Zinc in PDB 7dok: Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir

All present enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir:
2.7.7.48;

The structure of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir (pdb code 7dok). 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 Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir, PDB code: 7dok:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:37.2 occ:1.00 SG A:CYS310 2.4 20.7 1.0 SG A:CYS306 2.4 23.2 1.0 SG A:CYS301 2.5 23.1 1.0 ND1 A:HIS295 2.5 22.6 1.0 O A:CYS306 3.2 23.2 1.0 CE1 A:HIS295 3.4 22.6 1.0 CB A:CYS301 3.4 23.1 1.0 CB A:CYS306 3.5 23.2 1.0 CG A:HIS295 3.5 22.6 1.0 CB A:CYS310 3.7 20.7 1.0 C A:CYS306 3.7 23.2 1.0 CA A:CYS301 3.8 23.1 1.0 CB A:HIS295 3.8 22.6 1.0 CA A:CYS306 4.0 23.2 1.0 N A:HIS295 4.3 22.6 1.0 NE2 A:HIS295 4.5 22.6 1.0 N A:ILE307 4.5 21.5 1.0 O A:THR293 4.6 25.4 1.0 CD2 A:HIS295 4.6 22.6 1.0 CA A:HIS295 4.7 22.6 1.0 N A:CYS301 4.7 23.1 1.0 N A:LEU302 4.8 24.0 1.0 N A:CYS310 4.8 20.7 1.0 CA A:CYS310 4.8 20.7 1.0 C A:CYS301 4.9 23.1 1.0 ND1 A:HIS309 4.9 20.8 1.0

Zinc binding site 2 out of 2 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:40.4 occ:1.00 CD2 A:HIS642 2.3 27.2 1.0 SG A:CYS646 2.5 31.2 1.0 SG A:CYS487 2.5 29.9 1.0 SG A:CYS645 2.5 32.8 1.0 CG A:HIS642 3.1 27.2 1.0 CB A:HIS642 3.4 27.2 1.0 NE2 A:HIS642 3.5 27.2 1.0 CB A:CYS645 3.5 32.8 1.0 CB A:CYS487 3.5 29.9 1.0 CB A:CYS646 3.7 31.2 1.0 N A:CYS487 3.8 29.9 1.0 C A:CYS645 4.0 32.8 1.0 N A:CYS646 4.1 31.2 1.0 CA A:CYS487 4.2 29.9 1.0 O A:CYS645 4.3 32.8 1.0 CA A:HIS642 4.3 27.2 1.0 CE1 A:PHE571 4.3 25.6 1.0 CA A:CYS645 4.3 32.8 1.0 ND1 A:HIS642 4.4 27.2 1.0 CA A:CYS646 4.4 31.2 1.0 CE1 A:HIS642 4.5 27.2 1.0 C A:GLY486 4.6 26.3 1.0 CA A:GLY486 4.7 26.3 1.0 CD1 A:PHE571 4.7 25.6 1.0 CE A:LYS532 4.7 27.7 1.0 O A:HIS642 4.7 27.2 1.0 NZ A:LYS532 4.7 27.7 1.0 N A:CYS645 4.9 32.8 1.0 C A:HIS642 5.0 27.2 1.0

W.Yin, X.Luan, Z.Li, Y.Xie, Z.Zhou, J.Liu, M.Gao, X.Wang, F.Zhou, Q.Wang, Q.Wang, D.Shen, Y.Zhang, G.Tian, H.Aisa, D.Wei, Y.Jiang, G.Xiao, H.Jiang, L.Zhang, X.Yu, J.Shen, S.Zhang, H.Xu. Structural Basis For Repurpose and Design of Nucleotide Drugs For Treating Covid-19 To Be Published.