Zinc in PDB 8s8j: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5) also contains other interesting chemical elements:

Magnesium

(Mg)

115 atoms

The binding sites of Zinc atom in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-EIF5) (pdb code 8s8j). 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-EIF5), PDB code: 8s8j:
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-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:66.0 occ:1.00 SG a:CYS74 2.3 38.6 1.0 SG a:CYS26 2.3 45.6 1.0 SG a:CYS77 2.3 40.4 1.0 SG a:CYS23 2.3 48.4 1.0 CB a:CYS26 2.5 45.6 1.0 N a:CYS26 2.7 45.6 1.0 CB a:CYS74 2.9 38.6 1.0 CB a:CYS77 2.9 40.4 1.0 CA a:CYS26 3.1 45.6 1.0 CB a:CYS23 3.3 48.4 1.0 N a:CYS74 3.7 38.6 1.0 CA a:CYS74 3.9 38.6 1.0 C a:ASN25 3.9 46.1 1.0 N a:CYS77 3.9 40.4 1.0 C a:CYS26 3.9 45.6 1.0 N a:SER27 4.0 49.9 1.0 CA a:CYS77 4.0 40.4 1.0 CB a:ASN25 4.2 46.1 1.0 CA a:ASN25 4.4 46.1 1.0 N a:ASN25 4.4 46.1 1.0 C a:CYS74 4.6 38.6 1.0 CA a:CYS23 4.8 48.4 1.0 O a:ASN25 4.9 46.1 1.0 C a:TYR73 4.9 41.0 1.0 O a:CYS74 4.9 38.6 1.0 O a:CYS26 5.0 45.6 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-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:167.3 occ:1.00 OG b:SER58 2.2 142.5 1.0 SG b:CYS40 2.3 111.8 1.0 SG b:CYS56 2.3 143.1 1.0 SG b:CYS59 2.3 139.4 1.0 CB b:CYS56 2.9 143.1 1.0 N b:CYS59 3.0 139.4 1.0 CB b:CYS59 3.4 139.4 1.0 O b:CYS59 3.5 139.4 1.0 CB b:SER58 3.5 142.5 1.0 CA b:CYS59 3.6 139.4 1.0 C b:SER58 3.9 142.5 1.0 CB b:CYS40 3.9 111.8 1.0 C b:CYS59 4.0 139.4 1.0 CA b:SER58 4.0 142.5 1.0 N b:SER58 4.1 142.5 1.0 CA b:CYS56 4.2 143.1 1.0 C b:CYS56 4.4 143.1 1.0 O b:CYS56 4.6 143.1 1.0 CB b:ASN42 4.7 104.4 1.0 N b:CYS40 4.8 111.8 1.0 CA b:CYS40 4.9 111.8 1.0 O b:SER58 4.9 142.5 1.0 SG b:CYS37 5.0 92.5 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-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:251.3 occ:1.00 SG f:CYS124 2.3 100.7 1.0 SG f:CYS139 2.3 101.3 1.0 SG f:CYS121 2.3 86.2 1.0 CB f:CYS121 3.5 86.2 1.0 CB f:CYS139 3.7 101.3 1.0 CB f:CYS124 3.8 100.7 1.0 CD2 f:LEU130 4.1 96.1 1.0 N f:CYS124 4.2 100.7 1.0 CA f:CYS139 4.4 101.3 1.0 CB f:LYS141 4.5 97.2 1.0 CB f:ASN123 4.6 89.1 1.0 CA f:CYS124 4.6 100.7 1.0 N f:CYS142 4.6 99.5 1.0 CB f:PHE146 4.7 90.1 1.0 O f:CYS142 4.9 99.5 1.0 N f:LYS141 4.9 97.2 1.0 CA f:CYS121 4.9 86.2 1.0 CG2 f:ILE128 5.0 89.3 1.0 N f:GLY140 5.0 93.7 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-EIF5)


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-EIF5) within 5.0Å range: probe atom residue distance (Å) B Occ m:Zn501 b:31.3 occ:1.00 CB m:CYS99 2.0 22.9 1.0 SG m:CYS99 2.3 22.9 1.0 SG m:CYS124 2.3 22.3 1.0 CB m:CYS121 2.8 20.3 1.0 SG m:CYS121 3.3 20.3 1.0 CA m:CYS99 3.4 22.9 1.0 CG m:LYS126 3.8 15.0 1.0 N m:GLY100 3.8 23.2 1.0 OG1 m:THR128 3.9 13.7 1.0 C m:CYS99 4.0 22.9 1.0 CB m:CYS124 4.1 22.3 1.0 CA m:CYS121 4.1 20.3 1.0 N m:LYS126 4.4 15.0 1.0 N m:CYS99 4.4 22.9 1.0 CG2 m:THR107 4.4 20.1 1.0 N m:CYS121 4.5 20.3 1.0 N m:GLY125 4.5 20.2 1.0 CD m:LYS126 4.5 15.0 1.0 O m:LYS126 4.6 15.0 1.0 CE m:LYS126 4.7 15.0 1.0 CB m:LYS126 4.8 15.0 1.0 CA m:CYS124 5.0 22.3 1.0 CA m:GLY100 5.0 23.2 1.0 C m:CYS124 5.0 22.3 1.0 OG m:SER101 5.0 25.2 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