Zinc in PDB 8z1f: Cryo-Em Structure of Human ELAC2-Trna

All present enzymatic activity of Cryo-Em Structure of Human ELAC2-Trna:
3.1.26.11;

The binding sites of Zinc atom in the Cryo-Em Structure of Human ELAC2-Trna (pdb code 8z1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Human ELAC2-Trna, PDB code: 8z1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Human ELAC2-Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human ELAC2-Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:162.7 occ:1.00 HE1 A:HIS551 1.9 169.0 1.0 O1 A:PO4903 2.0 168.4 1.0 OD2 A:ASP666 2.3 179.6 1.0 ND1 A:HIS548 2.3 170.9 1.0 NE2 A:HIS546 2.3 177.6 1.0 ZN A:ZN902 2.3 150.4 1.0 CE1 A:HIS551 2.5 169.0 1.0 HE2 A:HIS644 3.0 184.1 1.0 CE1 A:HIS548 3.1 170.9 1.0 CE1 A:HIS546 3.1 177.6 1.0 ND1 A:HIS551 3.2 169.0 1.0 HE1 A:HIS546 3.2 177.6 1.0 HD1 A:HIS551 3.3 169.0 1.0 HE1 A:HIS548 3.3 170.9 1.0 CG A:HIS548 3.3 170.9 1.0 HB2 A:HIS548 3.3 170.9 1.0 NE2 A:HIS551 3.4 169.0 1.0 P A:PO4903 3.4 168.4 1.0 CD2 A:HIS546 3.4 177.6 1.0 CG A:ASP666 3.5 179.6 1.0 HD2 A:HIS546 3.6 177.6 1.0 CB A:HIS548 3.7 170.9 1.0 HB3 A:HIS548 3.7 170.9 1.0 NE2 A:HIS644 3.7 184.1 1.0 HB2 A:ASP666 3.8 179.6 1.0 O3 A:PO4903 3.8 168.4 1.0 O2 A:PO4903 4.0 168.4 1.0 HE2 A:HIS724 4.1 167.7 1.0 CB A:ASP666 4.1 179.6 1.0 OD1 A:ASP550 4.2 162.7 1.0 CG A:HIS551 4.2 169.0 1.0 NE2 A:HIS548 4.3 170.9 1.0 ND1 A:HIS546 4.3 177.6 1.0 CD2 A:HIS551 4.3 169.0 1.0 CD2 A:HIS548 4.3 170.9 1.0 HB3 A:ASP666 4.4 179.6 1.0 OD1 A:ASP666 4.4 179.6 1.0 HE1 A:HIS644 4.5 184.1 1.0 CG A:HIS546 4.5 177.6 1.0 CE1 A:HIS644 4.5 184.1 1.0 OD2 A:ASP550 4.6 162.7 1.0 O4 A:PO4903 4.6 168.4 1.0 NE2 A:HIS724 4.6 167.7 1.0 CD2 A:HIS644 4.7 184.1 1.0 HD2 A:HIS644 4.8 184.1 1.0 CG A:ASP550 4.9 162.7 1.0 NE2 A:HIS702 4.9 184.4 1.0 HE2 A:HIS548 5.0 170.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Human ELAC2-Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human ELAC2-Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:150.4 occ:1.00 HE2 A:HIS724 1.9 167.7 1.0 OD2 A:ASP666 2.0 179.6 1.0 HE1 A:HIS551 2.1 169.0 1.0 ZN A:ZN901 2.3 162.7 1.0 NE2 A:HIS724 2.3 167.7 1.0 O1 A:PO4903 2.4 168.4 1.0 O2 A:PO4903 2.6 168.4 1.0 P A:PO4903 2.6 168.4 1.0 O3 A:PO4903 2.7 168.4 1.0 CE1 A:HIS551 2.9 169.0 1.0 CE1 A:HIS724 3.0 167.7 1.0 CG A:ASP666 3.0 179.6 1.0 HE1 A:HIS724 3.1 167.7 1.0 CD2 A:HIS724 3.2 167.7 1.0 NE2 A:HIS551 3.4 169.0 1.0 OD1 A:ASP666 3.4 179.6 1.0 HD2 A:HIS724 3.5 167.7 1.0 ND1 A:HIS724 4.0 167.7 1.0 ND1 A:HIS551 4.1 169.0 1.0 CG A:HIS724 4.1 167.7 1.0 O4 A:PO4903 4.2 168.4 1.0 ND1 A:HIS548 4.2 170.9 1.0 HE1 A:HIS546 4.2 177.6 1.0 NE2 A:HIS546 4.3 177.6 1.0 OD2 A:ASP550 4.3 162.7 1.0 CB A:ASP666 4.4 179.6 1.0 HB2 A:ASP666 4.4 179.6 1.0 HD1 A:HIS551 4.4 169.0 1.0 OG A:SER490 4.5 163.5 1.0 HE1 A:HIS702 4.6 184.4 1.0 HE1 A:HIS548 4.6 170.9 1.0 HA A:SER490 4.6 163.5 1.0 CE1 A:HIS546 4.6 177.6 1.0 HD1 A:HIS724 4.7 167.7 1.0 HG A:SER490 4.7 163.5 1.0 CD2 A:HIS551 4.7 169.0 1.0 HB3 A:ASP666 4.8 179.6 1.0 CE1 A:HIS548 4.8 170.9 1.0 H A:ASP666 4.9 179.6 1.0 NE2 A:HIS702 4.9 184.4 1.0 HE2 A:HIS644 4.9 184.1 1.0 OD1 A:ASP550 4.9 162.7 1.0 CE1 A:HIS702 4.9 184.4 1.0

C.Xue, J.Tian, Y.Chen, Z.Liu. Structural Insights Into Human ELAC2 As A Trna 3' Processing Enzyme. Nucleic Acids Res. V. 52 13434 2024.
ISSN: ESSN 1362-4962
PubMed: 39494506
DOI: 10.1093/NAR/GKAE1014