Zinc in PDB 7b3b: Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1)

All present enzymatic activity of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1):
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The binding sites of Zinc atom in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1) (pdb code 7b3b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1), PDB code: 7b3b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:53.1 occ:1.00 ND1 A:HIS295 2.1 28.7 1.0 SG A:CYS310 2.3 28.7 1.0 SG A:CYS301 2.3 30.3 1.0 SG A:CYS306 2.3 30.3 1.0 CE1 A:HIS295 2.8 28.7 1.0 CG A:HIS295 2.8 28.7 1.0 CB A:CYS301 3.3 30.3 1.0 CB A:HIS295 3.4 28.7 1.0 CA A:CYS301 3.4 30.3 1.0 O A:CYS306 3.5 30.3 1.0 CB A:CYS306 3.6 30.3 1.0 NE2 A:HIS295 3.7 28.7 1.0 CD2 A:HIS295 3.7 28.7 1.0 C A:CYS306 3.9 30.3 1.0 CB A:CYS310 3.9 28.7 1.0 CA A:CYS306 4.2 30.3 1.0 O A:ASN300 4.3 30.7 1.0 N A:HIS295 4.3 28.7 1.0 N A:CYS301 4.3 30.3 1.0 CA A:HIS295 4.5 28.7 1.0 N A:LEU302 4.5 31.0 1.0 C A:CYS301 4.5 30.3 1.0 N A:ILE307 4.6 27.4 1.0 C A:ASN300 4.6 30.7 1.0 O A:THR293 4.9 31.6 1.0

Zinc binding site 2 out of 2 in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -3 (Structure 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:47.9 occ:1.00 SG A:CYS487 2.3 33.8 1.0 SG A:CYS646 2.3 33.1 1.0 ND1 A:HIS642 2.3 29.7 1.0 SG A:CYS645 2.3 37.0 1.0 CB A:CYS645 3.0 37.0 1.0 CG A:HIS642 3.2 29.7 1.0 CE1 A:HIS642 3.4 29.7 1.0 CB A:HIS642 3.4 29.7 1.0 CB A:CYS487 3.4 33.8 1.0 CB A:CYS646 3.5 33.1 1.0 C A:CYS645 3.5 37.0 1.0 N A:CYS646 3.6 33.1 1.0 N A:CYS487 3.7 33.8 1.0 CA A:CYS645 3.8 37.0 1.0 O A:CYS645 3.9 37.0 1.0 CA A:HIS642 4.1 29.7 1.0 CA A:CYS646 4.1 33.1 1.0 CA A:CYS487 4.2 33.8 1.0 O A:HIS642 4.3 29.7 1.0 N A:CYS645 4.4 37.0 1.0 CD2 A:HIS642 4.4 29.7 1.0 NE2 A:HIS642 4.4 29.7 1.0 C A:GLY486 4.5 32.5 1.0 C A:HIS642 4.7 29.7 1.0 CA A:GLY486 4.7 32.5 1.0 CE1 A:PHE571 4.8 30.4 1.0

G.Kokic, H.S.Hillen, D.Tegunov, C.Dienemann, F.Seitz, J.Schmitzova, L.Farnung, A.Siewert, C.Hoebartner, P.Cramer. Mechanism of Sars-Cov-2 Polymerase Stalling By Remdesivir Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-20542-0