Zinc in PDB 8kcx: Cryo-Em Structure of Human SIDT1

The binding sites of Zinc atom in the Cryo-Em Structure of Human SIDT1 (pdb code 8kcx). 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 SIDT1, PDB code: 8kcx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Human SIDT1


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 SIDT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:138.8 occ:1.00 NE2 A:HIS791 2.2 73.5 1.0 NE2 A:HIS563 2.2 83.2 1.0 CE1 A:HIS795 2.3 90.7 1.0 NE2 A:HIS795 2.4 88.5 1.0 CE1 A:HIS791 3.0 81.3 1.0 CD2 A:HIS563 3.1 86.3 1.0 CE1 A:HIS563 3.2 91.2 1.0 CD2 A:HIS791 3.3 79.4 1.0 ND1 A:HIS795 3.6 92.0 1.0 CD2 A:HIS795 3.7 91.6 1.0 ND1 A:HIS791 4.2 78.3 1.0 CG A:HIS563 4.3 81.9 1.0 ND1 A:HIS563 4.3 84.8 1.0 CG A:HIS795 4.3 85.9 1.0 CG A:HIS791 4.3 79.4 1.0 CD2 A:TYR562 4.6 93.0 1.0 CE2 A:TYR562 4.7 93.3 1.0 OG A:SER559 4.7 102.3 1.0 CB A:SER559 4.9 92.7 1.0 CD1 A:TRP794 5.0 76.3 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Human SIDT1


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 SIDT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:138.8 occ:1.00 NE2 C:HIS791 2.2 73.5 1.0 NE2 C:HIS563 2.2 83.2 1.0 CE1 C:HIS795 2.3 90.7 1.0 NE2 C:HIS795 2.4 88.5 1.0 CE1 C:HIS791 3.0 81.3 1.0 CD2 C:HIS563 3.1 86.3 1.0 CE1 C:HIS563 3.2 91.2 1.0 CD2 C:HIS791 3.3 79.4 1.0 ND1 C:HIS795 3.6 92.0 1.0 CD2 C:HIS795 3.7 91.6 1.0 ND1 C:HIS791 4.2 78.3 1.0 CG C:HIS563 4.3 81.9 1.0 ND1 C:HIS563 4.3 84.8 1.0 CG C:HIS795 4.3 85.9 1.0 CG C:HIS791 4.3 79.4 1.0 CD2 C:TYR562 4.6 93.0 1.0 CE2 C:TYR562 4.7 93.3 1.0 OG C:SER559 4.7 102.3 1.0 CB C:SER559 4.9 92.7 1.0 CD1 C:TRP794 5.0 76.3 1.0

Y.Hirano, U.Ohto, I.Ichi, R.Sato, K.Miyake, T.Shimizu. Cryo-Em Analysis Reveals Human Sid-1 Transmembrane Family Member 1 Dynamics Underlying Lipid Hydrolytic Activity. Commun Biol V. 7 664 2024.
ISSN: ESSN 2399-3642
PubMed: 38811802
DOI: 10.1038/S42003-024-06346-8