Zinc 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:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Human M-Aaa Protease AFG3L2, Substrate-Bound (pdb code 6nyy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human M-Aaa Protease AFG3L2, Substrate-Bound, PDB code: 6nyy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:92.3 occ:1.00 OD2 A:ASP649 2.1 79.2 1.0 NE2 A:HIS574 2.2 79.5 1.0 CE1 A:HIS578 2.8 80.3 1.0 CD2 A:HIS574 2.9 79.5 1.0 CG A:ASP649 3.0 79.2 1.0 OD1 A:ASP649 3.1 79.2 1.0 CE1 A:HIS574 3.4 79.5 1.0 NE2 A:HIS578 3.4 80.3 1.0 ND1 A:HIS578 3.6 80.3 1.0 NE2 A:GLN575 3.8 85.9 1.0 CG A:HIS574 4.1 79.5 1.0 ND1 A:HIS574 4.3 79.5 1.0 CD2 A:HIS578 4.4 80.3 1.0 CB A:ASP649 4.4 79.2 1.0 CG A:HIS578 4.5 80.3 1.0 CD A:GLN575 4.7 85.9 1.0 O A:GLY645 4.9 76.4 1.0

Zinc binding site 2 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:0.0 occ:1.00 OD2 B:ASP649 2.1 73.5 1.0 NE2 B:HIS574 2.2 70.1 1.0 NE2 B:HIS578 2.7 69.4 1.0 CG B:ASP649 3.0 73.5 1.0 CD2 B:HIS574 3.1 70.1 1.0 OD1 B:ASP649 3.2 73.5 1.0 CE1 B:HIS574 3.2 70.1 1.0 O H:ALA6 3.5 99.7 1.0 CD2 B:HIS578 3.5 69.4 1.0 CE1 B:HIS578 3.6 69.4 1.0 C H:ALA6 4.3 99.7 1.0 CG B:HIS574 4.3 70.1 1.0 ND1 B:HIS574 4.3 70.1 1.0 CB B:ASP649 4.4 73.5 1.0 CB H:ALA7 4.4 96.0 1.0 CA H:ALA7 4.4 96.0 1.0 CA B:ALA646 4.5 70.6 1.0 CB B:ALA646 4.5 70.6 1.0 CG B:HIS578 4.6 69.4 1.0 N H:ALA7 4.6 96.0 1.0 ND1 B:HIS578 4.6 69.4 1.0 O H:ALA5 4.6 0.3 1.0 N B:ALA646 4.7 70.6 1.0 NE2 B:GLN575 4.8 74.8 1.0 CG B:GLN575 4.9 74.8 1.0

Zinc binding site 3 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:88.9 occ:1.00 OD2 C:ASP649 2.1 67.0 1.0 O I:ALA5 2.1 73.9 1.0 NE2 C:HIS578 2.2 59.6 1.0 NE2 C:HIS574 2.3 61.2 1.0 CG C:ASP649 2.9 67.0 1.0 OD1 C:ASP649 2.9 67.0 1.0 CE1 C:HIS578 3.0 59.6 1.0 CD2 C:HIS574 3.1 61.2 1.0 C I:ALA5 3.2 73.9 1.0 CD2 C:HIS578 3.2 59.6 1.0 CE1 C:HIS574 3.3 61.2 1.0 N I:ALA6 3.9 73.3 1.0 CA I:ALA6 4.0 73.3 1.0 N I:ALA5 4.1 73.9 1.0 ND1 C:HIS578 4.1 59.6 1.0 CA I:ALA5 4.2 73.9 1.0 CG C:HIS574 4.3 61.2 1.0 CG C:HIS578 4.3 59.6 1.0 CB C:ASP649 4.3 67.0 1.0 ND1 C:HIS574 4.3 61.2 1.0 CB I:ALA6 4.4 73.3 1.0 NE2 C:GLN575 4.5 59.6 1.0 CB I:ALA4 4.9 75.1 1.0

Zinc binding site 4 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn803 b:82.7 occ:1.00 OD2 D:ASP649 2.1 67.0 1.0 O J:ALA5 2.1 76.0 1.0 NE2 D:HIS578 2.2 61.0 1.0 NE2 D:HIS574 2.3 63.2 1.0 CG D:ASP649 2.9 67.0 1.0 OD1 D:ASP649 2.9 67.0 1.0 C J:ALA5 3.0 76.0 1.0 CD2 D:HIS574 3.0 63.2 1.0 CD2 D:HIS578 3.0 61.0 1.0 CE1 D:HIS578 3.1 61.0 1.0 CE1 D:HIS574 3.4 63.2 1.0 N J:ALA5 3.6 76.0 1.0 CA J:ALA5 3.8 76.0 1.0 N J:ALA6 3.9 77.7 1.0 ND1 D:HIS578 4.1 61.0 1.0 CG D:HIS578 4.1 61.0 1.0 CG D:HIS574 4.2 63.2 1.0 CA J:ALA6 4.2 77.7 1.0 CB D:ASP649 4.3 67.0 1.0 NE2 D:GLN575 4.3 63.7 1.0 ND1 D:HIS574 4.4 63.2 1.0 C J:ALA4 4.4 77.9 1.0 CB J:ALA4 4.6 77.9 1.0 CB J:ALA6 4.7 77.7 1.0 CA J:ALA4 5.0 77.9 1.0

Zinc binding site 5 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn802 b:92.8 occ:1.00 OD2 E:ASP649 2.1 76.4 1.0 NE2 E:HIS574 2.2 76.4 1.0 CD2 E:HIS574 3.0 76.4 1.0 CG E:ASP649 3.0 76.4 1.0 NE2 E:HIS578 3.1 74.3 1.0 OD1 E:ASP649 3.3 76.4 1.0 CE1 E:HIS574 3.4 76.4 1.0 CD2 E:HIS578 3.7 74.3 1.0 NE2 E:GLN575 4.0 78.5 1.0 CE1 E:HIS578 4.1 74.3 1.0 CG E:HIS574 4.2 76.4 1.0 ND1 E:HIS574 4.4 76.4 1.0 CB E:ASP649 4.4 76.4 1.0 O E:GLY645 4.6 75.3 1.0 CG E:HIS578 4.9 74.3 1.0 CD E:GLN575 4.9 78.5 1.0

Zinc binding site 6 out of 6 in the Human M-Aaa Protease AFG3L2, Substrate-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human M-Aaa Protease AFG3L2, Substrate-Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:99.6 occ:1.00 OD2 F:ASP649 2.2 81.9 1.0 NE2 F:HIS574 2.2 87.2 1.0 NE2 F:HIS578 2.5 87.4 1.0 CD2 F:HIS574 3.0 87.2 1.0 CG F:ASP649 3.0 81.9 1.0 OD1 F:ASP649 3.2 81.9 1.0 CD2 F:HIS578 3.2 87.4 1.0 CE1 F:HIS574 3.3 87.2 1.0 CE1 F:HIS578 3.5 87.4 1.0 CG F:HIS574 4.2 87.2 1.0 ND1 F:HIS574 4.3 87.2 1.0 CG F:HIS578 4.4 87.4 1.0 ND1 F:HIS578 4.4 87.4 1.0 CB F:ASP649 4.5 81.9 1.0 OE1 F:GLN575 4.6 95.6 1.0 NE2 F:GLN575 4.7 95.6 1.0 CD F:GLN575 5.0 95.6 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