Zinc 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
Calcium	(Ca)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex, PDB code: 9vcl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


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 Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:59.1 occ:1.00 NE2 A:HIS83 2.0 37.8 1.0 SG A:CYS90 2.1 53.0 1.0 SG A:CYS77 2.2 43.1 1.0 SG A:CYS74 2.2 41.7 1.0 CB A:CYS74 2.7 41.7 1.0 CD2 A:HIS83 3.0 37.8 1.0 CB A:CYS90 3.0 53.0 1.0 CE1 A:HIS83 3.1 37.8 1.0 CB A:CYS77 3.6 43.1 1.0 N A:CYS77 3.9 43.1 1.0 CA A:CYS90 4.1 53.0 1.0 CG A:HIS83 4.1 37.8 1.0 CA A:CYS74 4.1 41.7 1.0 ND1 A:HIS83 4.1 37.8 1.0 CA A:CYS77 4.3 43.1 1.0 O A:CYS74 4.6 41.7 1.0 C A:CYS74 4.6 41.7 1.0 CB A:TYR76 4.6 35.8 1.0 C A:TYR76 4.8 35.8 1.0 CB A:LYS93 4.9 51.8 1.0 CB A:LEU92 4.9 55.0 1.0 N A:LYS93 4.9 51.8 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


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 Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:143.4 occ:1.00 CB A:CYS120 2.4 112.5 1.0 SG A:CYS128 3.2 115.4 1.0 SG A:CYS117 3.3 107.6 1.0 CA A:CYS120 3.4 112.5 1.0 CB A:CYS130 3.4 126.6 1.0 N A:CYS120 3.4 112.5 1.0 SG A:CYS130 3.6 126.6 1.0 SG A:CYS120 3.7 112.5 1.0 CA A:CYS130 4.1 126.6 1.0 N A:CYS130 4.4 126.6 1.0 C A:VAL119 4.6 110.0 1.0 CB A:CYS117 4.6 107.6 1.0 CB A:CYS128 4.7 115.4 1.0 C A:SER129 4.7 123.5 1.0 C A:CYS120 4.7 112.5 1.0 O A:SER129 4.8 123.5 1.0 CA A:CYS128 4.8 115.4 1.0 C A:CYS128 5.0 115.4 1.0 N A:SER129 5.0 123.5 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 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:Zn603 b:67.6 occ:1.00 ND1 B:HIS229 2.1 41.2 1.0 CE1 B:HIS229 2.1 41.2 1.0 SG B:CYS207 2.2 40.2 1.0 SG B:CYS226 2.3 33.3 1.0 CB B:CYS210 2.5 50.8 1.0 SG B:CYS210 2.8 50.8 1.0 CB B:CYS207 3.2 40.2 1.0 CG B:HIS229 3.4 41.2 1.0 NE2 B:HIS229 3.5 41.2 1.0 CB B:CYS226 3.5 33.3 1.0 NH1 B:ARG212 3.5 41.3 1.0 CA B:CYS210 3.9 50.8 1.0 N B:CYS226 4.0 33.3 1.0 CD2 B:HIS229 4.1 41.2 1.0 CB B:HIS229 4.4 41.2 1.0 N B:CYS210 4.4 50.8 1.0 O B:CYS208 4.4 47.2 1.0 CA B:CYS226 4.4 33.3 1.0 CD B:ARG212 4.5 41.3 1.0 CG B:ARG212 4.6 41.3 1.0 C B:CYS210 4.6 50.8 1.0 N B:ASP211 4.6 47.4 1.0 CA B:CYS207 4.6 40.2 1.0 CZ B:ARG212 4.7 41.3 1.0 CB B:ARG212 4.8 41.3 1.0 N B:ARG212 4.8 41.3 1.0 N B:HIS229 4.9 41.2 1.0 C B:CYS207 4.9 40.2 1.0 C B:LEU209 5.0 55.1 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 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:Zn604 b:69.8 occ:1.00 ND1 B:HIS264 2.1 52.9 1.0 NE2 B:HIS257 2.1 50.8 1.0 SG B:CYS279 2.2 33.4 1.0 SG B:CYS261 2.4 60.4 1.0 CB B:CYS261 2.7 60.4 1.0 CE1 B:HIS257 2.9 50.8 1.0 CE1 B:HIS264 3.0 52.9 1.0 CG B:HIS264 3.1 52.9 1.0 CD2 B:HIS257 3.3 50.8 1.0 CB B:CYS279 3.5 33.4 1.0 CB B:HIS264 3.5 52.9 1.0 ND1 B:HIS257 4.1 50.8 1.0 NE2 B:HIS264 4.1 52.9 1.0 CA B:CYS261 4.1 60.4 1.0 CD2 B:HIS264 4.2 52.9 1.0 CG B:HIS257 4.3 50.8 1.0 C B:CYS261 4.6 60.4 1.0 N B:ASP415 4.6 41.1 1.0 N B:HIS264 4.6 52.9 1.0 CA B:HIS264 4.7 52.9 1.0 CA B:CYS279 4.8 33.4 1.0 SG B:CYS414 4.9 55.1 1.0 N B:CYS261 4.9 60.4 1.0 N B:VAL263 4.9 56.3 1.0 N B:GLN262 4.9 60.5 1.0 O B:CYS279 4.9 33.4 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Atmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 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:Zn605 b:145.2 occ:1.00 SG B:CYS452 2.3 124.0 1.0 ND1 B:HIS487 2.3 105.6 1.0 SG B:CYS484 2.3 132.9 1.0 CB B:CYS452 2.4 120.7 1.0 CE1 B:HIS487 2.7 105.6 1.0 CA B:CYS452 3.1 121.0 1.0 CB B:CYS477 3.4 120.4 1.0 CG B:HIS487 3.4 103.3 1.0 CB B:CYS484 3.5 124.6 1.0 SG B:CYS477 3.8 117.9 1.0 NE2 B:HIS487 3.8 104.7 1.0 N B:CYS452 4.1 120.4 1.0 CB B:HIS487 4.1 102.8 1.0 C B:CYS452 4.1 123.0 1.0 CD2 B:HIS487 4.2 103.5 1.0 N B:GLU453 4.4 123.7 1.0 CD2 B:HIS486 4.4 113.5 1.0 CB B:HIS486 4.4 112.1 1.0 C B:HIS486 4.4 113.8 1.0 N B:HIS487 4.5 108.5 1.0 O B:HIS486 4.6 112.8 1.0 CG B:HIS486 4.6 112.5 1.0 O B:GLU453 4.7 120.3 1.0 CA B:CYS477 4.7 121.3 1.0 CA B:CYS484 4.8 123.8 1.0 N B:CYS477 4.9 121.7 1.0 CA B:HIS486 4.9 113.0 1.0 CA B:HIS487 4.9 104.0 1.0 C B:PRO451 4.9 109.2 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