Magnesium in PDB 6nyy: Human M-Aaa Protease AFG3L2, Substrate-Bound

The structure of Human M-Aaa Protease AFG3L2, Substrate-Bound also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the Human M-Aaa Protease AFG3L2, Substrate-Bound (pdb code 6nyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human M-Aaa Protease AFG3L2, Substrate-Bound, PDB code: 6nyy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:78.7 occ:1.00 O1B B:ANP801 2.1 74.2 1.0 OG1 B:THR355 2.1 85.4 1.0 O3G B:ANP801 2.1 74.2 1.0 O1G B:ANP801 2.1 74.2 1.0 PG B:ANP801 2.6 74.2 1.0 CB B:THR355 3.2 85.4 1.0 O1A B:ANP801 3.2 74.2 1.0 PB B:ANP801 3.3 74.2 1.0 N3B B:ANP801 3.5 74.2 1.0 OD2 B:ASP407 3.7 84.1 1.0 O2G B:ANP801 3.9 74.2 1.0 CG2 B:THR355 4.0 85.4 1.0 PA B:ANP801 4.0 74.2 1.0 OD1 B:ASP407 4.1 84.1 1.0 O3A B:ANP801 4.1 74.2 1.0 NH1 C:ARG468 4.3 72.1 1.0 O2A B:ANP801 4.3 74.2 1.0 CG B:ASP407 4.3 84.1 1.0 NE2 B:GLN408 4.3 83.5 1.0 N B:THR355 4.3 85.4 1.0 CA B:THR355 4.4 85.4 1.0 CG B:LYS354 4.4 82.2 1.0 O2B B:ANP801 4.5 74.2 1.0 O C:ASP439 4.6 78.9 1.0

Magnesium binding site 2 out of 3 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:59.6 occ:1.00 O3G C:ANP803 2.1 70.9 1.0 N3B C:ANP803 2.1 70.9 1.0 OG1 C:THR355 2.2 65.3 1.0 O1B C:ANP803 2.3 70.9 1.0 PG C:ANP803 2.5 70.9 1.0 PB C:ANP803 2.8 70.9 1.0 O2G C:ANP803 3.3 70.9 1.0 CB C:THR355 3.3 65.3 1.0 O2B C:ANP803 3.6 70.9 1.0 O1G C:ANP803 3.8 70.9 1.0 NH2 D:ARG468 4.0 61.6 1.0 O3A C:ANP803 4.0 70.9 1.0 O D:ASP439 4.1 67.3 1.0 O1A C:ANP803 4.2 70.9 1.0 CG2 C:THR355 4.2 65.3 1.0 OD2 C:ASP407 4.3 70.1 1.0 N C:THR355 4.3 65.3 1.0 CA C:THR355 4.4 65.3 1.0 OD1 C:ASP407 4.5 70.1 1.0 CG C:LYS354 4.6 63.1 1.0 PA C:ANP803 4.7 70.9 1.0 NH1 D:ARG465 4.8 60.7 1.0 CG C:ASP407 4.8 70.1 1.0 NE2 C:GLN408 4.8 68.5 1.0 CZ D:ARG468 4.9 61.6 1.0

Magnesium binding site 3 out of 3 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:72.7 occ:1.00 O3G D:ANP801 2.1 78.0 1.0 OG1 D:THR355 2.2 67.9 1.0 OD2 D:ASP407 3.2 73.4 1.0 CB D:THR355 3.2 67.9 1.0 O E:ASP439 3.3 75.4 1.0 PG D:ANP801 3.5 78.0 1.0 CG2 D:THR355 3.8 67.9 1.0 OD1 D:ASP407 3.8 73.4 1.0 O1B D:ANP801 3.8 78.0 1.0 O1G D:ANP801 3.9 78.0 1.0 CG D:ASP407 3.9 73.4 1.0 O1A D:ANP801 4.1 78.0 1.0 NH2 E:ARG468 4.1 69.2 1.0 O2G D:ANP801 4.1 78.0 1.0 C E:ASP439 4.4 75.4 1.0 CA E:GLY440 4.5 75.7 1.0 CA D:THR355 4.5 67.9 1.0 O3A D:ANP801 4.5 78.0 1.0 PB D:ANP801 4.6 78.0 1.0 NE2 D:GLN408 4.6 73.2 1.0 N D:THR355 4.6 67.9 1.0 N3B D:ANP801 4.7 78.0 1.0 PA D:ANP801 4.8 78.0 1.0 N E:GLY440 5.0 75.7 1.0 O2A D:ANP801 5.0 78.0 1.0

C.Puchades, B.Ding, A.Song, R.L.Wiseman, G.C.Lander, S.E.Glynn. Unique Structural Features of the Mitochondrial Aaa+ Protease AFG3L2 Reveal the Molecular Basis For Activity in Health and Disease. Mol.Cell V. 75 1073 2019.
ISSN: ISSN 1097-2765
PubMed: 31327635
DOI: 10.1016/J.MOLCEL.2019.06.016