Zinc in PDB 5it9: Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.

The structure of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. also contains other interesting chemical elements:

Magnesium

(Mg)

80 atoms

The binding sites of Zinc atom in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. (pdb code 5it9). 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 the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires., PDB code: 5it9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:10.1 occ:1.00 SG a:CYS23 2.0 10.8 1.0 CB a:CYS77 2.8 13.3 1.0 SG a:CYS74 2.8 13.5 1.0 SG a:CYS26 2.8 9.6 1.0 CB a:CYS26 3.0 9.6 1.0 CB a:CYS23 3.2 10.8 1.0 SG a:CYS77 3.2 13.3 1.0 N a:CYS26 3.3 9.7 1.0 N a:CYS74 3.4 13.8 1.0 CB a:CYS74 3.4 13.4 1.0 CA a:CYS26 3.7 9.6 1.0 CA a:CYS74 3.8 13.4 1.0 O a:CYS74 4.0 13.1 1.0 CB a:ASN25 4.2 10.0 1.0 CA a:CYS77 4.3 13.3 1.0 C a:ASN25 4.3 9.8 1.0 N a:ASN25 4.4 10.1 1.0 C a:CYS74 4.4 13.1 1.0 C a:TYR73 4.4 14.3 1.0 CA a:ASN25 4.6 10.0 1.0 CA a:CYS23 4.6 10.8 1.0 CA a:TYR73 4.6 14.9 1.0 N a:SER27 4.7 9.3 1.0 C a:CYS26 4.7 9.5 1.0 N a:CYS77 4.7 13.1 1.0 CB a:ARG28 4.9 8.9 1.0 C a:CYS23 5.0 10.7 1.0 N a:VAL24 5.0 10.6 1.0

Zinc binding site 2 out of 3 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:0.8 occ:1.00 SG b:CYS59 2.5 0.5 1.0 SG b:CYS40 3.0 0.7 1.0 CB b:CYS59 3.3 0.2 1.0 OG b:SER58 3.3 0.4 1.0 N b:CYS59 3.5 0.1 1.0 SG b:CYS56 3.7 0.8 1.0 CB b:CYS40 3.9 0.2 1.0 CG b:GLU57 4.0 0.3 1.0 CA b:CYS59 4.0 0.6 1.0 CD b:GLU57 4.2 1.0 1.0 CB b:CYS56 4.2 0.5 1.0 N b:SER58 4.3 0.1 1.0 OE1 b:GLU57 4.5 0.1 1.0 CB b:SER58 4.5 0.8 1.0 C b:SER58 4.6 0.1 1.0 OE2 b:GLU57 4.6 0.6 1.0 CA b:SER58 4.7 0.3 1.0 N b:GLU57 4.9 0.7 1.0

Zinc binding site 3 out of 3 in the Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Yeast Kluyveromyces Lactis Small Ribosomal Subunit in Complex with the Cricket Paralysis Virus Ires. within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn501 b:0.9 occ:1.00 CB f:CYS139 3.2 0.6 1.0 CB f:CYS142 3.3 0.3 1.0 SG f:CYS142 3.3 0.7 1.0 N f:CYS142 3.5 0.1 1.0 SG f:CYS121 3.6 0.3 1.0 CA f:CYS142 4.0 0.7 1.0 O f:CYS139 4.2 0.6 1.0 C f:CYS139 4.3 0.7 1.0 CA f:CYS139 4.3 0.7 1.0 SG f:CYS139 4.3 0.8 1.0 CZ f:PHE146 4.3 0.4 1.0 OG1 f:THR145 4.3 0.2 1.0 SG f:CYS124 4.4 0.2 1.0 C f:LYS141 4.6 0.3 1.0 N f:LYS141 4.6 0.2 1.0 CE1 f:PHE146 4.7 0.1 1.0 CB f:CYS121 4.7 0.7 1.0 C f:CYS142 4.7 0.2 1.0 CB f:LYS141 4.8 0.0 1.0 N f:GLY140 4.8 0.3 1.0 O f:CYS142 4.9 0.4 1.0 CA f:LYS141 4.9 0.2 1.0 N f:CYS139 4.9 0.5 1.0 CE2 f:PHE146 4.9 0.4 1.0 CB f:CYS124 5.0 0.7 1.0

J.Murray, C.G.Savva, B.S.Shin, T.E.Dever, V.Ramakrishnan, I.S.Fernandez. Structural Characterization of Ribosome Recruitment and Translocation By Type IV Ires. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27159451
DOI: 10.7554/ELIFE.13567