Zinc in PDB 7b3c: Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2)

Enzymatic activity of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2)

All present enzymatic activity of Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2):
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2) (pdb code 7b3c). 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 -4 (Structure 2), PDB code: 7b3c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7b3c

Go back to Zinc Binding Sites List in 7b3c
Zinc binding site 1 out of 2 in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2)


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 -4 (Structure 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:66.0
occ:1.00
ND1 A:HIS295 2.1 51.8 1.0
SG A:CYS301 2.3 56.7 1.0
SG A:CYS306 2.3 55.1 1.0
SG A:CYS310 2.3 50.1 1.0
CE1 A:HIS295 2.9 51.8 1.0
CG A:HIS295 3.2 51.8 1.0
CB A:CYS301 3.3 56.7 1.0
O A:CYS306 3.3 55.1 1.0
CA A:CYS301 3.4 56.7 1.0
CB A:CYS306 3.5 55.1 1.0
CB A:HIS295 3.7 51.8 1.0
C A:CYS306 3.7 55.1 1.0
CB A:CYS310 3.9 50.1 1.0
NE2 A:HIS295 4.0 51.8 1.0
CA A:CYS306 4.1 55.1 1.0
CD2 A:HIS295 4.2 51.8 1.0
N A:CYS301 4.3 56.7 1.0
O A:ASN300 4.3 54.7 1.0
N A:HIS295 4.4 51.8 1.0
N A:ILE307 4.4 52.6 1.0
N A:LEU302 4.5 56.5 1.0
C A:CYS301 4.5 56.7 1.0
CA A:HIS295 4.6 51.8 1.0
C A:ASN300 4.7 54.7 1.0
CA A:ILE307 4.9 52.6 1.0
O A:THR293 4.9 51.5 1.0
N A:CYS310 5.0 50.1 1.0

Zinc binding site 2 out of 2 in 7b3c

Go back to Zinc Binding Sites List in 7b3c
Zinc binding site 2 out of 2 in the Structure of Elongating Sars-Cov-2 Rna-Dependent Rna Polymerase with Remdesivir at Position -4 (Structure 2)


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 -4 (Structure 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:77.7
occ:1.00
SG A:CYS487 2.3 57.6 1.0
SG A:CYS646 2.3 58.7 1.0
ND1 A:HIS642 2.3 54.2 1.0
SG A:CYS645 2.4 64.2 1.0
CB A:CYS645 2.5 64.2 1.0
CE1 A:HIS642 3.2 54.2 1.0
CG A:HIS642 3.4 54.2 1.0
CB A:CYS487 3.4 57.6 1.0
C A:CYS645 3.5 64.2 1.0
N A:CYS646 3.5 58.7 1.0
CA A:CYS645 3.5 64.2 1.0
N A:CYS487 3.7 57.6 1.0
CB A:CYS646 3.7 58.7 1.0
CB A:HIS642 3.7 54.2 1.0
O A:CYS645 4.1 64.2 1.0
CA A:CYS646 4.1 58.7 1.0
CA A:CYS487 4.1 57.6 1.0
N A:CYS645 4.4 64.2 1.0
CA A:HIS642 4.4 54.2 1.0
NE2 A:HIS642 4.4 54.2 1.0
CD2 A:HIS642 4.5 54.2 1.0
NZ A:LYS532 4.5 57.2 1.0
C A:GLY486 4.5 55.1 1.0
CA A:GLY486 4.7 55.1 1.0
O A:HIS642 4.9 54.2 1.0
CE1 A:PHE571 4.9 53.4 1.0

Reference:

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
Page generated: Mon Jan 25 16:42:15 2021

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