Zinc in PDB 6zxh: Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2

All present enzymatic activity of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2:
2.7.11.1; 4.2.99.18;

The structure of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 also contains other interesting chemical elements:

Magnesium

(Mg)

131 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 (pdb code 6zxh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2, PDB code: 6zxh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range: probe atom residue distance (Å) B Occ h:Zn201 b:28.4 occ:1.00 SG h:CYS26 2.4 6.8 1.0 SG h:CYS74 2.4 5.8 1.0 SG h:CYS77 2.5 6.4 1.0 SG h:CYS23 2.5 5.8 1.0 CB h:CYS23 3.2 5.8 1.0 CB h:CYS26 3.3 6.8 1.0 CB h:CYS77 3.5 6.4 1.0 CB h:CYS74 3.6 5.8 1.0 N h:CYS26 3.7 6.8 1.0 CA h:CYS26 4.1 6.8 1.0 N h:CYS74 4.2 5.8 1.0 CA h:CYS74 4.5 5.8 1.0 CB h:ARG28 4.5 5.8 1.0 CB h:ASN25 4.5 7.1 1.0 N h:CYS77 4.5 6.4 1.0 ND2 h:ASN25 4.6 7.1 1.0 CA h:CYS77 4.6 6.4 1.0 C h:CYS26 4.6 6.8 1.0 CA h:CYS23 4.7 5.8 1.0 O h:CYS74 4.8 5.8 1.0 N h:ARG28 4.8 5.8 1.0 N h:ALA27 4.8 5.8 1.0 C h:ASN25 4.8 7.1 1.0 C h:CYS74 5.0 5.8 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn101 b:27.8 occ:1.00 SG d:CYS42 2.4 5.8 1.0 SG d:CYS39 2.4 5.8 1.0 SG d:CYS24 2.4 5.8 1.0 SG d:CYS21 2.9 5.8 1.0 CB d:CYS42 3.2 5.8 1.0 CB d:CYS24 3.5 5.8 1.0 CB d:CYS39 3.6 5.8 1.0 CB d:CYS21 3.7 5.8 1.0 N d:CYS42 4.1 5.8 1.0 N d:CYS24 4.2 5.8 1.0 CA d:CYS42 4.3 5.8 1.0 O2' 2:G1495 4.3 5.8 1.0 N d:CYS39 4.3 5.8 1.0 CA d:CYS24 4.4 5.8 1.0 CA d:CYS39 4.5 5.8 1.0 N3 2:G1495 4.7 5.8 1.0 CB d:VAL23 4.7 5.8 1.0 O d:CYS39 4.7 5.8 1.0 N2 2:G1495 4.8 5.8 1.0 C d:CYS39 4.9 5.8 1.0 CB d:ASN26 4.9 5.8 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:47.2 occ:1.00 SG f:CYS144 2.4 24.8 1.0 SG f:CYS121 2.4 21.9 1.0 SG f:CYS126 2.4 26.8 1.0 SG f:CYS141 2.5 22.0 1.0 CB f:CYS126 2.5 26.8 1.0 CB f:CYS144 3.4 24.8 1.0 CB f:CYS121 3.5 21.9 1.0 CB f:CYS141 3.5 22.0 1.0 CA f:CYS126 3.9 26.8 1.0 N f:CYS144 4.1 24.8 1.0 CB f:SER123 4.2 21.1 1.0 N f:CYS126 4.2 26.8 1.0 CA f:CYS144 4.3 24.8 1.0 O f:CYS126 4.4 26.8 1.0 C f:CYS126 4.6 26.8 1.0 CA f:CYS121 4.9 21.9 1.0 CB f:LEU146 4.9 22.4 1.0 OG f:SER123 4.9 21.1 1.0 C f:LYS143 4.9 23.8 1.0 CB f:LYS143 4.9 23.8 1.0 CA f:CYS141 4.9 22.0 1.0 C f:CYS144 5.0 24.8 1.0

M.Ameismeier, I.Zemp, J.Van Den Heuvel, M.Thoms, O.Berninghausen, U.Kutay, R.Beckmann. Structural Basis For the Final Steps of Human 40S Ribosome Maturation. Nature V. 587 683 2020.
ISSN: ESSN 1476-4687
PubMed: 33208940
DOI: 10.1038/S41586-020-2929-X