Zinc in PDB 9fhl: High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna

The structure of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna also contains other interesting chemical elements:

Magnesium

(Mg)

59 atoms

The binding sites of Zinc atom in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna (pdb code 9fhl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna, PDB code: 9fhl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:68.4 occ:1.00 SG C:CYS60 2.0 44.8 1.0 SG C:CYS57 2.1 38.4 1.0 SG C:CYS34 2.3 34.8 1.0 CB C:CYS60 2.7 40.5 1.0 SG C:CYS37 2.8 43.0 1.0 CB C:CYS57 3.0 34.0 1.0 CB C:CYS34 3.2 30.5 1.0 CB C:CYS37 3.3 35.2 1.0 N C:CYS37 3.6 33.2 1.0 CA C:CYS60 3.7 33.0 1.0 N C:CYS60 3.8 36.5 1.0 CA C:CYS37 4.1 34.0 1.0 CB C:PHE62 4.2 33.1 1.0 C C:CYS60 4.3 37.9 1.0 CB C:ASN36 4.3 35.4 1.0 N C:GLY61 4.4 37.1 1.0 CA C:CYS57 4.4 31.9 1.0 N C:PHE62 4.4 33.4 1.0 OD1 C:ASN59 4.6 46.0 1.0 C C:ASN36 4.6 36.5 1.0 CA C:CYS34 4.7 31.8 1.0 N C:GLY38 4.7 41.2 1.0 CA C:ASN36 4.8 34.7 1.0 N C:ASN36 4.8 36.6 1.0 ND2 C:ASN59 4.9 39.9 1.0 C C:CYS37 4.9 37.2 1.0 CG C:ASN59 4.9 39.2 1.0 CA C:PHE62 5.0 29.5 1.0

Zinc binding site 2 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:53.1 occ:1.00 OD2 C:ASP45 2.1 26.5 1.0 SG C:CYS48 2.3 23.4 1.0 SG C:CYS16 2.3 22.0 1.0 SG C:CYS19 2.3 40.2 1.0 CB C:CYS48 2.9 13.9 1.0 CG C:ASP45 2.9 17.6 1.0 CB C:CYS19 3.1 15.6 1.0 CB C:CYS16 3.2 10.9 1.0 OG C:SER18 3.4 18.5 1.0 OD1 C:ASP45 3.4 20.8 1.0 N C:CYS19 3.6 22.1 1.0 CA C:CYS19 3.9 14.6 1.0 CB C:ASP45 4.1 12.7 1.0 N C:ASP45 4.1 19.0 1.0 CA C:CYS48 4.1 14.4 1.0 N C:CYS48 4.2 8.8 1.0 NE I:ARG21 4.2 32.8 1.0 CD I:ARG21 4.5 29.7 1.0 CA C:ASP45 4.6 12.4 1.0 CA C:CYS16 4.7 18.9 1.0 CB C:SER18 4.7 13.7 1.0 C C:SER18 4.8 20.7 1.0 C C:CYS19 4.8 14.3 1.0 N C:GLY20 4.8 17.4 1.0 O C:ASP45 4.8 15.4 1.0

Zinc binding site 3 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:63.6 occ:1.00 CB F:CYS128 1.6 34.0 1.0 NE2 F:HIS132 2.1 19.2 1.0 SG F:CYS121 2.3 28.9 1.0 SG F:CYS126 2.3 25.1 1.0 SG F:CYS128 2.3 35.2 1.0 CD2 F:HIS132 2.9 11.7 1.0 CA F:CYS128 3.0 35.4 1.0 CE1 F:HIS132 3.1 12.5 1.0 CB F:CYS126 3.4 21.8 1.0 CB F:CYS121 3.4 22.3 1.0 N F:CYS128 3.4 28.9 1.0 O F:HOH407 3.8 30.0 1.0 C F:CYS128 3.9 32.6 1.0 N F:GLY129 4.0 33.5 1.0 CG F:HIS132 4.1 21.9 1.0 ND1 F:HIS132 4.1 22.1 1.0 CD F:LYS154 4.2 26.4 1.0 CA F:CYS121 4.4 19.4 1.0 CA F:CYS126 4.6 21.8 1.0 N F:LYS154 4.6 10.4 1.0 CG F:LYS154 4.6 23.0 1.0 C F:CYS126 4.6 26.8 1.0 O F:GLU130 4.7 33.3 1.0 C F:THR127 4.8 32.0 1.0 OD2 D:ASP91 4.8 53.3 1.0 N F:GLU130 4.8 30.6 1.0 O F:CYS126 4.8 35.2 1.0 O F:CYS128 4.9 34.4 1.0 N F:THR127 5.0 33.7 1.0 CB F:LYS154 5.0 17.9 1.0

Zinc binding site 4 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:55.8 occ:1.00 SG P:CYS22 2.3 32.5 1.0 SG P:CYS40 2.3 25.3 1.0 SG P:CYS37 2.3 31.0 1.0 CB P:CYS40 2.8 24.5 1.0 SG P:CYS19 2.8 35.3 1.0 CB P:CYS19 3.4 23.8 1.0 CB P:CYS22 3.4 27.0 1.0 CB P:CYS37 3.5 20.5 1.0 N P:CYS37 3.9 30.2 1.0 N P:CYS22 4.0 23.7 1.0 O2' 2:G1165 4.0 39.0 1.0 CA P:CYS40 4.1 18.6 1.0 CA P:CYS37 4.2 20.1 1.0 CA P:CYS22 4.3 26.1 1.0 N P:CYS40 4.3 20.2 1.0 CB P:ARG21 4.6 23.2 1.0 CB P:SER24 4.7 27.1 1.0 O P:CYS37 4.8 32.9 1.0 C P:ARG21 4.8 26.8 1.0 C P:CYS37 4.8 28.8 1.0 CA P:CYS19 4.9 24.0 1.0 C2' 2:G1165 4.9 37.2 1.0 N2 2:G1165 4.9 38.8 1.0 C P:CYS22 4.9 26.1 1.0 N3 2:G1165 4.9 37.9 1.0

Zinc binding site 5 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:61.4 occ:1.00 ND1 R:HIS31 2.1 30.2 1.0 SG R:CYS23 2.3 39.1 1.0 SG R:CYS84 2.3 39.1 1.0 SG R:CYS28 2.3 29.5 1.0 CE1 R:HIS31 2.8 24.1 1.0 CB R:CYS84 3.1 31.1 1.0 CG R:HIS31 3.2 31.2 1.0 CB R:CYS28 3.3 26.6 1.0 CB R:CYS23 3.6 36.7 1.0 CB R:HIS31 3.8 25.2 1.0 NE2 R:HIS31 4.0 28.1 1.0 N R:CYS23 4.0 33.4 1.0 N R:HIS31 4.1 24.8 1.0 CD2 R:HIS31 4.2 29.4 1.0 OD2 R:ASP25 4.3 43.5 1.0 CA R:CYS84 4.3 31.3 1.0 CB R:PRO82 4.3 25.0 1.0 N R:CYS84 4.3 33.3 1.0 CA R:CYS23 4.3 35.1 1.0 CB R:TYR30 4.4 23.3 1.0 CA R:HIS31 4.6 26.5 1.0 CA R:CYS28 4.7 24.9 1.0 CD2 R:TYR30 4.7 24.7 1.0 C R:CYS23 4.9 36.5 1.0 C R:TYR30 4.9 27.1 1.0 N R:TYR30 5.0 31.8 1.0 O R:CYS23 5.0 34.5 1.0 CA R:TYR30 5.0 24.9 1.0

Zinc binding site 6 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:84.4 occ:1.00 SG W:CYS43 2.3 59.8 1.0 SG W:CYS40 2.3 63.2 1.0 SG W:CYS24 2.3 59.4 1.0 SG W:CYS21 2.3 61.8 1.0 CB W:CYS21 3.2 47.9 1.0 CB W:CYS40 3.2 45.2 1.0 CB W:CYS43 3.4 51.0 1.0 CB W:CYS24 3.6 51.1 1.0 OG W:SER42 3.9 53.3 1.0 N W:CYS24 3.9 53.9 1.0 N W:CYS43 4.0 51.0 1.0 CA W:CYS43 4.2 50.3 1.0 CG2 W:THR45 4.3 42.9 1.0 CA W:CYS24 4.3 54.0 1.0 CB W:ASN23 4.4 56.7 1.0 CB W:ASN26 4.4 52.1 1.0 CA W:CYS40 4.6 47.5 1.0 CA W:CYS21 4.6 47.2 1.0 N W:ASN26 4.7 54.8 1.0 C W:ASN23 4.8 55.9 1.0 C W:CYS24 4.8 57.9 1.0 N W:GLY25 4.8 55.0 1.0 N W:GLY44 4.9 51.0 1.0 C W:CYS43 4.9 54.5 1.0 N W:ASN23 4.9 56.0 1.0 CA W:ASN23 4.9 56.3 1.0 ND2 W:ASN23 5.0 57.3 1.0

Zinc binding site 7 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn101 b:52.1 occ:1.00 SG a:CYS38 2.0 50.5 1.0 SG a:CYS61 2.2 43.6 1.0 SG a:CYS41 2.3 46.2 1.0 SG a:CYS64 2.4 46.7 1.0 CB a:CYS61 3.2 44.1 1.0 CB a:CYS38 3.4 41.0 1.0 CB a:CYS64 3.5 39.3 1.0 N a:CYS41 3.8 45.8 1.0 CB a:CYS41 3.9 46.5 1.0 N a:CYS64 4.0 35.8 1.0 CB a:LYS40 4.2 49.5 1.0 OG1 a:THR66 4.2 41.2 1.0 CA a:CYS64 4.3 38.7 1.0 CA a:CYS41 4.4 44.0 1.0 CG a:LYS40 4.5 46.8 1.0 O a:CYS38 4.5 44.3 1.0 CA a:CYS61 4.6 44.8 1.0 CA a:CYS38 4.6 40.7 1.0 CD a:LYS40 4.7 49.0 1.0 C a:LYS40 4.7 49.7 1.0 C a:CYS38 4.8 40.8 1.0 CB a:THR66 4.8 42.6 1.0 C a:TYR63 4.8 40.0 1.0 CB a:TYR63 4.8 40.2 1.0 CA a:LYS40 4.8 51.2 1.0 N a:LYS40 4.9 48.5 1.0 C a:CYS64 4.9 45.3 1.0

Zinc binding site 8 out of 8 in the High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of High-Resolution Cryo-Em Structure of Saccharolobus Solfataricus 30S Ribosomal Subunit Bound to Mrna and Initiator Trna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn102 b:71.2 occ:1.00 CB a:CYS24 1.9 40.2 1.0 SG a:CYS50 2.0 47.8 1.0 OD1 a:ASP53 2.2 40.8 1.0 SG a:CYS21 2.3 40.8 1.0 SG a:CYS24 2.6 50.0 1.0 CG a:ASP53 2.8 41.3 1.0 CB a:ASP53 3.2 41.4 1.0 CA a:CYS24 3.4 35.6 1.0 CB a:CYS21 3.4 37.5 1.0 CB a:CYS50 3.6 37.5 1.0 OD2 a:ASP53 3.7 42.2 1.0 N a:CYS24 3.7 40.2 1.0 N a:CYS50 4.2 37.3 1.0 N a:ASP53 4.2 41.2 1.0 CA a:ASP53 4.2 42.1 1.0 C a:CYS24 4.3 42.5 1.0 CA a:CYS50 4.5 33.5 1.0 N a:ASN25 4.6 37.8 1.0 CA a:CYS21 4.8 38.0 1.0 CB a:ARG26 4.8 33.9 1.0 O a:CYS24 5.0 45.6 1.0

G.Bourgeois, P.D.Coureux, C.Lazennec-Schurdevin, C.Madru, T.Gaillard, M.Duchateau, J.Chamot-Rooke, S.Bourcier, Y.Mechulam, E.Schmitt. Structures of Saccharolobus Solfataricus Initiation Complexes with Leaderless Mrnas Highlight Archaeal Features and Eukaryotic Proximity. Nat Commun V. 16 348 2025.
ISSN: ESSN 2041-1723
PubMed: 39753558
DOI: 10.1038/S41467-024-55718-5