Zinc in PDB 7oyg: Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase

Enzymatic activity of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase

All present enzymatic activity of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase:
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 Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase (pdb code 7oyg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase, PDB code: 7oyg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7oyg

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Zinc binding site 1 out of 4 in the Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase 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 4 in 7oyg

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Zinc binding site 2 out of 4 in the Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase 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:CYS645 3.5 31.0 1.0
CB A:CYS646 3.5 27.6 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

Zinc binding site 3 out of 4 in 7oyg

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Zinc binding site 3 out of 4 in the Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2000

b:43.9
occ:1.00
 ND1 D:HIS295 2.1 24.7 1.0
SG D:CYS301 2.3 25.1 1.0
SG D:CYS310 2.3 24.3 1.0
SG D:CYS306 2.3 26.0 1.0
CE1 D:HIS295 2.9 24.7 1.0
CG D:HIS295 3.2 24.7 1.0
CB D:CYS301 3.2 25.1 1.0
O D:CYS306 3.3 26.0 1.0
CA D:CYS301 3.3 25.1 1.0
CB D:CYS306 3.4 26.0 1.0
CB D:HIS295 3.6 24.7 1.0
C D:CYS306 3.7 26.0 1.0
CB D:CYS310 3.9 24.3 1.0
CA D:CYS306 4.0 26.0 1.0
NE2 D:HIS295 4.1 24.7 1.0
CD2 D:HIS295 4.2 24.7 1.0
O D:ASN300 4.2 25.3 1.0
N D:CYS301 4.3 25.1 1.0
N D:LEU302 4.3 25.5 1.0
C D:CYS301 4.4 25.1 1.0
N D:HIS295 4.4 24.7 1.0
N D:ILE307 4.4 24.1 1.0
CA D:HIS295 4.6 24.7 1.0
C D:ASN300 4.6 25.3 1.0
CA D:ILE307 4.9 24.1 1.0
N D:CYS310 5.0 24.3 1.0

Zinc binding site 4 out of 4 in 7oyg

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Zinc binding site 4 out of 4 in the Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dimeric Form of Sars-Cov-2 Rna-Dependent Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:41.0
occ:1.00
 SG D:CYS487 2.3 28.9 1.0
SG D:CYS645 2.3 31.0 1.0
SG D:CYS646 2.3 27.6 1.0
ND1 D:HIS642 2.3 26.2 1.0
CG D:HIS642 3.2 26.2 1.0
CE1 D:HIS642 3.3 26.2 1.0
CB D:CYS487 3.4 28.9 1.0
CB D:CYS646 3.5 27.6 1.0
CB D:CYS645 3.5 31.0 1.0
CB D:HIS642 3.5 26.2 1.0
C D:CYS645 3.7 31.0 1.0
N D:CYS646 3.8 27.6 1.0
N D:CYS487 3.9 28.9 1.0
O D:CYS645 3.9 31.0 1.0
CA D:CYS646 4.2 27.6 1.0
CA D:CYS645 4.2 31.0 1.0
CA D:CYS487 4.2 28.9 1.0
CE1 D:PHE571 4.3 26.0 1.0
CA D:HIS642 4.3 26.2 1.0
CD2 D:HIS642 4.4 26.2 1.0
NE2 D:HIS642 4.4 26.2 1.0
O D:HIS642 4.6 26.2 1.0
C D:GLY486 4.6 26.2 1.0
CD1 D:PHE571 4.8 26.0 1.0
N D:CYS645 4.8 31.0 1.0
C D:HIS642 4.9 26.2 1.0
CE D:LYS532 4.9 28.8 1.0
CA D:GLY486 4.9 26.2 1.0

Reference:

F.A.Jochheim, D.Tegunov, H.S.Hillen, J.Schmitzova, G.Kokic, C.Dienemann, P.Cramer. Dimeric Form of Sars-Cov-2 Polymerase To Be Published.
Page generated: Fri Sep 24 17:11:53 2021

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