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Zinc in PDB 5a2q: Structure of the Hcv Ires Bound to the Human Ribosome

Other elements in 5a2q:

The structure of Structure of the Hcv Ires Bound to the Human Ribosome also contains other interesting chemical elements:

Magnesium (Mg) 98 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Hcv Ires Bound to the Human Ribosome (pdb code 5a2q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Hcv Ires Bound to the Human Ribosome, PDB code: 5a2q:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5a2q

Go back to Zinc Binding Sites List in 5a2q
Zinc binding site 1 out of 3 in the Structure of the Hcv Ires Bound to the Human Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Hcv Ires Bound to the Human Ribosome within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn201

b:33.3
occ:1.00
SG a:CYS26 2.2 31.8 1.0
SG a:CYS77 2.4 32.9 1.0
SG a:CYS74 2.4 29.2 1.0
SG a:CYS23 2.6 28.5 1.0
CB a:CYS26 2.7 31.8 1.0
CB a:CYS77 3.0 32.9 1.0
CB a:CYS74 3.4 29.2 1.0
CB a:CYS23 3.5 28.5 1.0
N a:CYS26 3.5 30.1 1.0
CA a:CYS26 3.7 30.1 1.0
N a:CYS74 4.0 26.3 1.0
CA a:CYS77 4.1 29.6 1.0
N a:CYS77 4.1 29.6 1.0
CA a:CYS74 4.2 26.3 1.0
O a:CYS74 4.4 26.3 1.0
CB a:ASN25 4.5 36.2 1.0
CB a:ARG28 4.5 26.5 1.0
C a:ASN25 4.6 31.8 1.0
C a:CYS74 4.7 26.3 1.0
C a:CYS26 4.8 30.1 1.0
N a:ALA27 4.9 28.5 1.0
N a:ARG28 4.9 27.4 1.0
CG a:ARG28 4.9 26.5 1.0
CA a:ASN25 4.9 31.8 1.0
N a:ASN25 4.9 31.8 1.0
CA a:CYS23 4.9 29.1 1.0

Zinc binding site 2 out of 3 in 5a2q

Go back to Zinc Binding Sites List in 5a2q
Zinc binding site 2 out of 3 in the Structure of the Hcv Ires Bound to the Human Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Hcv Ires Bound to the Human Ribosome within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn201

b:0.6
occ:1.00
SG d:CYS39 2.4 0.1 1.0
SG d:CYS21 2.5 0.1 1.0
SG d:CYS24 2.5 0.2 1.0
SG d:CYS42 2.7 0.5 1.0
CB d:CYS21 3.1 0.1 1.0
CB d:CYS24 3.3 0.2 1.0
CB d:CYS42 3.5 0.5 1.0
N d:CYS24 3.7 0.3 1.0
CB d:CYS39 3.9 0.1 1.0
N d:CYS39 3.9 0.5 1.0
CA d:CYS24 4.1 0.3 1.0
O2' 2:G1495 4.1 0.9 1.0
CA d:CYS39 4.4 0.5 1.0
CB d:VAL23 4.5 0.8 1.0
CA d:CYS21 4.6 0.5 1.0
O d:CYS39 4.6 0.5 1.0
N d:CYS42 4.6 0.9 1.0
CA d:CYS42 4.7 0.9 1.0
C d:CYS24 4.8 0.3 1.0
C d:VAL23 4.9 0.6 1.0
C d:CYS39 4.9 0.5 1.0
N d:VAL23 4.9 0.6 1.0
N d:SER25 5.0 0.6 1.0
C d:CYS21 5.0 0.5 1.0
C d:MET38 5.0 0.0 1.0

Zinc binding site 3 out of 3 in 5a2q

Go back to Zinc Binding Sites List in 5a2q
Zinc binding site 3 out of 3 in the Structure of the Hcv Ires Bound to the Human Ribosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Hcv Ires Bound to the Human Ribosome within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn500

b:0.5
occ:1.00
SG f:CYS126 2.4 0.6 1.0
SG f:CYS121 2.4 0.9 1.0
SG f:CYS144 2.6 0.1 1.0
SG f:CYS141 2.6 0.8 1.0
CB f:CYS141 3.3 0.8 1.0
CB f:CYS121 3.4 0.9 1.0
CB f:CYS126 3.8 0.6 1.0
CB f:SER123 4.0 0.9 1.0
CB f:CYS144 4.1 0.1 1.0
N f:CYS144 4.1 0.8 1.0
OG f:SER123 4.3 0.9 1.0
CB f:LYS143 4.7 0.9 1.0
CA f:CYS144 4.7 0.8 1.0
CA f:CYS141 4.7 0.1 1.0
CB f:LEU146 4.7 0.4 1.0
CA f:CYS121 4.8 0.3 1.0
N f:SER123 4.9 0.9 1.0

Reference:

N.Quade, D.Boehringer, M.Leibundgut, J.Van Den Heuvel, N.Ban. Cryo-Em Structure of Hepatitis C Virus Ires Bound to the Human Ribosome at 3.9 Angstrom Resolution Nat.Commun. V. 6 7646 2015.
ISSN: ESSN 2041-1723
PubMed: 26155016
DOI: 10.1038/NCOMMS8646
Page generated: Wed Dec 16 06:01:27 2020

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