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

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

The structure of Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex (pdb code 9vck). 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:Smp Complex, PDB code: 9vck:
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:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:77.7 occ:1.00 OD2 B:ASP90 1.9 76.4 1.0 O10 P:K5X101 2.2 81.2 1.0 OD2 B:ASP273 2.3 86.3 1.0 CG B:ASP90 3.1 76.4 1.0 CG B:ASP273 3.1 86.3 1.0 P09 P:K5X101 3.5 81.2 1.0 OD1 B:ASP90 3.7 76.4 1.0 CB B:ASP273 3.7 86.3 1.0 O11 P:K5X101 3.8 81.2 1.0 OE2 B:GLU92 3.9 80.5 1.0 OD1 B:ASP273 4.0 86.3 1.0 CB B:ASP90 4.2 76.4 1.0 CA B:CA602 4.2 80.7 1.0 O08 P:K5X101 4.3 81.2 1.0 O B:VAL91 4.6 75.0 1.0 O3' P:C70 4.9 85.2 1.0 NE2 B:HIS268 4.9 85.8 1.0 C07 P:K5X101 4.9 81.2 1.0 CD B:GLU92 5.0 80.5 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:80.7 occ:1.00 OE2 B:GLU191 1.8 71.4 1.0 OD1 B:ASP90 2.6 76.4 1.0 CD B:GLU191 2.8 71.4 1.0 OE1 B:GLU191 3.2 71.4 1.0 O10 P:K5X101 3.3 81.2 1.0 CG B:ASP90 3.4 76.4 1.0 CB B:ALA187 3.5 70.0 1.0 OD2 B:ASP90 3.8 76.4 1.0 N B:ALA187 3.8 70.0 1.0 O3' P:C70 4.0 85.2 1.0 CG B:GLU191 4.1 71.4 1.0 P09 P:K5X101 4.2 81.2 1.0 CA B:CA601 4.2 77.7 1.0 CA B:ALA187 4.3 70.0 1.0 CB B:TRP186 4.6 74.8 1.0 CA B:ASP90 4.6 76.4 1.0 CB B:ASP90 4.6 76.4 1.0 N B:TRP186 4.6 74.8 1.0 C B:TRP186 4.7 74.8 1.0 CD1 B:TRP186 4.8 74.8 1.0 N B:VAL91 4.8 75.0 1.0 CA B:TRP186 4.9 74.8 1.0 O B:PHE190 4.9 74.5 1.0 O B:PHE89 4.9 76.8 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