Zinc in PDB 9ey2: Human Mitochondrial Rnase Z with Trna-His-Cca

All present enzymatic activity of Human Mitochondrial Rnase Z with Trna-His-Cca:
1.1.1.159; 1.1.1.178; 1.1.1.239; 1.1.1.35; 1.1.1.53; 1.1.1.62; 2.1.1.218; 2.1.1.221; 3.1.26.11;

The binding sites of Zinc atom in the Human Mitochondrial Rnase Z with Trna-His-Cca (pdb code 9ey2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Mitochondrial Rnase Z with Trna-His-Cca, PDB code: 9ey2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Mitochondrial Rnase Z with Trna-His-Cca


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Mitochondrial Rnase Z with Trna-His-Cca within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn901 b:19.9 occ:1.00 OD2 E:ASP666 2.1 15.9 1.0 OD2 E:ASP550 2.5 20.9 1.0 ND1 E:HIS724 2.7 23.2 1.0 CG E:ASP666 2.9 14.6 1.0 NE2 E:HIS551 2.9 15.9 1.0 OD1 E:ASP666 3.0 15.3 1.0 CE1 E:HIS724 3.4 24.1 1.0 CG E:ASP550 3.5 19.4 1.0 CD2 E:HIS551 3.8 15.9 1.0 ZN E:ZN902 3.8 15.8 1.0 OD1 E:ASP550 3.8 19.8 1.0 CG E:HIS724 3.8 21.3 1.0 CE1 E:HIS551 3.9 16.0 1.0 OG E:SER490 4.0 19.2 1.0 CA E:SER490 4.3 18.8 1.0 CB E:ASP666 4.3 14.3 1.0 CB E:SER490 4.4 19.1 1.0 NE2 E:HIS724 4.5 23.8 1.0 CB E:HIS724 4.5 17.6 1.0 N E:ALA491 4.7 21.5 1.0 CD2 E:HIS724 4.7 23.2 1.0 NE2 E:HIS546 4.8 13.8 1.0 CB E:ASP550 4.8 17.8 1.0 OG E:SER500 4.9 12.8 1.0 CG E:HIS551 4.9 16.0 1.0 O E:GLY489 4.9 19.9 1.0 CE1 E:HIS546 4.9 13.8 1.0 ND1 E:HIS551 4.9 16.0 1.0

Zinc binding site 2 out of 2 in the Human Mitochondrial Rnase Z with Trna-His-Cca


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Mitochondrial Rnase Z with Trna-His-Cca within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn902 b:15.8 occ:1.00 OD2 E:ASP666 2.1 15.9 1.0 NE2 E:HIS644 2.3 16.2 1.0 NE2 E:HIS546 2.5 13.8 1.0 ND1 E:HIS548 2.7 14.8 1.0 CG E:ASP666 2.9 14.6 1.0 CB E:ASP666 3.0 14.3 1.0 CD2 E:HIS644 3.2 16.4 1.0 CE1 E:HIS644 3.3 16.2 1.0 CE1 E:HIS546 3.4 13.8 1.0 CD2 E:HIS546 3.4 13.4 1.0 CE1 E:HIS548 3.6 14.8 1.0 CG E:HIS548 3.7 14.7 1.0 ZN E:ZN901 3.8 19.9 1.0 CB E:HIS548 3.9 14.3 1.0 OD1 E:ASP666 4.1 15.3 1.0 NE2 E:HIS702 4.3 21.1 1.0 CG E:HIS644 4.3 16.4 1.0 ND1 E:HIS644 4.3 16.1 1.0 ND1 E:HIS546 4.5 13.4 1.0 NE2 E:HIS551 4.5 15.9 1.0 CG E:HIS546 4.5 13.0 1.0 CA E:ASP666 4.5 14.4 1.0 OD1 E:ASP550 4.6 19.8 1.0 NE2 E:HIS548 4.7 14.6 1.0 CD2 E:HIS548 4.8 14.2 1.0 CE1 E:HIS551 4.8 16.0 1.0

G.Valentin Gese, B.M.Hallberg. Structural Basis of 3'-Trna Maturation By the Human Mitochondrial Rnase Z Complex. Embo J. 2024.
ISSN: ESSN 1460-2075
PubMed: 39516281
DOI: 10.1038/S44318-024-00297-W