Zinc in PDB 8s8i: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1) also contains other interesting chemical elements:

Magnesium

(Mg)

117 atoms

The binding sites of Zinc atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1) (pdb code 8s8i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1), PDB code: 8s8i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:118.6 occ:1.00 SG a:CYS74 2.3 91.0 1.0 SG a:CYS26 2.3 95.1 1.0 SG a:CYS77 2.3 91.6 1.0 SG a:CYS23 2.3 100.9 1.0 CB a:CYS26 2.5 95.1 1.0 N a:CYS26 2.7 95.1 1.0 CB a:CYS77 2.9 91.6 1.0 CB a:CYS74 3.0 91.0 1.0 CB a:CYS23 3.1 100.9 1.0 CA a:CYS26 3.1 95.1 1.0 N a:CYS74 3.6 91.0 1.0 CA a:CYS74 3.8 91.0 1.0 C a:ASN25 3.9 96.1 1.0 CB a:ASN25 4.1 96.1 1.0 C a:CYS26 4.1 95.1 1.0 CA a:CYS77 4.1 91.6 1.0 N a:CYS77 4.1 91.6 1.0 N a:SER27 4.2 98.5 1.0 CA a:ASN25 4.3 96.1 1.0 N a:ASN25 4.3 96.1 1.0 O a:CYS74 4.6 91.0 1.0 C a:CYS74 4.6 91.0 1.0 CA a:CYS23 4.6 100.9 1.0 C a:TYR73 4.8 99.4 1.0 O a:ASN25 4.9 96.1 1.0 C a:CYS23 5.0 100.9 1.0

Zinc binding site 2 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:338.8 occ:1.00 CB b:CYS56 2.1 256.1 1.0 O b:CYS59 2.3 277.6 1.0 N b:CYS59 2.3 277.6 1.0 SG b:CYS59 2.3 277.6 1.0 SG b:CYS56 2.3 256.1 1.0 CA b:CYS59 2.8 277.6 1.0 C b:CYS59 2.8 277.6 1.0 OG b:SER58 3.0 283.7 1.0 CB b:CYS59 3.0 277.6 1.0 OG1 b:THR61 3.1 238.2 1.0 CA b:CYS56 3.2 256.1 1.0 O b:CYS56 3.3 256.1 1.0 C b:CYS56 3.3 256.1 1.0 C b:SER58 3.4 283.7 1.0 N b:SER58 3.6 283.7 1.0 CA b:SER58 3.8 283.7 1.0 N b:CYS56 4.0 256.1 1.0 CB b:SER58 4.0 283.7 1.0 N b:SER60 4.1 257.5 1.0 N b:GLU57 4.1 263.9 1.0 N b:THR61 4.3 238.2 1.0 SG b:CYS37 4.3 209.2 1.0 CB b:THR61 4.4 238.2 1.0 C b:GLU57 4.4 263.9 1.0 O b:SER58 4.5 283.7 1.0 SG b:CYS40 4.6 229.9 1.0 CG2 b:THR61 4.7 238.2 1.0 CA b:GLU57 4.9 263.9 1.0 CA b:THR61 4.9 238.2 1.0 CA b:SER60 5.0 257.5 1.0 O b:THR61 5.0 238.2 1.0

Zinc binding site 3 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


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-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:323.0 occ:1.00 SG f:CYS139 2.3 256.4 1.0 SG f:CYS121 2.3 226.8 1.0 CB f:CYS139 2.4 256.4 1.0 CA f:CYS139 2.9 256.4 1.0 CB f:PHE146 3.1 236.3 1.0 CG f:PHE146 3.3 236.3 1.0 CD1 f:PHE146 3.5 236.3 1.0 N f:CYS139 3.6 256.4 1.0 CD2 f:LEU130 3.6 229.1 1.0 CB f:CYS121 3.7 226.8 1.0 CD2 f:PHE146 4.1 236.3 1.0 C f:CYS139 4.2 256.4 1.0 SG f:CYS124 4.3 212.8 1.0 C f:TYR138 4.4 242.3 1.0 CE1 f:PHE146 4.5 236.3 1.0 CA f:PHE146 4.5 236.3 1.0 N f:GLY140 4.5 255.2 1.0 CB f:ASN123 4.6 209.3 1.0 O f:TYR138 4.6 242.3 1.0 SG f:CYS142 4.8 259.6 1.0 O f:PHE146 4.8 236.3 1.0 O f:CYS142 4.8 259.6 1.0 CA f:CYS121 4.8 226.8 1.0 CE2 f:PHE146 4.9 236.3 1.0 C f:PHE146 5.0 236.3 1.0

Zinc binding site 4 out of 4 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF1) within 5.0Å range: probe atom residue distance (Å) B Occ l:Zn301 b:299.6 occ:1.00 SG l:CYS239 2.3 331.9 1.0 SG l:CYS259 2.3 285.5 1.0 CB l:CYS236 3.3 334.5 1.0 CB l:CYS259 3.6 285.5 1.0 SG l:CYS236 3.9 334.5 1.0 CB l:SER241 4.0 284.0 1.0 CB l:CYS239 4.1 331.9 1.0 OG l:SER261 4.3 260.6 1.0 NE2 k:GLN286 4.3 284.3 1.0 CB l:THR244 4.4 292.6 1.0 O l:CYS239 4.5 331.9 1.0 OG l:SER264 4.6 288.0 1.0 OG1 l:THR244 4.6 292.6 1.0 OG l:SER241 4.6 284.0 1.0 CA l:CYS259 4.7 285.5 1.0 CA l:CYS236 4.7 334.5 1.0 CG2 l:THR244 4.7 292.6 1.0 CA l:CYS239 4.8 331.9 1.0 OG1 l:THR238 4.8 338.2 1.0 C l:CYS239 4.8 331.9 1.0 N l:CYS239 4.8 331.9 1.0 N l:CYS236 4.9 334.5 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