Zinc in PDB 8z1g: Cryo-Em Structure of Human ELAC2-Pre-Trna

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

The binding sites of Zinc atom in the Cryo-Em Structure of Human ELAC2-Pre-Trna (pdb code 8z1g). 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-Pre-Trna, PDB code: 8z1g:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Human ELAC2-Pre-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-Pre-Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:84.2 occ:1.00 HE1 A:HIS644 2.1 97.1 1.0 O1 A:PO4903 2.2 103.8 1.0 ND1 A:HIS548 2.3 84.4 1.0 NE2 A:HIS546 2.3 85.0 1.0 ZN A:ZN902 2.3 72.5 1.0 O3 A:PO4903 2.3 103.8 1.0 P A:PO4903 2.8 103.8 1.0 CE1 A:HIS548 3.0 84.4 1.0 HE1 A:HIS548 3.0 84.4 1.0 CE1 A:HIS644 3.0 97.1 1.0 OD2 A:ASP666 3.1 90.2 1.0 CE1 A:HIS546 3.2 85.0 1.0 CD2 A:HIS546 3.3 85.0 1.0 NE2 A:HIS551 3.4 75.3 1.0 HE1 A:HIS546 3.4 85.0 1.0 HD2 A:HIS546 3.4 85.0 1.0 CG A:HIS548 3.4 84.4 1.0 HD2 A:HIS551 3.5 75.3 1.0 HB2 A:HIS548 3.6 84.4 1.0 HB2 A:ASP666 3.6 90.2 1.0 CD2 A:HIS551 3.8 75.3 1.0 NE2 A:HIS644 3.8 97.1 1.0 O2 A:PO4903 3.8 103.8 1.0 CB A:HIS548 3.9 84.4 1.0 O4 A:PO4903 4.0 103.8 1.0 HB3 A:HIS548 4.0 84.4 1.0 CG A:ASP666 4.1 90.2 1.0 ND1 A:HIS644 4.1 97.1 1.0 NE2 A:HIS548 4.2 84.4 1.0 HE2 A:HIS724 4.2 77.7 1.0 CB A:ASP666 4.2 90.2 1.0 HD1 A:HIS644 4.2 97.1 1.0 ND1 A:HIS546 4.3 85.0 1.0 CG A:HIS546 4.4 85.0 1.0 CD2 A:HIS548 4.4 84.4 1.0 HB3 A:ASP666 4.4 90.2 1.0 CE1 A:HIS551 4.5 75.3 1.0 NE2 A:HIS724 4.6 77.7 1.0 OD1 A:ASP550 4.6 69.9 1.0 HE1 A:HIS702 4.8 105.0 1.0 HE1 A:HIS724 4.8 77.7 1.0 OD2 A:ASP550 4.8 69.9 1.0 HE2 A:HIS548 4.9 84.4 1.0 HE1 A:HIS551 4.9 75.3 1.0 CE1 A:HIS724 4.9 77.7 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Human ELAC2-Pre-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-Pre-Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:72.5 occ:1.00 HE2 A:HIS724 1.9 77.7 1.0 O1 A:PO4903 2.1 103.8 1.0 OD2 A:ASP666 2.1 90.2 1.0 ZN A:ZN901 2.3 84.2 1.0 NE2 A:HIS551 2.3 75.3 1.0 NE2 A:HIS724 2.3 77.7 1.0 CE1 A:HIS724 2.9 77.7 1.0 HE1 A:HIS724 3.0 77.7 1.0 P A:PO4903 3.0 103.8 1.0 CD2 A:HIS724 3.2 77.7 1.0 CE1 A:HIS551 3.2 75.3 1.0 O3 A:PO4903 3.3 103.8 1.0 HE1 A:HIS551 3.3 75.3 1.0 CD2 A:HIS551 3.3 75.3 1.0 O4 A:PO4903 3.3 103.8 1.0 CG A:ASP666 3.4 90.2 1.0 OD2 A:ASP550 3.4 69.9 1.0 HD2 A:HIS551 3.5 75.3 1.0 HD2 A:HIS724 3.5 77.7 1.0 NE2 A:HIS546 3.8 85.0 1.0 ND1 A:HIS724 3.8 77.7 1.0 CG A:HIS724 4.0 77.7 1.0 HE1 A:HIS546 4.1 85.0 1.0 HB2 A:ASP666 4.1 90.2 1.0 HE1 A:HIS644 4.2 97.1 1.0 ND1 A:HIS548 4.2 84.4 1.0 OD1 A:ASP666 4.2 90.2 1.0 CG A:ASP550 4.2 69.9 1.0 OD1 A:ASP550 4.2 69.9 1.0 CB A:ASP666 4.3 90.2 1.0 CE1 A:HIS546 4.3 85.0 1.0 ND1 A:HIS551 4.4 75.3 1.0 O2 A:PO4903 4.4 103.8 1.0 CG A:HIS551 4.5 75.3 1.0 HB3 A:ASP666 4.5 90.2 1.0 HB2 A:HIS548 4.7 84.4 1.0 HB3 A:HIS548 4.9 84.4 1.0 HA A:SER490 4.9 81.2 1.0 CE1 A:HIS644 5.0 97.1 1.0 HE1 A:HIS702 5.0 105.0 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