Zinc in PDB 6az0: Mitochondrial Atpase Protease YME1

The structure of Mitochondrial Atpase Protease YME1 also contains other interesting chemical elements:

Magnesium

(Mg)

20 atoms

The binding sites of Zinc atom in the Mitochondrial Atpase Protease YME1 (pdb code 6az0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Mitochondrial Atpase Protease YME1, PDB code: 6az0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:64.2 occ:1.00 OD2 A:ASP618 2.1 38.2 1.0 NE2 A:HIS544 2.2 36.8 1.0 NE2 A:HIS540 2.2 39.3 1.0 OD1 A:ASP618 2.6 38.2 1.0 CG A:ASP618 2.7 38.2 1.0 CE1 A:HIS544 3.1 36.8 1.0 CD2 A:HIS544 3.1 36.8 1.0 CE1 A:HIS540 3.1 39.3 1.0 CD2 A:HIS540 3.2 39.3 1.0 ND1 A:HIS544 4.1 36.8 1.0 CG A:HIS544 4.2 36.8 1.0 CB A:ASP618 4.2 38.2 1.0 ND1 A:HIS540 4.3 39.3 1.0 CG A:HIS540 4.4 39.3 1.0

Zinc binding site 2 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:89.8 occ:1.00 OD2 B:ASP618 2.0 41.6 1.0 NE2 B:HIS544 2.1 42.2 1.0 NE2 B:HIS540 2.2 48.0 1.0 OD1 B:ASP618 2.5 41.6 1.0 CG B:ASP618 2.6 41.6 1.0 CE1 B:HIS540 2.7 48.0 1.0 CE1 B:HIS544 2.9 42.2 1.0 CD2 B:HIS544 3.3 42.2 1.0 CD2 B:HIS540 3.4 48.0 1.0 ND1 B:HIS540 3.9 48.0 1.0 CB B:ASP618 4.1 41.6 1.0 ND1 B:HIS544 4.1 42.2 1.0 CG B:HIS544 4.3 42.2 1.0 CG B:HIS540 4.3 48.0 1.0 CA B:GLY598 4.7 44.7 1.0 O B:GLY614 5.0 48.5 1.0 CA B:ASP618 5.0 41.6 1.0

Zinc binding site 3 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:72.0 occ:1.00 OD2 C:ASP618 2.0 40.0 1.0 NE2 C:HIS540 2.2 45.2 1.0 NE2 C:HIS544 2.2 42.7 1.0 OD1 C:ASP618 2.4 40.0 1.0 CG C:ASP618 2.5 40.0 1.0 CE1 C:HIS540 3.0 45.2 1.0 CE1 C:HIS544 3.0 42.7 1.0 CD2 C:HIS540 3.2 45.2 1.0 CD2 C:HIS544 3.2 42.7 1.0 CB C:ASP618 4.0 40.0 1.0 ND1 C:HIS544 4.2 42.7 1.0 ND1 C:HIS540 4.2 45.2 1.0 CG C:HIS540 4.2 45.2 1.0 CG C:HIS544 4.3 42.7 1.0 CA C:ASP618 4.9 40.0 1.0

Zinc binding site 4 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:75.4 occ:1.00 OD2 D:ASP618 2.0 45.5 1.0 NE2 D:HIS544 2.1 48.4 1.0 NE2 D:HIS540 2.1 53.4 1.0 CE1 D:HIS540 3.0 53.4 1.0 CE1 D:HIS544 3.1 48.4 1.0 CD2 D:HIS544 3.1 48.4 1.0 CG D:ASP618 3.1 45.5 1.0 CD2 D:HIS540 3.2 53.4 1.0 CB D:ASP618 3.8 45.5 1.0 OD1 D:ASP618 4.0 45.5 1.0 ND1 D:HIS540 4.2 53.4 1.0 ND1 D:HIS544 4.2 48.4 1.0 CG D:HIS544 4.2 48.4 1.0 CG D:HIS540 4.2 53.4 1.0 CA D:GLY598 5.0 51.2 1.0

Zinc binding site 5 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn802 b:45.0 occ:1.00 OD2 E:ASP618 2.0 43.6 1.0 NE2 E:HIS540 2.1 51.6 1.0 NE2 E:HIS544 2.2 47.0 1.0 OD1 E:ASP618 2.4 43.6 1.0 CG E:ASP618 2.5 43.6 1.0 CE1 E:HIS540 2.6 51.6 1.0 CE1 E:HIS544 3.0 47.0 1.0 CD2 E:HIS544 3.3 47.0 1.0 CD2 E:HIS540 3.4 51.6 1.0 ND1 E:HIS540 3.9 51.6 1.0 CB E:ASP618 4.0 43.6 1.0 ND1 E:HIS544 4.1 47.0 1.0 CG E:HIS540 4.3 51.6 1.0 CG E:HIS544 4.3 47.0 1.0 CA E:GLY598 4.9 46.9 1.0 CA E:ASP618 4.9 43.6 1.0

Zinc binding site 6 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mitochondrial Atpase Protease YME1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:0.8 occ:1.00 OD2 F:ASP618 1.7 56.5 1.0 NE2 F:HIS540 2.1 59.7 1.0 CG F:ASP618 2.5 56.5 1.0 NE2 F:HIS544 2.6 57.1 1.0 CE1 F:HIS540 2.7 59.7 1.0 OD1 F:ASP618 2.7 56.5 1.0 CD2 F:HIS540 3.3 59.7 1.0 CE1 F:HIS544 3.5 57.1 1.0 CD2 F:HIS544 3.5 57.1 1.0 CB F:ASP618 3.9 56.5 1.0 ND1 F:HIS540 3.9 59.7 1.0 CG F:HIS540 4.3 59.7 1.0 ND1 F:HIS544 4.6 57.1 1.0 CG F:HIS544 4.6 57.1 1.0 CA F:ASP618 5.0 56.5 1.0

C.Puchades, A.J.Rampello, M.Shin, C.J.Giuliano, R.L.Wiseman, S.E.Glynn, G.C.Lander. Structure of the Mitochondrial Inner Membrane Aaa+ Protease YME1 Gives Insight Into Substrate Processing. Science V. 358 2017.
ISSN: ESSN 1095-9203
PubMed: 29097521
DOI: 10.1126/SCIENCE.AAO0464