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Zinc in PDB 6zoj: Sars-Cov-2-NSP1-40S Complex, Composite Map

Enzymatic activity of Sars-Cov-2-NSP1-40S Complex, Composite Map

All present enzymatic activity of Sars-Cov-2-NSP1-40S Complex, Composite Map:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13; 4.2.99.18;

Other elements in 6zoj:

The structure of Sars-Cov-2-NSP1-40S Complex, Composite Map also contains other interesting chemical elements:

Magnesium (Mg) 166 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2-NSP1-40S Complex, Composite Map (pdb code 6zoj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Sars-Cov-2-NSP1-40S Complex, Composite Map, PDB code: 6zoj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6zoj

Go back to Zinc Binding Sites List in 6zoj
Zinc binding site 1 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2-NSP1-40S Complex, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn201

b:69.2
occ:1.00
SG a:CYS26 2.3 27.9 1.0
SG a:CYS74 2.3 26.4 1.0
SG a:CYS77 2.3 28.1 1.0
SG a:CYS23 2.3 27.0 1.0
CB a:CYS77 3.2 28.1 1.0
CB a:CYS23 3.3 27.0 1.0
CB a:CYS26 3.5 27.9 1.0
CB a:CYS74 3.8 26.4 1.0
N a:CYS26 3.8 27.9 1.0
N a:CYS74 4.1 26.4 1.0
CA a:CYS26 4.2 27.9 1.0
CB a:ASN25 4.3 28.0 1.0
N a:CYS77 4.3 28.1 1.0
CA a:CYS77 4.3 28.1 1.0
CA a:CYS74 4.5 26.4 1.0
CB a:ARG28 4.7 24.3 1.0
C a:ASN25 4.7 28.0 1.0
CA a:CYS23 4.8 27.0 1.0
C a:CYS26 4.8 27.9 1.0
CA a:ASN25 4.9 28.0 1.0
N a:ASN25 4.9 28.0 1.0
N a:ALA27 5.0 26.0 1.0

Zinc binding site 2 out of 3 in 6zoj

Go back to Zinc Binding Sites List in 6zoj
Zinc binding site 2 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2-NSP1-40S Complex, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn201

b:38.8
occ:1.00
SG d:CYS39 2.2 19.7 1.0
SG d:CYS24 2.3 22.4 1.0
SG d:CYS42 2.3 18.4 1.0
SG d:CYS21 2.3 22.3 1.0
CB d:CYS42 3.2 18.4 1.0
CB d:CYS21 3.3 22.3 1.0
CB d:CYS24 3.6 22.4 1.0
CB d:CYS39 3.7 19.7 1.0
N d:CYS24 3.8 22.4 1.0
N d:CYS39 4.0 19.7 1.0
CA d:CYS24 4.2 22.4 1.0
CA d:CYS39 4.4 19.7 1.0
CB d:VAL23 4.4 20.7 1.0
N d:CYS42 4.4 18.4 1.0
CA d:CYS42 4.4 18.4 1.0
C d:VAL23 4.7 20.7 1.0
CA d:CYS21 4.8 22.3 1.0
O d:CYS39 4.9 19.7 1.0
N d:VAL23 4.9 20.7 1.0
CA d:VAL23 4.9 20.7 1.0
C d:CYS24 4.9 22.4 1.0
C d:CYS39 4.9 19.7 1.0

Zinc binding site 3 out of 3 in 6zoj

Go back to Zinc Binding Sites List in 6zoj
Zinc binding site 3 out of 3 in the Sars-Cov-2-NSP1-40S Complex, Composite Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2-NSP1-40S Complex, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn500

b:0.3
occ:1.00
SG f:CYS144 2.3 69.3 1.0
SG f:CYS141 2.3 66.4 1.0
SG f:CYS121 2.4 74.1 1.0
SG f:CYS126 2.4 77.4 1.0
CB f:CYS126 3.2 77.4 1.0
CB f:CYS141 3.2 66.4 1.0
CB f:CYS121 3.2 74.1 1.0
CB f:CYS144 3.5 69.3 1.0
OG f:SER123 3.6 78.1 1.0
CB f:SER123 3.9 78.1 1.0
N f:CYS144 4.1 69.3 1.0
CA f:CYS144 4.4 69.3 1.0
CA f:CYS126 4.6 77.4 1.0
CA f:CYS141 4.7 66.4 1.0
CB f:LEU146 4.7 67.8 1.0
CA f:CYS121 4.7 74.1 1.0
O f:CYS126 4.8 77.4 1.0
C f:LYS143 4.9 67.1 1.0
CB f:LYS143 4.9 67.1 1.0
N f:SER123 5.0 78.1 1.0
N f:CYS126 5.0 77.4 1.0

Reference:

K.Schubert, E.D.Karousis, A.Jomaa, A.Scaiola, B.Echeverria, L.A.Gurzeler, M.Leibundgut, V.Thiel, O.Muhlemann, N.Ban. Sars-Cov-2 NSP1 Binds the Ribosomal Mrna Channel to Inhibit Translation. Nat.Struct.Mol.Biol. V. 27 959 2020.
ISSN: ESSN 1545-9985
PubMed: 32908316
DOI: 10.1038/S41594-020-0511-8
Page generated: Tue Oct 29 15:51:14 2024

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