Zinc in PDB 8s8d: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2) also contains other interesting chemical elements:

Magnesium

(Mg)

116 atoms

The binding sites of Zinc atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2) (pdb code 8s8d). 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 A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2), PDB code: 8s8d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-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 A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:72.8 occ:1.00 SG a:CYS74 2.3 47.4 1.0 SG a:CYS26 2.3 47.4 1.0 SG a:CYS77 2.3 45.5 1.0 SG a:CYS23 2.3 48.3 1.0 CB a:CYS74 2.9 47.4 1.0 CB a:CYS77 3.0 45.5 1.0 CB a:CYS26 3.2 47.4 1.0 CB a:CYS23 3.4 48.3 1.0 N a:CYS26 3.5 47.4 1.0 CA a:CYS26 3.9 47.4 1.0 N a:CYS74 3.9 47.4 1.0 N a:CYS77 3.9 45.5 1.0 CA a:CYS74 3.9 47.4 1.0 CA a:CYS77 4.1 45.5 1.0 CB a:ASN25 4.4 46.8 1.0 C a:CYS26 4.5 47.4 1.0 C a:ASN25 4.6 46.8 1.0 CB a:ARG28 4.6 46.5 1.0 C a:CYS74 4.7 47.4 1.0 N a:SER27 4.7 47.7 1.0 CA a:CYS23 4.8 48.3 1.0 N a:ASN25 4.8 46.8 1.0 CA a:ASN25 4.8 46.8 1.0

Zinc binding site 2 out of 3 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-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 A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:138.7 occ:1.00 SG b:CYS59 2.3 101.0 1.0 N b:CYS40 3.0 108.0 1.0 CB b:CYS59 3.2 101.0 1.0 SG b:CYS40 3.3 108.0 1.0 CB b:CYS40 3.5 108.0 1.0 C b:GLY39 3.5 106.2 1.0 CA b:GLY39 3.5 106.2 1.0 CA b:CYS40 3.9 108.0 1.0 N b:CYS59 4.3 101.0 1.0 N b:GLY39 4.3 106.2 1.0 CA b:CYS59 4.3 101.0 1.0 O b:GLY39 4.4 106.2 1.0 CB b:SER58 4.6 98.0 1.0 SG b:CYS56 4.8 98.0 1.0 SG b:CYS37 4.9 96.2 1.0 C b:SER58 4.9 98.0 1.0 C b:CYS40 4.9 108.0 1.0 CB b:CYS56 5.0 98.0 1.0 CB b:CYS37 5.0 96.2 1.0

Zinc binding site 3 out of 3 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:131.6 occ:1.00 SG f:CYS142 2.3 98.1 1.0 SG f:CYS139 2.3 99.1 1.0 SG f:CYS124 2.3 99.0 1.0 SG f:CYS121 2.3 92.9 1.0 CB f:CYS139 3.2 99.1 1.0 N f:CYS142 3.5 98.1 1.0 CB f:CYS121 3.6 92.9 1.0 CB f:CYS142 3.6 98.1 1.0 CB f:CYS124 3.9 99.0 1.0 CA f:CYS142 4.0 98.1 1.0 N f:CYS124 4.0 99.0 1.0 C f:CYS142 4.4 98.1 1.0 CB f:ASN123 4.4 95.2 1.0 CB f:LYS141 4.5 90.7 1.0 N f:LYS141 4.5 90.7 1.0 CA f:CYS124 4.6 99.0 1.0 C f:LYS141 4.6 90.7 1.0 CA f:CYS139 4.6 99.1 1.0 O f:CYS142 4.7 98.1 1.0 CA f:LYS141 4.8 90.7 1.0 CA f:CYS121 4.9 92.9 1.0 C f:ASN123 4.9 95.2 1.0 N f:GLY140 4.9 89.3 1.0 N f:HIS143 4.9 98.0 1.0 CG2 f:ILE128 4.9 94.5 1.0 N f:ASN123 4.9 95.2 1.0

L.Villamayor-Belinchon, P.Sharma, Y.Gordiyenko, J.L.Llacer, T.Hussain. Structural Basis of Auc Codon Discrimination During Translation Initiation in Yeast. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39193907
DOI: 10.1093/NAR/GKAE737