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

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

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State G (pdb code 6zxf). 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 G, PDB code: 6zxf:
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 G


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 G within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn101 b:67.8 occ:1.00 SG d:CYS21 2.4 40.1 1.0 SG d:CYS39 2.4 42.7 1.0 SG d:CYS24 2.4 42.2 1.0 SG d:CYS42 2.4 39.6 1.0 CB d:CYS39 3.0 42.7 1.0 CB d:CYS42 3.0 39.6 1.0 N d:CYS39 3.2 42.7 1.0 CB d:CYS21 3.3 40.1 1.0 CB d:CYS24 3.5 42.2 1.0 CA d:CYS39 3.6 42.7 1.0 O d:CYS39 4.0 42.7 1.0 N d:CYS24 4.0 42.2 1.0 C d:CYS39 4.2 42.7 1.0 CG1 d:VAL23 4.2 40.8 1.0 CA d:CYS42 4.3 39.6 1.0 N d:CYS42 4.3 39.6 1.0 CA d:CYS24 4.4 42.2 1.0 C d:MET38 4.4 40.3 1.0 CA d:CYS21 4.6 40.1 1.0 CA d:MET38 4.7 40.3 1.0 CB d:MET38 5.0 40.3 1.0 C d:CYS24 5.0 42.2 1.0

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


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 G within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn500 b:0.2 occ:1.00 N f:CYS144 2.2 0.8 1.0 SG f:CYS144 2.5 0.8 1.0 SG f:CYS141 2.6 0.2 1.0 CB f:CYS144 2.7 0.8 1.0 CA f:CYS144 2.9 0.8 1.0 C f:LYS143 3.0 0.3 1.0 CB f:LYS143 3.1 0.3 1.0 CA f:LYS143 3.3 0.3 1.0 N f:LYS143 3.6 0.3 1.0 SG f:CYS121 3.6 0.4 1.0 CB f:CYS141 3.7 0.2 1.0 O f:LYS143 4.0 0.3 1.0 CG f:LYS143 4.1 0.3 1.0 C f:CYS144 4.1 0.8 1.0 N f:CYS145 4.5 1.0 1.0 CD f:LYS143 4.6 0.3 1.0 CB f:CYS121 4.7 0.4 1.0 C f:CYS141 4.8 0.2 1.0 O f:CYS141 4.8 0.2 1.0 C f:GLY142 4.8 0.4 1.0 CA f:CYS141 4.9 0.2 1.0 CE f:LYS143 4.9 0.3 1.0 CB f:CYS126 5.0 0.6 1.0 OG f:SER123 5.0 0.1 1.0 O f:CYS144 5.0 0.8 1.0

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


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 G within 5.0Å range: probe atom residue distance (Å) B Occ y:Zn500 b:0.7 occ:1.00 SG y:CYS270 2.3 57.2 1.0 SG y:CYS285 2.4 59.7 1.0 SG y:CYS273 2.4 63.1 1.0 CB y:CYS288 2.4 65.0 1.0 SG y:CYS288 2.4 65.0 1.0 N y:CYS288 2.9 65.0 1.0 CA y:CYS288 3.2 65.0 1.0 CB y:CYS270 3.2 57.2 1.0 CB y:CYS285 3.3 59.7 1.0 CB y:CYS273 3.5 63.1 1.0 N y:CYS273 3.9 63.1 1.0 OG1 y:THR292 4.0 52.8 1.0 N y:GLY289 4.2 58.1 1.0 C y:HIS287 4.2 66.0 1.0 C y:CYS288 4.2 65.0 1.0 CA y:CYS273 4.3 63.1 1.0 N y:HIS287 4.6 66.0 1.0 CB y:HIS287 4.6 66.0 1.0 CA y:CYS285 4.7 59.7 1.0 CA y:HIS287 4.7 66.0 1.0 CA y:CYS270 4.7 57.2 1.0 C y:CYS285 4.9 59.7 1.0 C y:GLY272 4.9 54.1 1.0 C y:CYS273 5.0 63.1 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