Zinc in PDB 7b3d: Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Amp at Position -4 (Structure 3)

All present enzymatic activity of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Amp at Position -4 (Structure 3):
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 Amp at Position -4 (Structure 3) (pdb code 7b3d). 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 Amp at Position -4 (Structure 3), PDB code: 7b3d:
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 Amp at Position -4 (Structure 3)


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 Amp at Position -4 (Structure 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:43.9 occ:1.00 ND1 A:HIS295 2.1 24.7 1.0 SG A:CYS301 2.3 25.1 1.0 SG A:CYS310 2.3 24.3 1.0 SG A:CYS306 2.3 26.0 1.0 CE1 A:HIS295 2.9 24.7 1.0 CG A:HIS295 3.2 24.7 1.0 CB A:CYS301 3.2 25.1 1.0 O A:CYS306 3.3 26.0 1.0 CA A:CYS301 3.3 25.1 1.0 CB A:CYS306 3.4 26.0 1.0 CB A:HIS295 3.6 24.7 1.0 C A:CYS306 3.7 26.0 1.0 CB A:CYS310 3.9 24.3 1.0 CA A:CYS306 4.0 26.0 1.0 NE2 A:HIS295 4.1 24.7 1.0 CD2 A:HIS295 4.2 24.7 1.0 O A:ASN300 4.2 25.3 1.0 N A:CYS301 4.3 25.1 1.0 N A:LEU302 4.3 25.5 1.0 C A:CYS301 4.4 25.1 1.0 N A:HIS295 4.4 24.7 1.0 N A:ILE307 4.4 24.1 1.0 CA A:HIS295 4.6 24.7 1.0 C A:ASN300 4.6 25.3 1.0 CA A:ILE307 4.9 24.1 1.0 N A:CYS310 5.0 24.3 1.0

Zinc binding site 2 out of 2 in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Amp at Position -4 (Structure 3)


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 Amp at Position -4 (Structure 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:41.0 occ:1.00 SG A:CYS487 2.3 28.9 1.0 SG A:CYS645 2.3 31.0 1.0 SG A:CYS646 2.3 27.6 1.0 ND1 A:HIS642 2.3 26.2 1.0 CG A:HIS642 3.2 26.2 1.0 CE1 A:HIS642 3.3 26.2 1.0 CB A:CYS487 3.4 28.9 1.0 CB A:CYS646 3.5 27.6 1.0 CB A:CYS645 3.5 31.0 1.0 CB A:HIS642 3.5 26.2 1.0 C A:CYS645 3.7 31.0 1.0 N A:CYS646 3.8 27.6 1.0 N A:CYS487 3.9 28.9 1.0 O A:CYS645 3.9 31.0 1.0 CA A:CYS646 4.2 27.6 1.0 CA A:CYS645 4.2 31.0 1.0 CA A:CYS487 4.2 28.9 1.0 CE1 A:PHE571 4.3 26.0 1.0 CA A:HIS642 4.3 26.2 1.0 CD2 A:HIS642 4.4 26.2 1.0 NE2 A:HIS642 4.4 26.2 1.0 O A:HIS642 4.6 26.2 1.0 C A:GLY486 4.6 26.2 1.0 CD1 A:PHE571 4.8 26.0 1.0 N A:CYS645 4.8 31.0 1.0 C A:HIS642 4.9 26.2 1.0 CE A:LYS532 4.9 28.8 1.0 CA A:GLY486 4.9 26.2 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