Zinc 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:

Calcium	(Ca)	2 atoms
Fluorine	(F)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp Complex, PDB code: 9vck:
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:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:113.0 occ:1.00 NE2 A:HIS83 2.0 73.4 1.0 SG A:CYS90 2.3 85.6 1.0 SG A:CYS74 2.3 77.9 1.0 SG A:CYS77 2.4 75.1 1.0 CB A:CYS90 2.5 85.6 1.0 CD2 A:HIS83 2.5 73.4 1.0 CE1 A:HIS83 3.2 73.4 1.0 CB A:CYS74 3.3 77.9 1.0 CA A:CYS90 3.6 85.6 1.0 CG A:HIS83 3.8 73.4 1.0 CB A:CYS77 3.8 75.1 1.0 ND1 A:HIS83 4.1 73.4 1.0 N A:CYS77 4.1 75.1 1.0 CA A:CYS77 4.5 75.1 1.0 N A:CYS90 4.5 85.6 1.0 CB A:TYR76 4.6 73.2 1.0 C A:CYS90 4.6 85.6 1.0 CA A:CYS74 4.7 77.9 1.0 CD2 A:TYR76 5.0 73.2 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:145.3 occ:1.00 NZ A:LYS124 2.1 112.5 1.0 SG A:CYS128 2.3 118.0 1.0 CD A:LYS124 2.4 112.5 1.0 CE A:LYS124 2.5 112.5 1.0 SG A:CYS130 2.9 116.7 1.0 CB A:CYS130 3.0 116.7 1.0 O A:CYS128 3.3 118.0 1.0 CB A:CYS128 3.7 118.0 1.0 SG A:CYS117 3.7 118.0 1.0 CG A:LYS124 3.8 112.5 1.0 N A:CYS130 4.1 116.7 1.0 CA A:CYS130 4.1 116.7 1.0 C A:CYS128 4.2 118.0 1.0 CB A:CYS117 4.4 118.0 1.0 CB A:LYS124 4.5 112.5 1.0 CA A:CYS128 4.5 118.0 1.0 CA A:LYS124 4.8 112.5 1.0 C A:CYS130 4.9 116.7 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:113.2 occ:1.00 ND1 B:HIS229 2.0 81.5 1.0 SG B:CYS207 2.3 86.9 1.0 SG B:CYS226 2.4 86.9 1.0 CB B:CYS210 2.4 92.8 1.0 SG B:CYS210 2.6 92.8 1.0 CG B:HIS229 2.8 81.5 1.0 CE1 B:HIS229 2.9 81.5 1.0 CB B:HIS229 3.2 81.5 1.0 CB B:CYS207 3.3 86.9 1.0 CD2 B:HIS229 3.8 81.5 1.0 NE2 B:HIS229 3.8 81.5 1.0 CA B:CYS210 3.8 92.8 1.0 CB B:CYS226 3.8 86.9 1.0 O B:LEU209 3.9 88.9 1.0 N B:CYS226 4.2 86.9 1.0 O B:CYS208 4.4 87.5 1.0 N B:CYS210 4.4 92.8 1.0 C B:LEU209 4.4 88.9 1.0 CA B:HIS229 4.5 81.5 1.0 N B:HIS229 4.5 81.5 1.0 CA B:CYS226 4.5 86.9 1.0 CA B:CYS207 4.6 86.9 1.0 O B:CYS207 4.7 86.9 1.0 NH1 B:ARG212 4.7 88.2 1.0 C B:CYS207 4.8 86.9 1.0 C B:CYS210 4.9 92.8 1.0 N B:ASP211 5.0 88.3 1.0 C B:CYS226 5.0 86.9 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:121.2 occ:1.00 NE2 B:HIS257 2.2 94.0 1.0 ND1 B:HIS264 2.2 90.2 1.0 SG B:CYS279 2.3 86.0 1.0 CB B:CYS261 2.7 101.4 1.0 CD2 B:HIS257 2.9 94.0 1.0 CE1 B:HIS264 3.0 90.2 1.0 SG B:CYS261 3.0 101.4 1.0 CG B:HIS264 3.3 90.2 1.0 CE1 B:HIS257 3.3 94.0 1.0 CB B:CYS279 3.3 86.0 1.0 CB B:HIS264 3.8 90.2 1.0 CA B:CYS261 4.1 101.4 1.0 NE2 B:HIS264 4.1 90.2 1.0 CG B:HIS257 4.2 94.0 1.0 ND1 B:HIS257 4.3 94.0 1.0 CD2 B:HIS264 4.3 90.2 1.0 N B:CYS261 4.7 101.4 1.0 SG B:CYS414 4.7 169.4 1.0 CA B:CYS279 4.8 86.0 1.0 N B:ASP415 4.9 186.0 1.0 N B:HIS264 4.9 90.2 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10/NSP14:Rna:Smp 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:Smp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn605 b:275.7 occ:1.00 CB B:CYS452 2.2 272.4 1.0 ND1 B:HIS487 2.3 223.6 1.0 SG B:CYS452 2.3 272.4 1.0 SG B:CYS484 2.3 256.4 1.0 CE1 B:HIS487 2.5 223.6 1.0 CA B:CYS452 3.0 272.4 1.0 CG B:HIS487 3.4 223.6 1.0 CB B:CYS477 3.5 281.1 1.0 CB B:CYS484 3.6 256.4 1.0 NE2 B:HIS487 3.6 223.6 1.0 SG B:CYS477 3.9 281.1 1.0 N B:CYS452 4.0 272.4 1.0 CD2 B:HIS487 4.1 223.6 1.0 CB B:HIS486 4.1 241.8 1.0 C B:CYS452 4.1 272.4 1.0 CB B:HIS487 4.2 223.6 1.0 CD2 B:HIS486 4.3 241.8 1.0 N B:GLU453 4.4 278.6 1.0 CG B:HIS486 4.5 241.8 1.0 C B:HIS486 4.5 241.8 1.0 N B:HIS487 4.5 223.6 1.0 CA B:HIS486 4.8 241.8 1.0 CA B:CYS477 4.8 281.1 1.0 O B:GLU453 4.8 278.6 1.0 O B:HIS486 4.8 241.8 1.0 CA B:CYS484 4.9 256.4 1.0 N B:CYS477 4.9 281.1 1.0 C B:PRO451 4.9 252.4 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