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

Enzymatic activity of 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;

Other elements in 7dok:

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

Zinc Binding Sites:

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 7dok

Go back to Zinc Binding Sites List in 7dok
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 7dok

Go back to Zinc Binding Sites List in 7dok
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

Reference:

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.
Page generated: Fri Dec 17 11:48:58 2021

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