Zinc in PDB 9fs8: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna also contains other interesting chemical elements:

Magnesium

(Mg)

57 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna (pdb code 9fs8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna, PDB code: 9fs8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


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 Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:164.6 occ:1.00 SG C:CYS37 1.9 126.3 1.0 SG C:CYS34 2.1 119.8 1.0 SG C:CYS60 2.2 126.2 1.0 SG C:CYS57 2.2 118.4 1.0 CB C:CYS34 2.5 119.8 1.0 CB C:CYS37 3.0 126.3 1.0 CB C:CYS60 3.3 126.2 1.0 CB C:CYS57 3.3 118.4 1.0 N C:CYS37 3.5 126.3 1.0 CA C:CYS37 3.7 126.3 1.0 OD1 C:ASN59 3.9 123.1 1.0 N C:GLY38 4.0 125.7 1.0 CA C:CYS34 4.0 119.8 1.0 N C:CYS60 4.3 126.2 1.0 C C:CYS37 4.3 126.3 1.0 CA C:CYS60 4.4 126.2 1.0 OE1 C:GLU39 4.4 124.6 1.0 CG2 C:VAL40 4.5 117.2 1.0 C C:CYS34 4.5 119.8 1.0 CA C:CYS57 4.6 118.4 1.0 C C:ASN36 4.7 121.7 1.0 O C:CYS34 4.7 119.8 1.0 CB C:ASN36 4.8 121.7 1.0 N C:ASN36 4.8 121.7 1.0 N C:CYS34 4.8 119.8 1.0 N C:GLU39 4.8 124.6 1.0 CG C:ASN59 4.9 123.1 1.0 CB C:PHE62 4.9 113.4 1.0 CA C:ASN36 5.0 121.7 1.0

Zinc binding site 2 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


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 Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:147.9 occ:1.00 OD1 C:ASP45 2.0 110.6 1.0 CB C:CYS19 2.1 110.0 1.0 SG C:CYS48 2.2 114.5 1.0 SG C:CYS19 2.2 110.0 1.0 SG C:CYS16 2.2 107.5 1.0 CG C:ASP45 2.8 110.6 1.0 N C:CYS19 3.0 110.0 1.0 OD2 C:ASP45 3.0 110.6 1.0 CA C:CYS19 3.1 110.0 1.0 CB C:CYS16 3.1 107.5 1.0 CB C:CYS48 3.2 114.5 1.0 OG C:SER18 3.5 107.3 1.0 C C:CYS19 4.1 110.0 1.0 NE I:ARG21 4.1 126.9 1.0 CB C:ASP45 4.1 110.6 1.0 C C:SER18 4.3 107.3 1.0 N C:GLY20 4.3 107.1 1.0 CA C:CYS48 4.3 114.5 1.0 N C:ASP45 4.4 110.6 1.0 N C:CYS48 4.4 114.5 1.0 CD I:ARG21 4.4 126.9 1.0 CA C:CYS16 4.5 107.5 1.0 CB C:SER18 4.7 107.3 1.0 CA C:ASP45 4.8 110.6 1.0 CA C:SER18 4.9 107.3 1.0 N C:SER18 4.9 107.3 1.0 C C:CYS16 5.0 107.5 1.0

Zinc binding site 3 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


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 Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:168.4 occ:1.00 CB F:CYS128 1.0 140.3 1.0 NE2 F:HIS132 2.1 114.3 1.0 CA F:CYS128 2.2 140.3 1.0 SG F:CYS128 2.2 140.3 1.0 SG F:CYS121 2.3 118.1 1.0 SG F:CYS126 2.4 121.7 1.0 N F:CYS128 2.7 140.3 1.0 CD2 F:HIS132 2.8 114.3 1.0 C F:CYS128 2.9 140.3 1.0 CB F:CYS121 3.1 118.1 1.0 N F:GLY129 3.1 132.0 1.0 CE1 F:HIS132 3.1 114.3 1.0 O F:CYS128 3.9 140.3 1.0 CB F:CYS126 4.0 121.7 1.0 CG F:HIS132 4.0 114.3 1.0 C F:THR127 4.0 128.4 1.0 ND1 F:HIS132 4.1 114.3 1.0 N F:GLU130 4.2 128.8 1.0 CD F:LYS154 4.2 106.3 1.0 CA F:GLY129 4.4 132.0 1.0 CA F:CYS121 4.4 118.1 1.0 O F:GLU130 4.4 128.8 1.0 C F:GLY129 4.7 132.0 1.0 O F:THR127 4.7 128.4 1.0 C F:CYS126 4.8 121.7 1.0 N F:THR127 4.8 128.4 1.0 CG F:LYS154 4.8 106.3 1.0 CA F:CYS126 4.9 121.7 1.0 CA F:THR127 4.9 128.4 1.0

Zinc binding site 4 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:148.8 occ:1.00 CB P:CYS40 2.1 104.1 1.0 SG P:CYS37 2.2 109.5 1.0 SG P:CYS19 2.2 101.7 1.0 SG P:CYS22 2.3 100.1 1.0 SG P:CYS40 2.3 104.1 1.0 N P:CYS37 2.7 109.5 1.0 CB P:CYS37 2.9 109.5 1.0 CB P:CYS19 3.2 101.7 1.0 CA P:CYS37 3.3 109.5 1.0 CA P:CYS40 3.5 104.1 1.0 C P:LEU36 3.8 102.8 1.0 N P:CYS40 3.8 104.1 1.0 O P:CYS37 3.8 109.5 1.0 CB P:CYS22 3.9 100.1 1.0 C P:CYS37 3.9 109.5 1.0 CA P:LEU36 4.1 102.8 1.0 N P:CYS22 4.3 100.1 1.0 CB P:LEU36 4.3 102.8 1.0 C P:CYS40 4.4 104.1 1.0 CA P:CYS19 4.6 101.7 1.0 CB P:ARG21 4.7 98.4 1.0 CA P:CYS22 4.7 100.1 1.0 N P:PHE41 4.7 95.7 1.0 O2' 2:G1165 4.8 137.1 1.0 O P:LEU36 4.9 102.8 1.0

Zinc binding site 5 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:183.8 occ:1.00 ND1 R:HIS31 2.0 138.4 1.0 SG R:CYS28 2.3 141.6 1.0 SG R:CYS23 2.3 149.7 1.0 SG R:CYS84 2.3 145.6 1.0 CE1 R:HIS31 2.7 138.4 1.0 CB R:CYS84 2.9 145.6 1.0 CB R:CYS28 3.2 141.6 1.0 CG R:HIS31 3.2 138.4 1.0 CB R:CYS23 3.5 149.7 1.0 CB R:HIS31 3.9 138.4 1.0 NE2 R:HIS31 3.9 138.4 1.0 N R:CYS23 4.0 149.7 1.0 N R:HIS31 4.1 138.4 1.0 CD2 R:HIS31 4.2 138.4 1.0 CA R:CYS84 4.2 145.6 1.0 CA R:CYS23 4.2 149.7 1.0 CB R:TYR30 4.3 136.0 1.0 N R:CYS84 4.3 145.6 1.0 CB R:PRO82 4.4 132.1 1.0 CD2 R:TYR30 4.4 136.0 1.0 CA R:CYS28 4.6 141.6 1.0 CA R:HIS31 4.6 138.4 1.0 C R:CYS23 4.8 149.7 1.0 CG R:TYR30 4.9 136.0 1.0 N R:TYR30 4.9 136.0 1.0 CG R:PRO19 4.9 141.2 1.0 C R:TYR30 4.9 136.0 1.0 CA R:TYR30 5.0 136.0 1.0 O R:CYS23 5.0 149.7 1.0

Zinc binding site 6 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:186.3 occ:1.00 CB W:CYS24 2.1 158.6 1.0 SG W:CYS43 2.3 150.7 1.0 SG W:CYS21 2.3 146.2 1.0 SG W:CYS40 2.4 146.6 1.0 CA W:CYS24 2.9 158.6 1.0 N W:CYS24 3.0 158.6 1.0 SG W:CYS24 3.0 158.6 1.0 CB W:CYS21 3.3 146.2 1.0 CB W:CYS43 3.4 150.7 1.0 OG W:SER42 3.4 149.9 1.0 C W:CYS24 3.5 158.6 1.0 N W:GLY25 3.7 150.2 1.0 CB W:CYS40 3.7 146.6 1.0 N W:ASN26 4.0 144.8 1.0 CB W:ASN26 4.1 144.8 1.0 N W:CYS43 4.1 150.7 1.0 C W:ASN23 4.2 154.9 1.0 CA W:CYS43 4.4 150.7 1.0 O W:CYS24 4.4 158.6 1.0 CB W:ASN23 4.6 154.9 1.0 CB W:SER42 4.7 149.9 1.0 CA W:CYS21 4.7 146.2 1.0 CA W:ASN26 4.7 144.8 1.0 CG W:ASN23 4.8 154.9 1.0 OD1 W:ASN23 4.8 154.9 1.0 CA W:ASN23 4.8 154.9 1.0 O W:CYS21 4.9 146.2 1.0 CA W:GLY25 4.9 150.2 1.0 CG2 W:THR45 4.9 139.3 1.0 N W:ASN23 4.9 154.9 1.0 C W:GLY25 5.0 150.2 1.0 C W:CYS21 5.0 146.2 1.0

Zinc binding site 7 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn101 b:169.9 occ:1.00 CB a:CYS61 2.1 130.0 1.0 SG a:CYS61 2.1 130.0 1.0 SG a:CYS64 2.2 129.2 1.0 SG a:CYS38 2.3 134.4 1.0 SG a:CYS41 2.4 139.3 1.0 CB a:CYS38 3.4 134.4 1.0 CB a:CYS64 3.4 129.2 1.0 NZ a:LYS40 3.5 136.7 1.0 CA a:CYS61 3.6 130.0 1.0 N a:CYS64 3.7 129.2 1.0 CA a:CYS64 4.0 129.2 1.0 OG1 a:THR66 4.0 125.9 1.0 CB a:CYS41 4.1 139.3 1.0 C a:CYS61 4.1 130.0 1.0 O a:CYS61 4.2 130.0 1.0 N a:GLY65 4.3 126.5 1.0 N a:THR66 4.3 125.9 1.0 N a:CYS61 4.4 130.0 1.0 C a:CYS64 4.4 129.2 1.0 CB a:THR66 4.4 125.9 1.0 CG a:LYS40 4.5 136.7 1.0 C a:TYR63 4.6 121.8 1.0 N a:TYR63 4.7 121.8 1.0 CE a:LYS40 4.7 136.7 1.0 CA a:CYS38 4.7 134.4 1.0 CD a:LYS40 4.7 136.7 1.0 CB a:TYR63 4.8 121.8 1.0 N a:CYS41 4.9 139.3 1.0 CA a:THR66 4.9 125.9 1.0 CA a:TYR63 5.0 121.8 1.0 N a:PRO62 5.0 117.2 1.0

Zinc binding site 8 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn102 b:160.5 occ:1.00 OD2 a:ASP53 2.0 134.4 1.0 CB a:CYS24 2.1 122.9 1.0 SG a:CYS21 2.2 123.0 1.0 SG a:CYS24 2.3 122.9 1.0 SG a:CYS50 2.3 130.9 1.0 CB a:CYS21 2.8 123.0 1.0 CA a:CYS24 3.0 122.9 1.0 CG a:ASP53 3.1 134.4 1.0 N a:CYS24 3.1 122.9 1.0 C a:CYS24 3.7 122.9 1.0 CB a:CYS50 3.8 130.9 1.0 OD1 a:ASP53 3.8 134.4 1.0 N a:ASN25 3.9 112.2 1.0 CB a:ASP53 4.1 134.4 1.0 CG a:ARG26 4.2 111.7 1.0 CB a:ARG26 4.3 111.7 1.0 N a:ARG26 4.3 111.7 1.0 CA a:CYS21 4.3 123.0 1.0 O a:CYS24 4.4 122.9 1.0 N a:CYS50 4.5 130.9 1.0 C a:ILE23 4.5 119.0 1.0 CA a:CYS50 4.8 130.9 1.0 C a:CYS21 4.9 123.0 1.0 CA a:ARG26 5.0 111.7 1.0

Zinc binding site 9 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AEF1A-Like Mrna within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:109.2 occ:1.00 CB b:CYS26 2.3 111.1 1.0 SG b:CYS73 2.3 86.7 1.0 SG b:CYS23 2.3 100.0 1.0 CB b:CYS73 3.0 86.7 1.0 CB b:CYS70 3.1 91.8 1.0 N b:CYS26 3.2 111.1 1.0 SG b:CYS70 3.2 91.8 1.0 CA b:CYS26 3.3 111.1 1.0 N b:CYS70 3.4 91.8 1.0 CB b:CYS23 3.4 100.0 1.0 OD1 b:ASN72 3.4 87.3 1.0 SG b:CYS26 3.7 111.1 1.0 ND2 b:ASN72 3.8 87.3 1.0 CA b:CYS70 3.8 91.8 1.0 CG b:ASN72 3.9 87.3 1.0 N b:CYS73 4.0 86.7 1.0 CA b:CYS73 4.1 86.7 1.0 C b:GLN25 4.4 104.2 1.0 C b:TYR69 4.5 86.5 1.0 C b:CYS26 4.5 111.1 1.0 CA b:TYR69 4.6 86.5 1.0 C b:CYS70 4.6 91.8 1.0 CB b:GLN25 4.7 104.2 1.0 CB b:TYR69 4.8 86.5 1.0 O b:CYS70 4.8 91.8 1.0 CA b:CYS23 4.8 100.0 1.0 N b:GLY27 4.8 105.3 1.0 NE2 b:GLN25 4.9 104.2 1.0 CD1 b:TYR69 5.0 86.5 1.0 CA b:GLN25 5.0 104.2 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