Zinc in PDB 8rw1: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation

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

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation 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 (pdb code 8rw1). 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, PDB code: 8rw1:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:76.1 occ:1.00 CB a:CYS74 1.8 49.1 1.0 SG a:CYS26 2.3 48.5 1.0 SG a:CYS77 2.3 45.2 1.0 SG a:CYS23 2.3 49.3 1.0 SG a:CYS74 2.4 49.1 1.0 CB a:CYS77 3.2 45.2 1.0 CA a:CYS74 3.2 49.1 1.0 CB a:CYS23 3.3 49.3 1.0 CB a:CYS26 3.4 48.5 1.0 N a:CYS74 3.7 49.1 1.0 N a:CYS26 3.9 48.5 1.0 N a:CYS77 4.0 45.2 1.0 C a:CYS74 4.1 49.1 1.0 CA a:CYS26 4.2 48.5 1.0 CA a:CYS77 4.2 45.2 1.0 CB a:ARG28 4.2 46.7 1.0 N a:ILE75 4.5 42.1 1.0 C a:CYS26 4.7 48.5 1.0 CA a:CYS23 4.8 49.3 1.0 N a:SER27 4.8 48.2 1.0 N a:ARG28 4.8 46.7 1.0 CB a:ASN25 4.9 47.8 1.0 O a:CYS74 5.0 49.1 1.0 C a:TYR73 5.0 46.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:161.0 occ:1.00 SG b:CYS59 2.3 112.9 1.0 N b:CYS40 3.0 120.9 1.0 CB b:CYS59 3.1 112.9 1.0 SG b:CYS40 3.3 120.9 1.0 CA b:GLY39 3.4 119.3 1.0 C b:GLY39 3.4 119.3 1.0 CB b:CYS40 3.5 120.9 1.0 CA b:CYS40 3.9 120.9 1.0 N b:GLY39 4.3 119.3 1.0 N b:CYS59 4.3 112.9 1.0 CA b:CYS59 4.3 112.9 1.0 O b:GLY39 4.4 119.3 1.0 CB b:SER58 4.6 111.6 1.0 SG b:CYS56 4.8 108.7 1.0 C b:SER58 4.9 111.6 1.0 C b:CYS40 4.9 120.9 1.0 CB b:CYS56 5.0 108.7 1.0

Zinc binding site 3 out of 3 in the Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation


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 within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:135.6 occ:1.00 SG f:CYS139 2.3 100.1 1.0 SG f:CYS142 2.3 101.2 1.0 SG f:CYS124 2.3 103.6 1.0 SG f:CYS121 2.3 98.5 1.0 CB f:CYS139 3.3 100.1 1.0 N f:CYS142 3.5 101.2 1.0 CB f:CYS142 3.5 101.2 1.0 CB f:CYS121 3.6 98.5 1.0 CB f:CYS124 3.8 103.6 1.0 CA f:CYS142 3.9 101.2 1.0 N f:CYS124 4.0 103.6 1.0 C f:CYS142 4.4 101.2 1.0 CB f:ASN123 4.4 97.9 1.0 CB f:LYS141 4.5 84.7 1.0 N f:LYS141 4.5 84.7 1.0 CA f:CYS124 4.5 103.6 1.0 C f:LYS141 4.6 84.7 1.0 CA f:CYS139 4.7 100.1 1.0 CA f:LYS141 4.8 84.7 1.0 O f:CYS142 4.8 101.2 1.0 N f:HIS143 4.8 98.3 1.0 CG2 f:ILE128 4.8 102.3 1.0 N f:GLY140 4.9 86.8 1.0 C f:ASN123 4.9 97.9 1.0 CA f:CYS121 4.9 98.5 1.0 N f:ASN123 5.0 97.9 1.0 CB f:PHE146 5.0 99.8 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