Zinc in PDB 3j81: Cryoem Structure of A Partial Yeast 48S Preinitiation Complex

The structure of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex also contains other interesting chemical elements:

Magnesium

(Mg)

81 atoms

The binding sites of Zinc atom in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex (pdb code 3j81). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex, PDB code: 3j81:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn500 b:0.4 occ:1.00 SG a:CYS23 2.3 0.1 1.0 SG a:CYS74 2.5 83.3 1.0 SG a:CYS26 2.6 0.9 1.0 CB a:CYS77 3.1 0.7 1.0 CB a:CYS74 3.2 87.5 1.0 N a:CYS74 3.3 97.8 1.0 O a:CYS74 3.3 90.0 1.0 CB a:CYS23 3.4 0.9 1.0 OD1 a:ASN25 3.4 0.8 1.0 CA a:CYS74 3.6 90.1 1.0 N a:CYS77 3.6 93.8 1.0 CA a:CYS77 3.7 96.1 1.0 C a:CYS74 3.8 89.0 1.0 C a:CYS77 4.0 92.7 1.0 C a:TYR73 4.2 1.0 1.0 CB a:CYS26 4.2 0.3 1.0 O a:CYS77 4.3 91.9 1.0 SG a:CYS77 4.3 0.1 1.0 N a:ALA78 4.5 94.4 1.0 N a:CYS26 4.6 0.2 1.0 CG a:ASN25 4.6 0.1 1.0 CA a:TYR73 4.7 0.3 1.0 CA a:CYS23 4.8 0.2 1.0 O a:HIS72 4.9 0.5 1.0 CG a:ARG28 4.9 1.0 1.0 C a:SER76 4.9 92.3 1.0 CA a:CYS26 5.0 0.6 1.0

Zinc binding site 2 out of 3 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:0.0 occ:1.00 CA b:GLY39 3.2 0.7 1.0 N b:GLY39 3.6 0.0 1.0 OG1 b:THR61 3.8 0.2 1.0 SG b:CYS59 4.1 0.6 1.0 CG2 b:THR61 4.2 0.2 1.0 C b:GLY39 4.2 0.8 1.0 N b:CYS40 4.4 0.8 1.0 CB b:THR61 4.4 0.2 1.0 C b:PRO38 4.7 1.0 1.0

Zinc binding site 3 out of 3 in the Cryoem Structure of A Partial Yeast 48S Preinitiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of A Partial Yeast 48S Preinitiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:0.7 occ:1.00 SG f:CYS124 2.5 0.2 1.0 SG f:CYS121 3.1 0.2 1.0 CB f:CYS142 3.3 0.7 1.0 SG f:CYS139 3.3 0.6 1.0 CB f:CYS139 3.5 0.6 1.0 CB f:PHE146 3.6 20.0 1.0 O f:CYS142 3.7 0.7 1.0 CD1 f:PHE146 3.8 20.0 1.0 CG f:PHE146 3.8 20.0 1.0 OG1 f:THR145 4.0 20.0 1.0 CB f:CYS124 4.0 0.4 1.0 CA f:CYS142 4.2 1.0 1.0 C f:CYS142 4.3 1.0 1.0 SG f:CYS142 4.4 0.1 1.0 N f:CYS142 4.4 1.0 1.0 CB f:CYS121 4.4 1.0 1.0 N f:CYS124 4.5 0.6 1.0 CE1 f:PHE146 4.7 20.0 1.0 CB f:ASN123 4.7 0.1 1.0 CA f:PHE146 4.8 0.0 1.0 CD2 f:PHE146 4.8 20.0 1.0 CA f:CYS124 4.8 0.8 1.0 N f:PHE146 4.8 0.0 1.0

T.Hussain, J.L.Llacer, I.S.Fernandez, A.Munoz, P.Martin-Marcos, C.G.Savva, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan. Structural Changes Enable Start Codon Recognition By the Eukaryotic Translation Initiation Complex Cell(Cambridge,Mass.) V. 159 597 2014.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2014.10.001