Magnesium 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:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State G, PDB code: 6zxf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 z:Mg601 b:53.1 occ:1.00 O2B z:ATP603 2.0 56.6 1.0 O2G z:ATP603 2.1 56.6 1.0 OE1 z:GLU191 2.2 65.6 1.0 O1G z:ATP603 2.2 56.6 1.0 OD2 z:ASP341 2.3 56.9 1.0 PG z:ATP603 2.3 56.6 1.0 PB z:ATP603 2.4 56.6 1.0 MG z:MG602 2.5 56.5 1.0 O3B z:ATP603 2.6 56.6 1.0 CD z:GLU191 3.0 65.6 1.0 O1B z:ATP603 3.1 56.6 1.0 CG z:ASP341 3.1 56.9 1.0 OD1 z:ASP341 3.5 56.9 1.0 OE2 z:GLU191 3.8 65.6 1.0 CG z:GLU191 3.8 65.6 1.0 O3G z:ATP603 3.8 56.6 1.0 CE z:LYS190 3.9 47.2 1.0 O3A z:ATP603 3.9 56.6 1.0 ND2 z:ASN329 4.0 65.6 1.0 O2A z:ATP603 4.0 56.6 1.0 CB z:ASP341 4.2 56.9 1.0 PA z:ATP603 4.4 56.6 1.0 OD1 z:ASN329 4.4 65.6 1.0 CG z:LYS190 4.4 47.2 1.0 NZ z:LYS190 4.5 47.2 1.0 CD z:LYS190 4.6 47.2 1.0 CG z:ASN329 4.6 65.6 1.0 OE1 z:GLN344 4.6 65.6 1.0 CB z:GLU191 4.7 65.6 1.0 O1A z:ATP603 4.8 56.6 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 z:Mg602 b:56.5 occ:1.00 O2G z:ATP603 1.9 56.6 1.0 O2A z:ATP603 2.0 56.6 1.0 O3B z:ATP603 2.0 56.6 1.0 OD1 z:ASN329 2.3 65.6 1.0 O2B z:ATP603 2.4 56.6 1.0 PG z:ATP603 2.4 56.6 1.0 MG z:MG601 2.5 53.1 1.0 PB z:ATP603 2.7 56.6 1.0 OD2 z:ASP341 2.8 56.9 1.0 PA z:ATP603 3.1 56.6 1.0 CG z:ASN329 3.1 65.6 1.0 ND2 z:ASN329 3.2 65.6 1.0 O3A z:ATP603 3.2 56.6 1.0 CG z:ASP341 3.3 56.9 1.0 O3G z:ATP603 3.4 56.6 1.0 CB z:ASP341 3.5 56.9 1.0 O1G z:ATP603 3.6 56.6 1.0 O1A z:ATP603 4.0 56.6 1.0 O1B z:ATP603 4.0 56.6 1.0 OD1 z:ASP341 4.2 56.9 1.0 O5' z:ATP603 4.3 56.6 1.0 OE1 z:GLU191 4.5 65.6 1.0 CB z:ASN329 4.5 65.6 1.0 C5' z:ATP603 4.5 56.6 1.0 O z:PHE328 4.6 65.6 1.0 CA z:ASP341 4.9 65.6 1.0 CD1 z:ILE340 5.0 65.6 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