Zinc in PDB 8s8e: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.1) 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-3.1) (pdb code 8s8e). 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-3.1), PDB code: 8s8e:
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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:93.4 occ:1.00 SG a:CYS26 2.3 70.2 1.0 SG a:CYS74 2.3 61.1 1.0 SG a:CYS23 2.3 76.5 1.0 SG a:CYS77 2.3 55.3 1.0 CB a:CYS77 3.0 55.3 1.0 CB a:CYS74 3.4 61.1 1.0 CB a:CYS26 3.4 70.2 1.0 CB a:CYS23 3.4 76.5 1.0 N a:CYS26 3.5 70.2 1.0 N a:CYS74 3.8 61.1 1.0 CA a:CYS26 4.0 70.2 1.0 N a:CYS77 4.0 55.3 1.0 CA a:CYS77 4.1 55.3 1.0 CA a:CYS74 4.1 61.1 1.0 O a:CYS74 4.3 61.1 1.0 CB a:ASN25 4.4 68.2 1.0 C a:CYS74 4.5 61.1 1.0 C a:CYS26 4.5 70.2 1.0 C a:ASN25 4.6 68.2 1.0 N a:SER27 4.6 69.0 1.0 N a:ASN25 4.6 68.2 1.0 CA a:ASN25 4.8 68.2 1.0 CA a:CYS23 4.8 76.5 1.0 C a:TYR73 4.9 65.3 1.0 N a:ARG28 5.0 66.0 1.0 CB a:ARG28 5.0 66.0 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:212.6 occ:1.00 SG b:CYS59 2.3 161.8 1.0 SG b:CYS37 2.3 157.7 1.0 CG2 b:THR61 2.4 152.0 1.0 CB b:THR61 3.1 152.0 1.0 CB b:CYS37 3.1 157.7 1.0 SG b:CYS40 3.3 166.1 1.0 OG1 b:THR61 3.3 152.0 1.0 N b:CYS40 4.0 166.1 1.0 CB b:CYS59 4.0 161.8 1.0 CB b:CYS40 4.2 166.1 1.0 OG b:SER58 4.5 160.9 1.0 CA b:THR61 4.5 152.0 1.0 CA b:CYS37 4.5 157.7 1.0 O b:CYS59 4.5 161.8 1.0 N b:GLY39 4.6 169.2 1.0 CA b:GLY39 4.6 169.2 1.0 CA b:CYS40 4.7 166.1 1.0 C b:GLY39 4.8 169.2 1.0 CB b:CYS56 4.8 148.5 1.0 CA b:CYS59 4.8 161.8 1.0 C b:CYS59 4.9 161.8 1.0 N b:CYS59 4.9 161.8 1.0 SG b:CYS56 5.0 148.5 1.0 N b:THR61 5.0 152.0 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-3.1)


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-3.1) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:194.4 occ:1.00 SG f:CYS121 2.3 139.2 1.0 SG f:CYS124 2.3 143.4 1.0 SG f:CYS139 2.3 144.9 1.0 CB f:ASN123 3.1 133.9 1.0 N f:CYS124 3.3 143.4 1.0 SG f:CYS142 3.4 143.3 1.0 CB f:CYS139 3.4 144.9 1.0 CB f:CYS124 3.7 143.4 1.0 OG1 f:THR145 3.7 150.5 1.0 C f:ASN123 3.7 133.9 1.0 CB f:PHE146 3.8 145.9 1.0 CA f:ASN123 3.8 133.9 1.0 N f:ASN123 4.0 133.9 1.0 CA f:CYS124 4.0 143.4 1.0 CB f:CYS121 4.0 139.2 1.0 O f:CYS142 4.3 143.3 1.0 CA f:CYS139 4.5 144.9 1.0 CG f:PHE146 4.6 145.9 1.0 O f:ASN123 4.6 133.9 1.0 N f:CYS142 4.8 143.3 1.0 N f:PHE146 4.8 145.9 1.0 CA f:CYS121 4.9 139.2 1.0 CB f:THR145 4.9 150.5 1.0 CA f:PHE146 4.9 145.9 1.0 CD2 f:LEU130 4.9 136.1 1.0 CB f:CYS142 4.9 143.3 1.0 CD2 f:PHE146 5.0 145.9 1.0 C f:CYS142 5.0 143.3 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