Zinc in PDB 9bkd: The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit

All present enzymatic activity of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit:
4.2.99.18;

The structure of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit also contains other interesting chemical elements:

Potassium	(K)	19 atoms
Magnesium	(Mg)	88 atoms

The binding sites of Zinc atom in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit (pdb code 9bkd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit, PDB code: 9bkd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn201 b:73.3 occ:1.00 SG Q:CYS26 2.3 38.2 1.0 SG Q:CYS74 2.3 27.4 1.0 SG Q:CYS77 2.3 41.6 1.0 SG Q:CYS23 2.3 30.6 1.0 CB Q:CYS77 3.1 14.2 1.0 CB Q:CYS23 3.2 8.3 1.0 CB Q:CYS26 3.4 13.9 1.0 CB Q:CYS74 3.6 7.7 1.0 N Q:CYS26 3.8 15.0 1.0 N Q:CYS74 4.1 13.5 1.0 CA Q:CYS26 4.1 9.8 1.0 N Q:CYS77 4.3 16.6 1.0 CA Q:CYS77 4.3 5.7 1.0 CB Q:ASN25 4.3 15.2 1.0 CA Q:CYS74 4.4 8.3 1.0 CB Q:ARG28 4.6 14.7 1.0 CA Q:CYS23 4.7 11.6 1.0 C Q:ASN25 4.7 21.4 1.0 C Q:CYS26 4.8 21.7 1.0 N Q:ALA27 4.9 19.6 1.0 N Q:ARG28 4.9 18.6 1.0 CA Q:ASN25 4.9 14.2 1.0 O Q:CYS74 4.9 22.9 1.0 N Q:ASN25 4.9 19.3 1.0 C Q:CYS74 5.0 18.6 1.0

Zinc binding site 2 out of 3 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ i:Zn101 b:77.0 occ:1.00 SG i:CYS24 2.3 44.8 1.0 SG i:CYS21 2.3 39.6 1.0 SG i:CYS39 2.3 60.3 1.0 SG i:CYS42 2.3 41.8 1.0 CB i:CYS39 2.9 28.8 1.0 CB i:CYS21 3.1 30.1 1.0 CB i:CYS24 3.4 35.9 1.0 CB i:CYS42 3.5 29.9 1.0 N i:CYS39 3.8 33.3 1.0 N i:CYS24 3.9 37.9 1.0 CA i:CYS39 3.9 28.2 1.0 CA i:CYS24 4.2 32.2 1.0 CB i:VAL23 4.5 33.6 1.0 CA i:CYS21 4.5 30.7 1.0 N i:CYS42 4.6 29.0 1.0 O2' A:G1495 4.6 30.6 1.0 CA i:CYS42 4.7 25.8 1.0 C i:CYS24 4.7 33.0 1.0 CB i:ASN26 4.8 28.9 1.0 N i:SER25 4.8 37.7 1.0 C i:VAL23 4.9 32.3 1.0 N i:ASN26 4.9 34.7 1.0 C i:MET38 5.0 33.3 1.0

Zinc binding site 3 out of 3 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ k:Zn201 b:145.9 occ:1.00 SG k:CYS144 2.3 109.4 1.0 SG k:CYS126 2.3 104.3 1.0 SG k:CYS141 2.3 111.9 1.0 SG k:CYS121 2.3 108.9 1.0 CB k:CYS126 3.2 99.2 1.0 CB k:CYS144 3.2 107.1 1.0 CB k:CYS121 3.3 103.2 1.0 CB k:CYS141 3.4 108.1 1.0 N k:CYS144 3.8 107.1 1.0 CA k:CYS144 4.1 107.6 1.0 CB k:LYS143 4.4 107.6 1.0 CB k:SER123 4.4 97.0 1.0 C k:LYS143 4.4 107.2 1.0 O k:CYS121 4.5 101.4 1.0 CA k:CYS126 4.6 99.3 1.0 CG1 k:VAL130 4.7 99.3 1.0 CG2 k:VAL130 4.7 100.5 1.0 CA k:CYS121 4.7 102.8 1.0 OG k:SER123 4.8 96.5 1.0 CA k:LYS143 4.8 106.6 1.0 N k:LYS143 4.8 107.6 1.0 CA k:CYS141 4.8 109.2 1.0 C k:CYS121 4.9 102.1 1.0

J.Brito Querido, M.Sokabe, I.Diaz-Lopez, Y.Gordiyenko, P.Zuber, Y.Du, L.Albacete-Albacete, V.Ramakrishnan, C.S.Fraser. Human Tumor Suppressor Protein PDCD4 Binds at the Mrna Entry Channel in the 40S Small Ribosomal Subunit. Nat Commun V. 15 6633 2024.
ISSN: ESSN 2041-1723
PubMed: 39117603
DOI: 10.1038/S41467-024-50672-8