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Zinc in PDB 7dfh: Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin

Enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin

All present enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin:
2.7.7.48;

Other elements in 7dfh:

The structure of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 7dfh

Go back to Zinc Binding Sites List in 7dfh
Zinc binding site 1 out of 2 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin


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 Bound to Ribavirin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:59.7
occ:1.00
ND1 A:HIS295 2.2 44.3 1.0
SG A:CYS310 2.5 37.3 1.0
SG A:CYS306 2.5 43.8 1.0
SG A:CYS301 2.5 48.8 1.0
CG A:HIS295 3.1 44.3 1.0
CE1 A:HIS295 3.1 44.3 1.0
CB A:HIS295 3.4 44.3 1.0
O A:CYS306 3.5 43.8 1.0
CB A:CYS301 3.6 48.8 1.0
CB A:CYS306 3.6 43.8 1.0
CA A:CYS301 3.8 48.8 1.0
CB A:CYS310 3.9 37.3 1.0
C A:CYS306 4.0 43.8 1.0
N A:HIS295 4.2 44.3 1.0
NE2 A:HIS295 4.2 44.3 1.0
CD2 A:HIS295 4.2 44.3 1.0
CA A:CYS306 4.3 43.8 1.0
CA A:HIS295 4.4 44.3 1.0
O A:ASN300 4.6 44.3 1.0
N A:CYS301 4.6 48.8 1.0
N A:ILE307 4.9 40.4 1.0
N A:LEU302 4.9 49.9 1.0
O A:HIS295 4.9 44.3 1.0
C A:ASN300 4.9 44.3 1.0
C A:CYS301 4.9 48.8 1.0
O A:THR293 5.0 48.8 1.0

Zinc binding site 2 out of 2 in 7dfh

Go back to Zinc Binding Sites List in 7dfh
Zinc binding site 2 out of 2 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin


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 Bound to Ribavirin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:74.8
occ:1.00
CD2 A:HIS642 2.3 49.2 1.0
SG A:CYS487 2.4 54.0 1.0
SG A:CYS646 2.4 57.6 1.0
SG A:CYS645 2.4 59.7 1.0
CG A:HIS642 3.2 49.2 1.0
NE2 A:HIS642 3.4 49.2 1.0
CB A:CYS646 3.4 57.6 1.0
CB A:CYS645 3.5 59.7 1.0
CB A:CYS487 3.6 54.0 1.0
CB A:HIS642 3.7 49.2 1.0
C A:CYS645 3.8 59.7 1.0
N A:CYS487 3.8 54.0 1.0
N A:CYS646 3.8 57.6 1.0
O A:CYS645 4.0 59.7 1.0
CA A:CYS646 4.1 57.6 1.0
CA A:CYS645 4.2 59.7 1.0
CA A:CYS487 4.3 54.0 1.0
CE1 A:PHE571 4.4 44.9 1.0
ND1 A:HIS642 4.4 49.2 1.0
CA A:HIS642 4.4 49.2 1.0
CE1 A:HIS642 4.5 49.2 1.0
O A:HIS642 4.5 49.2 1.0
C A:GLY486 4.6 49.5 1.0
N A:CYS645 4.7 59.7 1.0
CA A:GLY486 4.7 49.5 1.0
CD1 A:PHE571 4.8 44.9 1.0
C A:HIS642 4.9 49.2 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: Tue Oct 29 18:55:28 2024

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