 3.6 12.6 1.0 CA B:THR323 3.6 22.2 1.0 CD B:LYS301 3.6 134.2 1.0 F3 B:ALF1002 3.6 14.3 1.0 CG2 B:THR323 3.7 34.1 1.0 O3A B:GDP1001 4.0 7.3 1.0 OD1 B:ASP398 4.2 121.1 1.0 CB B:LYS301 4.2 134.2 1.0 HA B:THR323 4.2 22.2 1.0 HG3 B:MET321 4.2 31.7 1.0 HG1 B:THR302 4.2 134.2 1.0 HG22 B:THR323 4.2 34.1 1.0 HG23 B:THR323 4.3 34.1 1.0 HD2 B:LYS301 4.3 134.2 1.0 NZ B:LYS301 4.3 134.2 1.0 HB2 B:LYS301 4.4 134.2 1.0 HG2 B:MET321 4.4 31.7 1.0 HZ1 B:LYS301 4.4 134.2 1.0 H B:MET322 4.4 24.4 1.0 HA B:PRO400 4.5 90.2 1.0 OG1 B:THR302 4.5 134.2 1.0 CG B:LYS301 4.5 134.2 1.0 HB2 B:MET322 4.5 33.6 1.0 H B:GLY401 4.6 89.2 1.0 C B:THR323 4.7 23.8 1.0 O B:LEU399 4.7 91.6 1.0 C B:MET322 4.7 27.9 1.0 N B:MET322 4.7 24.4 1.0 O B:THR323 4.7 24.9 1.0 HZ2 B:LYS301 4.8 134.2 1.0 OD2 B:ASP398 4.8 121.1 1.0 HA B:MET321 4.8 26.7 1.0 CG B:MET321 4.8 31.7 1.0 HZ3 B:LYS301 4.9 134.2 1.0 CG B:ASP398 4.9 121.1 1.0 H B:THR302 4.9 89.8 1.0 HG2 B:LYS301 5.0 134.2 1.0

Magnesium binding site 3 out of 4 in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:7.9 occ:1.00 O3B C:GDP1001 2.2 9.7 1.0 HG21 C:THR302 2.5 134.1 1.0 HB2 C:MET322 2.7 33.6 1.0 HG1 C:THR323 2.7 32.5 1.0 HE2 C:PHE314 2.8 35.8 1.0 OG1 C:THR323 3.0 32.5 1.0 HG23 C:THR302 3.2 134.1 1.0 OG1 C:THR302 3.2 134.1 1.0 O1B C:GDP1001 3.2 7.1 1.0 CG2 C:THR302 3.2 134.1 1.0 PB C:GDP1001 3.2 7.8 1.0 H C:THR323 3.2 25.9 1.0 F4 C:ALF1002 3.6 16.1 1.0 CB C:MET322 3.6 33.6 1.0 O1A C:GDP1001 3.6 6.8 1.0 AL C:ALF1002 3.6 14.3 1.0 HB3 C:MET322 3.6 33.6 1.0 CE2 C:PHE314 3.7 35.8 1.0 CB C:THR302 3.8 134.1 1.0 HG1 C:THR302 3.9 134.1 1.0 N C:THR323 3.9 25.9 1.0 F1 C:ALF1002 4.0 15.2 1.0 HG22 C:THR302 4.1 134.1 1.0 HG3 C:MET322 4.1 33.6 1.0 F2 C:ALF1002 4.1 15.3 1.0 HZ C:PHE314 4.1 35.8 1.0 HB C:THR302 4.2 134.1 1.0 O3A C:GDP1001 4.2 9.1 1.0 CB C:THR323 4.3 32.5 1.0 H C:MET322 4.4 24.4 1.0 O2B C:GDP1001 4.4 6.3 1.0 CZ C:PHE314 4.4 35.8 1.0 CG C:MET322 4.4 33.6 1.0 PA C:GDP1001 4.4 8.3 1.0 H C:THR302 4.4 89.8 1.0 F3 C:ALF1002 4.5 15.9 1.0 HB C:THR323 4.6 32.5 1.0 CA C:MET322 4.6 22.5 1.0 HD2 C:PHE314 4.6 35.8 1.0 CA C:THR323 4.6 22.2 1.0 C C:MET322 4.6 27.9 1.0 CD2 C:PHE314 4.7 35.8 1.0 HG2 C:MET322 4.7 33.6 1.0 HZ3 C:LYS301 4.7 134.2 1.0 HA C:THR323 4.8 22.2 1.0 HA C:ARG316 4.9 23.5 1.0 O2A C:GDP1001 4.9 8.8 1.0 N C:MET322 4.9 24.4 1.0 O C:PRO315 5.0 27.0 1.0

Magnesium binding site 4 out of 4 in the Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem of the Soluble OPA1 Tetramer From the Gdp-Alfx Bound Helical Assembly on A Lipid Membrane within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1003 b:8.2 occ:1.00 O2B D:GDP1001 2.0 8.5 1.0 HB D:THR323 2.1 34.1 1.0 F4 D:ALF1002 2.2 13.6 1.0 OG1 D:THR323 2.2 34.1 1.0 F1 D:ALF1002 2.2 11.9 1.0 AL D:ALF1002 2.4 10.9 1.0 O3B D:GDP1001 2.4 8.0 1.0 HE3 D:LYS301 2.6 134.2 1.0 CB D:THR323 2.6 34.1 1.0 PB D:GDP1001 2.6 7.9 1.0 HE2 D:LYS301 2.7 134.2 1.0 H D:THR323 2.8 25.9 1.0 CE D:LYS301 3.0 134.2 1.0 HD3 D:LYS301 3.2 134.2 1.0 O1B D:GDP1001 3.3 5.6 1.0 HB3 D:LYS301 3.3 134.2 1.0 N D:THR323 3.5 25.9 1.0 HG21 D:THR323 3.6 34.1 1.0 F2 D:ALF1002 3.6 12.6 1.0 CA D:THR323 3.6 22.2 1.0 CD D:LYS301 3.6 134.2 1.0 F3 D:ALF1002 3.6 14.3 1.0 CG2 D:THR323 3.7 34.1 1.0 O3A D:GDP1001 4.0 7.3 1.0 OD1 D:ASP398 4.2 121.1 1.0 CB D:LYS301 4.2 134.2 1.0 HA D:THR323 4.2 22.2 1.0 HG3 D:MET321 4.2 31.7 1.0 HG22 D:THR323 4.2 34.1 1.0 HG1 D:THR302 4.3 134.2 1.0 HG23 D:THR323 4.3 34.1 1.0 NZ D:LYS301 4.3 134.2 1.0 HD2 D:LYS301 4.3 134.2 1.0 HG2 D:MET321 4.4 31.7 1.0 HB2 D:LYS301 4.4 134.2 1.0 HZ1 D:LYS301 4.4 134.2 1.0 H D:MET322 4.4 24.4 1.0 HA D:PRO400 4.5 90.2 1.0 OG1 D:THR302 4.5 134.2 1.0 CG D:LYS301 4.5 134.2 1.0 HB2 D:MET322 4.5 33.6 1.0 H D:GLY401 4.6 89.2 1.0 C D:THR323 4.7 23.8 1.0 O D:LEU399 4.7 91.6 1.0 C D:MET322 4.7 27.9 1.0 N D:MET322 4.7 24.4 1.0 O D:THR323 4.7 24.9 1.0 HZ2 D:LYS301 4.8 134.2 1.0 OD2 D:ASP398 4.8 121.1 1.0 HA D:MET321 4.8 26.7 1.0 CG D:MET321 4.8 31.7 1.0 HZ3 D:LYS301 4.9 134.2 1.0 CG D:ASP398 4.9 121.1 1.0 H D:THR302 4.9 89.8 1.0 HG2 D:LYS301 5.0 134.2 1.0

S.B.Nyenhuis, X.Wu, A.E.Stanton, M.P.Strub, Y.I.Yim, B.Canagarajah, J.E.Hinshaw. OPA1 Helical Structures Give Perspective to Mitochondrial Dysfunction Nature 2023.
ISSN: ESSN 1476-4687