Zinc in PDB 8woq: Cryo-Em Structure of Human SIDT1 Protein with C1 Symmetry at Neutral pH

The structure of Cryo-Em Structure of Human SIDT1 Protein with C1 Symmetry at Neutral pH also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Human SIDT1 Protein with C1 Symmetry at Neutral pH (pdb code 8woq). 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 Protein with C1 Symmetry at Neutral pH, PDB code: 8woq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Human SIDT1 Protein with C1 Symmetry at Neutral pH


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 Protein with C1 Symmetry at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:155.9 occ:1.00 O A:HOH1002 2.1 134.5 1.0 NE2 A:HIS796 2.3 113.7 1.0 NE2 A:HIS563 2.3 103.9 1.0 NE2 A:HIS800 2.3 108.2 1.0 CE1 A:HIS800 3.1 101.6 1.0 CE1 A:HIS563 3.1 101.8 1.0 CD2 A:HIS796 3.1 110.0 1.0 CE1 A:HIS796 3.3 112.8 1.0 CD2 A:HIS563 3.4 107.2 1.0 CD2 A:HIS800 3.4 108.9 1.0 ND1 A:HIS563 4.3 99.6 1.0 ND1 A:HIS800 4.3 104.0 1.0 CG A:HIS796 4.3 106.2 1.0 ND1 A:HIS796 4.4 112.9 1.0 CG A:HIS563 4.4 101.7 1.0 CG A:HIS800 4.5 105.4 1.0 CD1 A:TRP799 4.8 97.4 1.0 NE1 A:TRP799 4.8 103.5 1.0 CE2 A:TYR562 4.9 113.7 1.0 O A:HOH1001 4.9 113.8 1.0 CB A:SER559 4.9 110.8 1.0 CD2 A:TYR562 4.9 113.8 1.0 OG A:SER559 4.9 116.9 1.0 O1 A:SPL913 5.0 143.2 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Human SIDT1 Protein with C1 Symmetry at Neutral pH


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 Protein with C1 Symmetry at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:166.8 occ:1.00 O B:HOH1002 2.0 129.1 1.0 NE2 B:HIS796 2.3 111.1 1.0 NE2 B:HIS563 2.3 98.5 1.0 NE2 B:HIS800 2.3 103.8 1.0 CD2 B:HIS796 3.1 107.6 1.0 CE1 B:HIS800 3.1 98.6 1.0 CE1 B:HIS563 3.2 96.9 1.0 CD2 B:HIS563 3.3 100.9 1.0 CE1 B:HIS796 3.4 109.3 1.0 CD2 B:HIS800 3.4 103.8 1.0 CG B:HIS796 4.3 102.9 1.0 ND1 B:HIS800 4.3 100.0 1.0 OG B:SER559 4.3 109.8 1.0 ND1 B:HIS563 4.3 93.2 1.0 ND1 B:HIS796 4.4 107.8 1.0 CG B:HIS563 4.4 92.2 1.0 CG B:HIS800 4.5 98.6 1.0 O B:HOH1001 4.6 124.6 1.0 CE2 B:TYR562 4.9 106.2 1.0 CD1 B:TRP799 4.9 96.9 1.0 CD2 B:TYR562 5.0 106.9 1.0 NE1 B:TRP799 5.0 101.8 1.0

W.Liu, M.Tang, J.Wang, F.Wang, G.Song, X.Zhang, S.Wu, H.Ru. Structural Insights Into Cholesterol Transport and Hydrolase Activity of A Putative Human Rna Transport Protein SIDT1. Cell Discov V. 10 21 2024.
ISSN: ESSN 2056-5968
PubMed: 38378654
DOI: 10.1038/S41421-024-00647-2