Zinc in PDB 8s8h: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.2) 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-2.2) (pdb code 8s8h). 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-2.2), PDB code: 8s8h:
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-2.2)


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-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:139.3 occ:1.00 SG a:CYS26 2.3 46.9 1.0 SG a:CYS74 2.3 48.7 1.0 SG a:CYS77 2.3 47.8 1.0 SG a:CYS23 2.3 46.5 1.0 CB a:CYS77 3.0 47.8 1.0 CB a:CYS26 3.3 46.9 1.0 CB a:CYS23 3.3 46.5 1.0 N a:CYS26 3.4 46.9 1.0 CB a:CYS74 3.5 48.7 1.0 CA a:CYS26 3.9 46.9 1.0 N a:CYS77 4.0 47.8 1.0 CA a:CYS77 4.1 47.8 1.0 CB a:ASN25 4.2 46.9 1.0 N a:CYS74 4.2 48.7 1.0 CB a:ARG28 4.3 44.8 1.0 CA a:CYS74 4.4 48.7 1.0 C a:CYS26 4.4 46.9 1.0 C a:ASN25 4.4 46.9 1.0 O a:CYS74 4.6 48.7 1.0 N a:SER27 4.7 42.6 1.0 N a:ARG28 4.7 44.8 1.0 CA a:ASN25 4.7 46.9 1.0 CA a:CYS23 4.8 46.5 1.0 C a:CYS74 4.8 48.7 1.0 N a:ASN25 4.8 46.9 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-2.2)


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-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:199.1 occ:1.00 SG b:CYS59 2.3 124.4 1.0 CB b:CYS56 2.4 124.3 1.0 SG b:CYS56 2.8 124.3 1.0 SG b:CYS37 2.9 113.9 1.0 CG2 b:THR61 3.4 105.9 1.0 CB b:CYS37 3.5 113.9 1.0 CA b:CYS56 3.9 124.3 1.0 CB b:CYS59 4.1 124.4 1.0 O b:CYS59 4.1 124.4 1.0 CD1 b:LEU63 4.2 86.1 1.0 SG b:CYS40 4.2 111.8 1.0 N b:CYS56 4.4 124.3 1.0 N b:CYS59 4.6 124.4 1.0 C b:CYS59 4.6 124.4 1.0 CA b:CYS59 4.7 124.4 1.0 N b:CYS40 4.8 111.8 1.0 OG b:SER58 4.8 122.3 1.0 C b:CYS56 4.9 124.3 1.0 CB b:THR61 4.9 105.9 1.0 CA b:CYS37 5.0 113.9 1.0 O b:THR61 5.0 105.9 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-2.2)


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-2.2) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:251.8 occ:1.00 SG f:CYS142 2.3 155.6 1.0 SG f:CYS124 2.3 135.2 1.0 SG f:CYS139 2.3 154.5 1.0 SG f:CYS121 2.3 134.2 1.0 N f:CYS142 3.5 155.6 1.0 CB f:CYS142 3.5 155.6 1.0 CB f:CYS124 3.6 135.2 1.0 N f:CYS124 3.6 135.2 1.0 CB f:CYS121 3.7 134.2 1.0 CB f:CYS139 3.7 154.5 1.0 CA f:CYS142 3.9 155.6 1.0 O f:CYS142 3.9 155.6 1.0 CB f:ASN123 4.1 127.7 1.0 C f:CYS142 4.2 155.6 1.0 CA f:CYS124 4.2 135.2 1.0 C f:ASN123 4.4 127.7 1.0 CB f:PHE146 4.5 142.6 1.0 CB f:LYS141 4.6 149.8 1.0 C f:LYS141 4.6 149.8 1.0 CA f:ASN123 4.7 127.7 1.0 CG2 f:ILE128 4.7 128.7 1.0 N f:LYS141 4.8 149.8 1.0 CA f:LYS141 4.9 149.8 1.0 CA f:CYS139 4.9 154.5 1.0 O f:CYS121 4.9 134.2 1.0 OG1 f:THR145 4.9 153.4 1.0 N f:ASN123 5.0 127.7 1.0 CA f:CYS121 5.0 134.2 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