Zinc in PDB 8s8g: Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1)

All present enzymatic activity of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1):
3.6.5.3;

The structure of Structure of A Yeast 48S-Auc Preinitiation Complex in Closed Conformation (Model PY48S-Auc-2.1) 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-2.1) (pdb code 8s8g). 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-2.1), PDB code: 8s8g:
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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:72.5 occ:1.00 SG a:CYS74 2.3 44.0 1.0 SG a:CYS26 2.3 45.2 1.0 SG a:CYS77 2.3 46.4 1.0 SG a:CYS23 2.3 43.4 1.0 CB a:CYS77 3.1 46.4 1.0 CB a:CYS26 3.1 45.2 1.0 CB a:CYS74 3.1 44.0 1.0 N a:CYS26 3.4 45.2 1.0 CB a:CYS23 3.5 43.4 1.0 N a:CYS74 3.6 44.0 1.0 CA a:CYS26 3.8 45.2 1.0 CA a:CYS74 3.9 44.0 1.0 N a:CYS77 4.0 46.4 1.0 CA a:CYS77 4.1 46.4 1.0 C a:CYS26 4.4 45.2 1.0 CB a:ARG28 4.4 50.9 1.0 O a:CYS74 4.5 44.0 1.0 C a:CYS74 4.5 44.0 1.0 CB a:ASN25 4.5 45.2 1.0 C a:ASN25 4.6 45.2 1.0 N a:SER27 4.7 43.1 1.0 N a:ARG28 4.8 50.9 1.0 N a:ASN25 4.8 45.2 1.0 C a:TYR73 4.8 47.0 1.0 CA a:ASN25 4.9 45.2 1.0 CA a:CYS23 4.9 43.4 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:210.8 occ:1.00 CB b:CYS56 2.3 142.5 1.0 SG b:CYS56 2.3 142.5 1.0 SG b:CYS59 2.3 150.6 1.0 OG b:SER58 2.8 147.0 1.0 OG1 b:THR61 3.1 128.4 1.0 N b:CYS59 3.3 150.6 1.0 O b:CYS59 3.4 150.6 1.0 SG b:CYS40 3.6 114.5 1.0 CB b:CYS59 3.7 150.6 1.0 CA b:CYS56 3.7 142.5 1.0 CA b:CYS59 3.8 150.6 1.0 C b:CYS59 3.9 150.6 1.0 CB b:SER58 4.1 147.0 1.0 C b:CYS56 4.1 142.5 1.0 C b:SER58 4.2 147.0 1.0 N b:SER58 4.2 147.0 1.0 CB b:THR61 4.3 128.4 1.0 CA b:SER58 4.4 147.0 1.0 CG2 b:THR61 4.4 128.4 1.0 N b:CYS56 4.4 142.5 1.0 O b:CYS56 4.5 142.5 1.0 CB b:CYS40 4.7 114.5 1.0 N b:CYS40 4.7 114.5 1.0 N b:GLU57 4.8 141.8 1.0 SG b:CYS37 4.8 110.4 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-2.1)


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-2.1) within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:197.1 occ:1.00 SG f:CYS139 2.3 162.6 1.0 SG f:CYS142 2.3 167.3 1.0 SG f:CYS121 2.3 145.4 1.0 CB f:CYS139 3.1 162.6 1.0 CB f:PHE146 3.7 155.2 1.0 CB f:ASN123 3.9 132.6 1.0 CG f:PHE146 4.0 155.2 1.0 CB f:CYS142 4.0 167.3 1.0 CB f:CYS121 4.0 145.4 1.0 O f:CYS142 4.0 167.3 1.0 CA f:CYS139 4.2 162.6 1.0 CD2 f:PHE146 4.3 155.2 1.0 N f:CYS142 4.4 167.3 1.0 N f:ASN123 4.4 132.6 1.0 C f:CYS142 4.5 167.3 1.0 CA f:CYS142 4.5 167.3 1.0 CD2 f:LEU130 4.5 155.0 1.0 N f:CYS124 4.6 136.0 1.0 CD1 f:PHE146 4.7 155.2 1.0 CA f:ASN123 4.7 132.6 1.0 CD f:PRO122 4.7 136.4 1.0 CA f:CYS121 4.9 145.4 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