Zinc in PDB 9fra: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna

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

Magnesium

(Mg)

58 atoms

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

Zinc binding site 1 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:174.1 occ:1.00 SG C:CYS37 2.2 108.9 1.0 SG C:CYS60 2.2 106.4 1.0 SG C:CYS34 2.2 94.9 1.0 SG C:CYS57 2.2 112.3 1.0 CB C:CYS34 2.6 91.9 1.0 CB C:CYS37 3.1 97.0 1.0 CB C:CYS60 3.2 90.9 1.0 CB C:CYS57 3.4 97.6 1.0 N C:CYS37 3.4 94.6 1.0 CA C:CYS37 3.7 94.9 1.0 OD1 C:ASN59 3.8 105.1 1.0 N C:GLY38 4.0 101.1 1.0 CA C:CYS34 4.0 88.1 1.0 N C:CYS60 4.2 94.9 1.0 C C:CYS37 4.3 97.0 1.0 CA C:CYS60 4.3 93.5 1.0 CG2 C:VAL40 4.5 92.1 1.0 C C:CYS34 4.5 92.3 1.0 C C:ASN36 4.6 90.1 1.0 N C:GLU39 4.6 98.1 1.0 O C:CYS34 4.7 97.4 1.0 CA C:CYS57 4.7 89.5 1.0 CB C:ASN36 4.8 93.1 1.0 N C:ASN36 4.8 92.4 1.0 N C:CYS34 4.8 92.1 1.0 CG C:ASN59 4.8 102.0 1.0 CA C:ASN36 5.0 90.8 1.0 CB C:PHE62 5.0 80.4 1.0

Zinc binding site 2 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:149.4 occ:1.00 OD1 C:ASP45 2.0 91.0 1.0 CB C:CYS19 2.1 83.9 1.0 SG C:CYS48 2.2 103.0 1.0 SG C:CYS19 2.2 111.5 1.0 SG C:CYS16 2.3 88.2 1.0 CG C:ASP45 2.8 83.9 1.0 N C:CYS19 3.0 87.9 1.0 OD2 C:ASP45 3.1 82.2 1.0 CA C:CYS19 3.1 84.7 1.0 CB C:CYS16 3.1 71.0 1.0 CB C:CYS48 3.2 83.4 1.0 OG C:SER18 3.5 84.2 1.0 C C:CYS19 4.1 83.5 1.0 NE I:ARG21 4.1 94.1 1.0 CB C:ASP45 4.2 75.8 1.0 C C:SER18 4.3 80.0 1.0 N C:GLY20 4.3 72.5 1.0 CA C:CYS48 4.3 78.9 1.0 N C:CYS48 4.4 78.2 1.0 N C:ASP45 4.4 79.0 1.0 CD I:ARG21 4.4 87.1 1.0 CA C:CYS16 4.5 67.7 1.0 CB C:SER18 4.7 80.0 1.0 CA C:ASP45 4.9 72.6 1.0 CA C:SER18 4.9 78.0 1.0 N C:SER18 4.9 82.7 1.0 C C:CYS16 5.0 79.2 1.0

Zinc binding site 3 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:201.4 occ:1.00 CB F:CYS128 1.0 130.0 1.0 NE2 F:HIS132 2.1 99.0 1.0 CA F:CYS128 2.2 125.0 1.0 SG F:CYS128 2.2 141.5 1.0 SG F:CYS121 2.3 116.6 1.0 SG F:CYS126 2.4 104.1 1.0 N F:CYS128 2.7 124.5 1.0 CD2 F:HIS132 2.8 96.8 1.0 C F:CYS128 2.9 122.2 1.0 CB F:CYS121 3.1 97.3 1.0 N F:GLY129 3.1 112.9 1.0 CE1 F:HIS132 3.1 89.2 1.0 O F:CYS128 3.9 118.0 1.0 CB F:CYS126 4.0 99.7 1.0 CG F:HIS132 4.0 85.5 1.0 C F:THR127 4.0 107.2 1.0 ND1 F:HIS132 4.1 82.0 1.0 CD F:LYS154 4.2 84.2 1.0 N F:GLU130 4.3 108.8 1.0 CA F:GLY129 4.4 109.9 1.0 CA F:CYS121 4.4 95.2 1.0 O F:GLU130 4.4 112.6 1.0 C F:GLY129 4.7 115.7 1.0 O F:THR127 4.7 109.4 1.0 C F:CYS126 4.8 102.9 1.0 N F:THR127 4.8 105.2 1.0 CG F:LYS154 4.8 85.1 1.0 CA F:CYS126 4.9 96.7 1.0 CA F:THR127 5.0 105.7 1.0

Zinc binding site 4 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:169.2 occ:1.00 CB P:CYS40 2.1 79.0 1.0 SG P:CYS19 2.2 84.6 1.0 SG P:CYS37 2.2 115.0 1.0 SG P:CYS40 2.3 87.8 1.0 SG P:CYS22 2.3 80.0 1.0 N P:CYS37 2.8 85.2 1.0 CB P:CYS37 2.9 79.8 1.0 CB P:CYS19 3.2 74.1 1.0 CA P:CYS37 3.3 74.0 1.0 CA P:CYS40 3.5 63.9 1.0 N P:CYS40 3.9 72.1 1.0 CB P:CYS22 3.9 71.4 1.0 C P:LEU36 3.9 76.5 1.0 O P:CYS37 3.9 88.0 1.0 C P:CYS37 4.0 79.1 1.0 CA P:LEU36 4.1 72.2 1.0 N P:CYS22 4.3 77.2 1.0 CB P:LEU36 4.3 68.8 1.0 C P:CYS40 4.4 59.6 1.0 CA P:CYS19 4.5 71.6 1.0 CB P:ARG21 4.6 68.5 1.0 CA P:CYS22 4.7 78.4 1.0 N P:PHE41 4.7 56.9 1.0 O2' 2:G1165 4.8 76.7 1.0 CD2 P:LEU36 4.9 77.7 1.0 O P:LEU36 5.0 76.2 1.0

Zinc binding site 5 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:175.3 occ:1.00 ND1 R:HIS31 2.1 99.4 1.0 SG R:CYS28 2.3 117.4 1.0 SG R:CYS23 2.3 118.7 1.0 SG R:CYS84 2.3 116.8 1.0 CE1 R:HIS31 2.7 94.8 1.0 CB R:CYS84 2.9 99.3 1.0 CB R:CYS28 3.2 101.1 1.0 CG R:HIS31 3.3 90.1 1.0 CB R:CYS23 3.5 107.8 1.0 CB R:HIS31 3.9 85.3 1.0 NE2 R:HIS31 3.9 89.6 1.0 N R:CYS23 4.0 106.6 1.0 N R:HIS31 4.1 85.1 1.0 CD2 R:HIS31 4.2 89.4 1.0 CA R:CYS84 4.2 97.8 1.0 CA R:CYS23 4.3 106.2 1.0 CB R:TYR30 4.3 82.2 1.0 N R:CYS84 4.3 97.1 1.0 CB R:PRO82 4.4 83.0 1.0 CD2 R:TYR30 4.4 93.1 1.0 CA R:CYS28 4.6 96.0 1.0 CA R:HIS31 4.6 85.7 1.0 C R:CYS23 4.9 107.1 1.0 CG R:TYR30 4.9 86.7 1.0 OD1 R:ASP25 4.9 112.5 1.0 CG R:PRO19 4.9 104.7 1.0 N R:TYR30 4.9 94.7 1.0 C R:TYR30 4.9 90.8 1.0 CA R:TYR30 5.0 91.4 1.0

Zinc binding site 6 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:197.7 occ:1.00 SG W:CYS43 2.3 119.7 1.0 SG W:CYS21 2.3 115.8 1.0 SG W:CYS40 2.4 122.2 1.0 SG W:CYS24 2.8 152.7 1.0 CB W:CYS24 2.8 132.5 1.0 N W:CYS24 3.1 131.4 1.0 CB W:CYS43 3.4 116.1 1.0 CA W:CYS24 3.4 130.1 1.0 CB W:CYS21 3.4 106.2 1.0 OG W:SER42 3.4 115.3 1.0 N W:GLY25 3.6 114.2 1.0 CB W:CYS40 3.7 104.0 1.0 C W:CYS24 4.0 128.0 1.0 CB W:ASN26 4.1 110.2 1.0 N W:CYS43 4.1 116.2 1.0 N W:ASN26 4.1 114.9 1.0 C W:ASN23 4.2 120.5 1.0 CB W:ASN23 4.3 121.3 1.0 CA W:CYS43 4.4 112.7 1.0 CA W:ASN23 4.6 119.5 1.0 CB W:SER42 4.7 110.0 1.0 CA W:GLY25 4.7 110.6 1.0 CA W:CYS21 4.8 100.6 1.0 CA W:ASN26 4.8 109.3 1.0 N W:ASN23 4.8 118.6 1.0 C W:GLY25 4.9 112.3 1.0 O W:CYS21 4.9 106.1 1.0 CG2 W:THR45 4.9 101.8 1.0 C W:CYS21 5.0 103.2 1.0

Zinc binding site 7 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn101 b:176.4 occ:1.00 CB a:CYS61 2.1 105.0 1.0 SG a:CYS61 2.1 125.3 1.0 SG a:CYS64 2.2 113.5 1.0 SG a:CYS38 2.3 119.7 1.0 SG a:CYS41 2.4 133.1 1.0 CB a:CYS38 3.4 104.2 1.0 CB a:CYS64 3.4 97.9 1.0 NZ a:LYS40 3.6 109.8 1.0 CA a:CYS61 3.6 101.6 1.0 N a:CYS64 3.7 102.1 1.0 OG1 a:THR66 4.0 103.0 1.0 CA a:CYS64 4.0 103.5 1.0 C a:CYS61 4.1 101.8 1.0 CB a:CYS41 4.1 108.7 1.0 O a:CYS61 4.2 105.0 1.0 N a:GLY65 4.3 101.1 1.0 N a:THR66 4.3 98.7 1.0 N a:CYS61 4.4 108.0 1.0 C a:CYS64 4.4 104.1 1.0 CB a:THR66 4.4 101.1 1.0 CG a:LYS40 4.5 106.7 1.0 C a:TYR63 4.6 95.1 1.0 N a:TYR63 4.7 92.9 1.0 CE a:LYS40 4.7 110.4 1.0 CD a:LYS40 4.7 108.8 1.0 CA a:CYS38 4.7 99.3 1.0 CB a:TYR63 4.9 95.5 1.0 N a:CYS41 4.9 109.1 1.0 CA a:TYR63 5.0 95.2 1.0 CA a:THR66 5.0 101.5 1.0 N a:PRO62 5.0 89.7 1.0

Zinc binding site 8 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless 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-Map Leaderless Mrna within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn102 b:166.7 occ:1.00 CB a:CYS24 2.0 105.0 1.0 OD2 a:ASP53 2.0 113.3 1.0 SG a:CYS21 2.2 117.2 1.0 SG a:CYS50 2.3 104.3 1.0 SG a:CYS24 2.5 122.0 1.0 CB a:CYS21 2.8 97.6 1.0 CA a:CYS24 3.0 100.2 1.0 CG a:ASP53 3.1 104.9 1.0 N a:CYS24 3.2 103.0 1.0 C a:CYS24 3.6 102.7 1.0 OD1 a:ASP53 3.7 102.5 1.0 CB a:CYS50 3.8 99.7 1.0 N a:ASN25 3.9 95.9 1.0 CB a:ASP53 4.1 103.5 1.0 N a:ARG26 4.3 98.3 1.0 CB a:ARG26 4.3 92.2 1.0 CA a:CYS21 4.3 96.5 1.0 O a:CYS24 4.4 104.8 1.0 N a:CYS50 4.4 92.5 1.0 C a:ILE23 4.5 100.8 1.0 CA a:CYS50 4.7 96.8 1.0 C a:CYS21 4.9 93.1 1.0 CA a:ARG26 4.9 93.8 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