Zinc in PDB 7n0b: Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna Complex

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

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna Complex (pdb code 7n0b). 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 (Wt)-Rna Complex, PDB code: 7n0b:
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 (Wt)-Rna 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 (Wt)-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:113.2 occ:1.00 NE2 A:HIS83 1.8 39.0 1.0 SG A:CYS90 2.1 53.7 1.0 SG A:CYS77 2.1 35.4 1.0 SG A:CYS74 2.2 45.6 1.0 CD2 A:HIS83 2.7 39.0 1.0 CE1 A:HIS83 2.9 39.0 1.0 CB A:CYS90 2.9 53.7 1.0 CB A:CYS74 3.2 45.6 1.0 CB A:CYS77 3.3 35.4 1.0 N A:CYS77 3.6 35.4 1.0 CG A:HIS83 3.8 39.0 1.0 CA A:CYS77 3.9 35.4 1.0 ND1 A:HIS83 3.9 39.0 1.0 CA A:CYS90 3.9 53.7 1.0 CA A:CYS74 4.5 45.6 1.0 C A:TYR76 4.6 34.8 1.0 CB A:TYR76 4.7 34.8 1.0 O A:CYS74 4.7 45.6 1.0 C A:CYS74 4.9 45.6 1.0 CB A:LYS93 4.9 43.8 1.0 C A:CYS90 4.9 53.7 1.0 N A:CYS90 4.9 53.7 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna 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 (Wt)-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:180.8 occ:1.00 SG A:CYS120 2.2 89.8 1.0 SG A:CYS130 2.2 83.5 1.0 SG A:CYS128 2.3 79.9 1.0 SG A:CYS117 2.3 87.1 1.0 CB A:CYS117 3.1 87.1 1.0 CB A:CYS120 3.5 89.8 1.0 CB A:CYS128 3.6 79.9 1.0 CB A:CYS130 3.9 83.5 1.0 CG2 A:VAL119 4.1 82.4 1.0 N A:CYS120 4.2 89.8 1.0 CA A:CYS128 4.2 79.9 1.0 CA A:CYS120 4.4 89.8 1.0 N A:SER129 4.4 77.1 1.0 C A:CYS128 4.5 79.9 1.0 CA A:CYS117 4.6 87.1 1.0 N A:CYS130 4.8 83.5 1.0 CA A:CYS130 4.9 83.5 1.0 C A:CYS120 4.9 89.8 1.0 C A:CYS117 5.0 87.1 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna 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 (Wt)-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:121.7 occ:1.00 ND1 B:HIS229 1.8 44.9 1.0 SG B:CYS226 2.1 33.7 1.0 SG B:CYS207 2.5 32.4 1.0 CE1 B:HIS229 2.6 44.9 1.0 SG B:CYS210 2.6 42.3 1.0 CG B:HIS229 2.7 44.9 1.0 CB B:CYS210 3.1 42.3 1.0 CB B:CYS226 3.4 33.7 1.0 CB B:HIS229 3.5 44.9 1.0 NE2 B:HIS229 3.5 44.9 1.0 CD2 B:HIS229 3.6 44.9 1.0 CB B:CYS207 3.9 32.4 1.0 N B:CYS226 4.0 33.7 1.0 O B:CYS208 4.2 40.4 1.0 CA B:CYS226 4.3 33.7 1.0 N B:HIS229 4.5 44.9 1.0 CA B:CYS210 4.6 42.3 1.0 CA B:HIS229 4.7 44.9 1.0 NH1 B:ARG212 4.7 33.7 1.0 C B:CYS226 4.9 33.7 1.0 O B:LEU209 4.9 45.4 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna 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 (Wt)-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:76.0 occ:1.00 NE2 B:HIS257 1.8 36.1 1.0 ND1 B:HIS264 1.8 48.1 1.0 SG B:CYS261 2.3 44.8 1.0 SG B:CYS279 2.4 18.0 1.0 CE1 B:HIS264 2.7 48.1 1.0 CE1 B:HIS257 2.8 36.1 1.0 CD2 B:HIS257 2.9 36.1 1.0 CB B:CYS261 3.0 44.8 1.0 CG B:HIS264 3.0 48.1 1.0 CB B:CYS279 3.3 18.0 1.0 CB B:HIS264 3.7 48.1 1.0 NE2 B:HIS264 3.9 48.1 1.0 ND1 B:HIS257 3.9 36.1 1.0 CG B:HIS257 4.0 36.1 1.0 CD2 B:HIS264 4.0 48.1 1.0 CA B:CYS261 4.5 44.8 1.0 N B:HIS264 4.5 48.1 1.0 N B:ASP415 4.7 36.5 1.0 CA B:HIS264 4.7 48.1 1.0 CA B:CYS279 4.8 18.0 1.0 SG B:CYS414 5.0 30.8 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of Sars-Cov-2 NSP10-NSP14 (Wt)-Rna 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 (Wt)-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn605 b:165.1 occ:1.00 ND1 B:HIS487 1.8 92.0 1.0 SG B:CYS484 2.1 96.4 1.0 SG B:CYS452 2.3 95.7 1.0 CE1 B:HIS487 2.6 92.0 1.0 CG B:HIS487 2.9 92.0 1.0 CB B:CYS452 3.0 95.7 1.0 SG B:CYS477 3.3 91.3 1.0 CB B:CYS484 3.3 96.4 1.0 CA B:CYS452 3.4 95.7 1.0 CB B:CYS477 3.4 91.3 1.0 CB B:HIS487 3.7 92.0 1.0 NE2 B:HIS487 3.8 92.0 1.0 CD2 B:HIS487 3.9 92.0 1.0 N B:HIS487 4.1 92.0 1.0 C B:HIS486 4.3 89.7 1.0 C B:CYS452 4.4 95.7 1.0 N B:CYS452 4.4 95.7 1.0 CB B:HIS486 4.4 89.7 1.0 CA B:HIS487 4.5 92.0 1.0 N B:GLU453 4.6 93.8 1.0 CA B:CYS484 4.6 96.4 1.0 O B:GLU453 4.7 93.8 1.0 O B:HIS486 4.7 89.7 1.0 ND1 B:HIS486 4.7 89.7 1.0 CA B:HIS486 4.7 89.7 1.0 CA B:CYS477 4.8 91.3 1.0 N B:CYS484 4.8 96.4 1.0 N B:HIS486 4.8 89.7 1.0 N B:CYS477 4.9 91.3 1.0 C B:CYS484 5.0 96.4 1.0

C.Liu, W.Shi, S.T.Becker, D.G.Schatz, B.Liu, Y.Yang. Structural Basis of Mismatch Recognition By A Sars-Cov-2 Proofreading Enzyme Science 2021.
ISSN: ESSN 1095-9203