Zinc in PDB 9fsf: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna with H44 in Up Position

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna with H44 in Up Position also contains other interesting chemical elements:

Magnesium

(Mg)

56 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna with H44 in Up Position (pdb code 9fsf). 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 with H44 in Up Position, PDB code: 9fsf:
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 with H44 in Up Position


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 with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:161.0 occ:1.00 CB C:CYS60 1.6 97.3 1.0 SG C:CYS37 2.3 87.0 1.0 SG C:CYS57 2.3 99.1 1.0 SG C:CYS60 2.3 111.4 1.0 SG C:CYS34 2.3 83.8 1.0 CA C:CYS60 3.1 91.1 1.0 CB C:CYS57 3.1 85.4 1.0 CB C:CYS37 3.1 78.3 1.0 N C:CYS37 3.6 77.6 1.0 N C:CYS60 3.6 92.2 1.0 CB C:CYS34 3.6 77.7 1.0 C C:CYS60 3.9 87.3 1.0 CB C:PHE62 3.9 76.7 1.0 CA C:CYS37 4.0 76.5 1.0 OD1 C:ASN59 4.1 94.7 1.0 N C:PHE62 4.2 79.7 1.0 N C:GLY61 4.2 86.2 1.0 CB C:ASN36 4.4 78.8 1.0 CA C:CYS57 4.6 80.2 1.0 C C:ASN36 4.6 77.3 1.0 O C:CYS60 4.7 83.4 1.0 CA C:PHE62 4.7 75.7 1.0 N C:GLY38 4.7 85.9 1.0 CG C:ASN36 4.8 79.9 1.0 CA C:ASN36 4.9 78.9 1.0 N C:ASN36 4.9 78.8 1.0 OD1 C:ASN36 4.9 77.5 1.0 C C:ASN59 4.9 84.6 1.0 C C:CYS37 4.9 82.8 1.0 CA C:CYS34 5.0 73.3 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 with H44 in Up Position


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 with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:135.5 occ:1.00 OD1 C:ASP45 2.0 83.8 1.0 CB C:CYS19 2.1 80.4 1.0 SG C:CYS48 2.2 88.3 1.0 SG C:CYS19 2.2 98.0 1.0 SG C:CYS16 2.2 84.8 1.0 CG C:ASP45 2.8 75.3 1.0 N C:CYS19 3.0 81.8 1.0 CB C:CYS48 3.0 72.6 1.0 OD2 C:ASP45 3.0 73.1 1.0 CA C:CYS19 3.1 82.1 1.0 CB C:CYS16 3.1 65.5 1.0 OG C:SER18 3.6 69.6 1.0 C C:CYS19 4.1 77.8 1.0 CB C:ASP45 4.2 68.4 1.0 CA C:CYS48 4.2 70.5 1.0 C C:SER18 4.2 69.7 1.0 N C:GLY20 4.3 64.8 1.0 N C:CYS48 4.4 72.9 1.0 N C:ASP45 4.4 70.7 1.0 NE I:ARG21 4.4 82.2 1.0 CA C:CYS16 4.5 64.8 1.0 CB C:SER18 4.7 67.5 1.0 N C:SER18 4.8 73.6 1.0 CA C:SER18 4.8 66.9 1.0 CA C:ASP45 4.9 63.0 1.0 C C:CYS16 4.9 74.5 1.0 CD I:ARG21 4.9 77.2 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 with H44 in Up Position


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 with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:178.0 occ:1.00 CB F:CYS128 1.2 109.8 1.0 NE2 F:HIS132 2.1 83.2 1.0 SG F:CYS128 2.2 120.5 1.0 SG F:CYS121 2.3 101.6 1.0 CA F:CYS128 2.3 105.1 1.0 SG F:CYS126 2.4 85.9 1.0 CD2 F:HIS132 2.8 84.0 1.0 N F:CYS128 2.8 108.1 1.0 CB F:CYS121 2.8 91.0 1.0 C F:CYS128 3.0 105.2 1.0 CE1 F:HIS132 3.1 76.5 1.0 N F:GLY129 3.2 97.8 1.0 CB F:CYS126 3.9 85.6 1.0 CG F:HIS132 3.9 75.0 1.0 O F:CYS128 4.0 104.3 1.0 ND1 F:HIS132 4.1 70.5 1.0 C F:THR127 4.1 89.5 1.0 CA F:CYS121 4.2 90.1 1.0 N F:GLU130 4.2 97.5 1.0 CD F:LYS154 4.3 75.3 1.0 O F:GLU130 4.4 101.8 1.0 CG F:LYS154 4.4 74.0 1.0 CA F:GLY129 4.4 95.0 1.0 C F:GLY129 4.7 98.7 1.0 C F:CYS126 4.8 90.5 1.0 N F:THR127 4.8 85.9 1.0 O F:THR127 4.8 89.5 1.0 CA F:CYS126 4.8 84.8 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 with H44 in Up Position


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 with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:164.1 occ:1.00 ND1 R:HIS31 2.0 98.1 1.0 SG R:CYS28 2.3 115.4 1.0 SG R:CYS23 2.3 116.5 1.0 SG R:CYS84 2.3 118.8 1.0 CE1 R:HIS31 2.7 96.0 1.0 CB R:CYS84 2.8 98.8 1.0 CB R:CYS28 3.1 98.6 1.0 CG R:HIS31 3.3 90.4 1.0 CB R:CYS23 3.6 107.1 1.0 NE2 R:HIS31 3.9 92.6 1.0 CB R:HIS31 3.9 88.2 1.0 N R:CYS23 4.1 105.9 1.0 CA R:CYS84 4.1 94.6 1.0 N R:HIS31 4.2 86.4 1.0 CD2 R:HIS31 4.2 90.4 1.0 N R:CYS84 4.3 96.0 1.0 CB R:PRO82 4.4 83.3 1.0 CB R:TYR30 4.4 86.0 1.0 CA R:CYS23 4.4 105.1 1.0 CD2 R:TYR30 4.5 88.0 1.0 CA R:CYS28 4.5 94.4 1.0 CA R:HIS31 4.7 88.2 1.0 CG R:TYR30 4.9 87.9 1.0 CG R:PRO19 4.9 98.6 1.0 N R:TYR30 4.9 92.1 1.0 OD1 R:ASP25 5.0 106.0 1.0 C R:CYS23 5.0 104.2 1.0 C R:TYR30 5.0 90.8 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 with H44 in Up Position


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 with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:188.5 occ:1.00 SG W:CYS21 2.5 114.0 1.0 SG W:CYS43 2.6 121.9 1.0 SG W:CYS24 2.8 137.9 1.0 CB W:CYS24 2.8 120.8 1.0 SG W:CYS40 3.1 121.7 1.0 CB W:CYS21 3.2 101.4 1.0 OG W:SER42 3.3 107.5 1.0 N W:CYS24 3.4 119.9 1.0 CB W:CYS43 3.4 113.9 1.0 CA W:CYS24 3.6 118.2 1.0 CB W:CYS40 3.6 101.1 1.0 N W:GLY25 3.8 110.3 1.0 CB W:ASN26 3.8 100.5 1.0 N W:ASN26 4.0 108.0 1.0 N W:CYS43 4.0 110.8 1.0 C W:CYS24 4.2 119.5 1.0 CA W:CYS43 4.4 110.3 1.0 CA W:ASN26 4.5 103.6 1.0 CA W:CYS21 4.6 98.3 1.0 CB W:SER42 4.6 99.4 1.0 C W:ASN23 4.6 113.2 1.0 CB W:ASN23 4.7 118.5 1.0 O W:CYS40 4.7 101.1 1.0 OD1 W:ASN23 4.8 118.1 1.0 CA W:GLY25 4.9 105.4 1.0 O W:CYS21 4.9 105.1 1.0 C W:GLY25 4.9 107.8 1.0 C W:CYS21 4.9 103.4 1.0 CA W:CYS40 4.9 95.3 1.0 C W:SER42 5.0 107.0 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 with H44 in Up Position


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 with H44 in Up Position 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 7 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna with H44 in Up Position


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 with H44 in Up Position 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

Zinc binding site 8 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-Map Leaderless Mrna with H44 in Up Position


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 with H44 in Up Position 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 CA P:CYS40 4.1 18.6 1.0 O2' 2:G1165 4.2 76.9 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 N2 2:G1165 4.8 74.5 1.0 C P:ARG21 4.8 26.8 1.0 C P:CYS37 4.8 28.8 1.0 N3 2:G1165 4.9 77.7 1.0 CA P:CYS19 4.9 24.0 1.0 C P:CYS22 4.9 26.1 1.0 C2' 2:G1165 4.9 72.1 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