Zinc in PDB 8s8f: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-3.2) 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-3.2) (pdb code 8s8f). 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-3.2), PDB code: 8s8f:
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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:112.2 occ:1.00 SG a:CYS26 2.3 37.2 1.0 SG a:CYS74 2.3 36.9 1.0 SG a:CYS77 2.3 33.9 1.0 SG a:CYS23 2.3 38.0 1.0 CB a:CYS74 2.8 36.9 1.0 CB a:CYS77 2.8 33.9 1.0 CB a:CYS26 2.9 37.2 1.0 N a:CYS26 3.3 37.2 1.0 CB a:CYS23 3.4 38.0 1.0 CA a:CYS26 3.6 37.2 1.0 N a:CYS74 3.6 36.9 1.0 N a:CYS77 3.6 33.9 1.0 CA a:CYS74 3.8 36.9 1.0 CA a:CYS77 3.8 33.9 1.0 C a:CYS26 4.3 37.2 1.0 C a:ASN25 4.5 37.5 1.0 C a:CYS74 4.5 36.9 1.0 N a:SER27 4.5 35.7 1.0 CB a:ASN25 4.8 37.5 1.0 N a:ASN25 4.8 37.5 1.0 CA a:CYS23 4.8 38.0 1.0 C a:SER76 4.9 34.8 1.0 C a:TYR73 4.9 38.0 1.0 CA a:ASN25 4.9 37.5 1.0 C a:CYS77 5.0 33.9 1.0 N a:ILE75 5.0 31.0 1.0 N a:ARG28 5.0 37.5 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:180.8 occ:1.00 OG1 b:THR61 2.1 103.3 1.0 SG b:CYS37 2.3 102.5 1.0 SG b:CYS59 2.3 116.7 1.0 CB b:THR61 3.2 103.3 1.0 CB b:CYS37 3.3 102.5 1.0 SG b:CYS40 3.4 115.6 1.0 CG2 b:THR61 3.5 103.3 1.0 CB b:CYS56 3.8 108.5 1.0 CB b:CYS59 4.1 116.7 1.0 CA b:THR61 4.4 103.3 1.0 N b:CYS40 4.5 115.6 1.0 OG b:SER58 4.5 119.3 1.0 O b:CYS59 4.5 116.7 1.0 O b:THR61 4.6 103.3 1.0 SG b:CYS56 4.6 108.5 1.0 N b:THR61 4.7 103.3 1.0 CA b:CYS37 4.7 102.5 1.0 C b:CYS59 4.8 116.7 1.0 CA b:CYS59 4.8 116.7 1.0 CB b:CYS40 4.9 115.6 1.0 N b:CYS59 4.9 116.7 1.0 C b:THR61 5.0 103.3 1.0 N b:GLY39 5.0 114.8 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:204.7 occ:1.00 SG f:CYS142 2.3 133.4 1.0 SG f:CYS124 2.3 125.2 1.0 SG f:CYS139 2.3 136.1 1.0 SG f:CYS121 2.3 126.8 1.0 CB f:CYS139 3.6 136.1 1.0 N f:CYS142 3.7 133.4 1.0 CB f:CYS121 3.7 126.8 1.0 CB f:CYS142 3.7 133.4 1.0 CB f:CYS124 3.9 125.2 1.0 CA f:CYS142 4.1 133.4 1.0 O f:CYS142 4.3 133.4 1.0 CD2 f:PHE146 4.3 128.9 1.0 N f:CYS124 4.4 125.2 1.0 C f:CYS142 4.4 133.4 1.0 CB f:PHE146 4.5 128.9 1.0 CB f:LYS141 4.6 120.0 1.0 CA f:CYS124 4.7 125.2 1.0 N f:LYS141 4.7 120.0 1.0 C f:LYS141 4.7 120.0 1.0 CA f:CYS139 4.8 136.1 1.0 CG f:PHE146 4.8 128.9 1.0 CA f:LYS141 4.9 120.0 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-3.2)


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-3.2) within 5.0Å range: probe atom residue distance (Å) B Occ k:Zn602 b:188.6 occ:1.00 NE2 k:GLN286 4.6 161.0 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