Zinc in PDB 8kcw: Cryo-Em Structure of Human SIDT1 Bound to Cholesterol

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

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


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 Bound to Cholesterol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:129.6 occ:1.00 OD1 A:ASP574 2.1 94.2 1.0 NE2 A:HIS791 2.2 61.8 1.0 NE2 A:HIS563 2.2 59.1 1.0 NE2 A:HIS795 2.2 74.9 1.0 CE1 A:HIS795 2.3 74.7 1.0 OD2 A:ASP574 2.6 92.4 1.0 CG A:ASP574 2.7 93.9 1.0 CD2 A:HIS791 2.9 68.9 1.0 CD2 A:HIS563 3.2 59.8 1.0 CE1 A:HIS563 3.2 72.9 1.0 CE1 A:HIS791 3.3 74.5 1.0 CD2 A:HIS795 3.6 70.4 1.0 ND1 A:HIS795 3.6 73.2 1.0 CG A:HIS791 4.1 68.1 1.0 CB A:ASP574 4.2 85.5 1.0 CG A:HIS795 4.2 61.8 1.0 ND1 A:HIS791 4.3 74.0 1.0 ND1 A:HIS563 4.3 74.2 1.0 CG A:HIS563 4.3 63.3 1.0 CD2 A:TYR562 4.4 72.4 1.0 CE2 A:TYR562 4.4 68.4 1.0 CD1 A:TRP794 4.8 64.5 1.0 CA A:ASP574 4.8 83.2 1.0 NE1 A:TRP794 5.0 69.0 1.0 CB A:SER559 5.0 76.3 1.0

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


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 Bound to Cholesterol within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:129.6 occ:1.00 OD1 C:ASP574 2.1 94.2 1.0 NE2 C:HIS791 2.2 61.8 1.0 NE2 C:HIS563 2.2 59.1 1.0 NE2 C:HIS795 2.2 74.9 1.0 CE1 C:HIS795 2.3 74.7 1.0 OD2 C:ASP574 2.6 92.4 1.0 CG C:ASP574 2.7 93.9 1.0 CD2 C:HIS791 2.9 68.9 1.0 CD2 C:HIS563 3.2 59.8 1.0 CE1 C:HIS563 3.2 72.9 1.0 CE1 C:HIS791 3.3 74.5 1.0 CD2 C:HIS795 3.6 70.4 1.0 ND1 C:HIS795 3.6 73.2 1.0 CG C:HIS791 4.1 68.1 1.0 CB C:ASP574 4.2 85.5 1.0 CG C:HIS795 4.2 61.8 1.0 ND1 C:HIS791 4.3 74.0 1.0 ND1 C:HIS563 4.3 74.2 1.0 CG C:HIS563 4.3 63.3 1.0 CD2 C:TYR562 4.4 72.4 1.0 CE2 C:TYR562 4.4 68.4 1.0 CD1 C:TRP794 4.8 64.5 1.0 CA C:ASP574 4.8 83.2 1.0 NE1 C:TRP794 5.0 69.0 1.0 CB C:SER559 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