Calcium in PDB 9vcl: Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex

All present enzymatic activity of Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex:
2.1.1.56;

The structure of Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	5 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex (pdb code 9vcl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex, PDB code: 9vcl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:65.9 occ:1.00 OD2 B:ASP90 1.8 27.4 1.0 OE1 B:GLU92 1.8 39.2 1.0 OD2 B:ASP273 1.9 34.6 1.0 CG B:ASP90 2.8 27.4 1.0 CG B:ASP273 3.0 34.6 1.0 CD B:GLU92 3.0 39.2 1.0 OD1 B:ASP90 3.1 27.4 1.0 CB B:ASP273 3.4 34.6 1.0 O B:HOH702 3.4 30.0 1.0 CG B:GLU92 3.7 39.2 1.0 O3 P:EIF101 3.8 62.4 1.0 OE2 B:GLU92 4.0 39.2 1.0 O B:VAL269 4.1 46.6 1.0 OD1 B:ASP273 4.1 34.6 1.0 CB B:ASP90 4.1 27.4 1.0 O4 P:EIF101 4.3 62.4 1.0 O B:HOH701 4.3 30.0 1.0 P P:EIF101 4.7 62.4 1.0 O B:ASP273 4.7 34.6 1.0 CA B:ASP273 4.8 34.6 1.0 O B:HIS268 4.9 70.6 1.0 CA B:ALA270 5.0 34.4 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:51.5 occ:1.00 OE2 B:GLU191 2.3 25.4 1.0 OE1 B:GLU191 2.5 25.4 1.0 CD B:GLU191 2.7 25.4 1.0 O3 P:EIF101 2.8 62.4 1.0 CB B:ALA187 3.0 27.4 1.0 O3' P:C70 3.6 77.2 1.0 P P:EIF101 3.9 62.4 1.0 OD1 B:ASP90 4.0 27.4 1.0 N B:ALA187 4.1 27.4 1.0 CA B:ALA187 4.1 27.4 1.0 CG B:GLU191 4.1 25.4 1.0 O2' P:C70 4.3 79.3 1.0 O B:VAL91 4.6 24.4 1.0 O B:HOH702 4.6 30.0 1.0 C3' P:C70 4.6 78.2 1.0 C4' P:C70 4.7 78.7 1.0 CG B:ASP90 4.7 27.4 1.0 O1 P:EIF101 4.8 62.4 1.0 C4 P:EIF101 4.9 62.4 1.0 N B:GLU191 5.0 25.4 1.0

J.Wang, Y.Pan, Y.Liu, B.Huang, G.Jin, L.Zhang, F.Zhou, X.Chang, Y.Huang, L.Yan, Y.Dong, Z.Rao, D.Liu, Z.Lou. Structural Basis and Rational Design of Nucleotide Analogue Inhibitor Evading the Sars-Cov-2 Proofreading Enzyme. J.Am.Chem.Soc. V. 147 21896 2025.
ISSN: ESSN 1520-5126
PubMed: 40509573
DOI: 10.1021/JACS.5C05014