Zinc in PDB 9frl: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd Mrna with H44 in Up Position

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

Magnesium

(Mg)

53 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd Mrna with H44 in Up Position (pdb code 9frl). 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 Sd Mrna with H44 in Up Position, PDB code: 9frl:
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 Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:170.6 occ:1.00 SG C:CYS60 2.2 86.6 1.0 SG C:CYS34 2.3 109.3 1.0 SG C:CYS37 2.3 102.5 1.0 SG C:CYS57 2.3 79.9 1.0 CB C:CYS34 2.3 91.8 1.0 CB C:CYS37 3.2 91.7 1.0 N C:CYS37 3.4 89.0 1.0 CB C:CYS60 3.4 82.0 1.0 CB C:CYS57 3.4 77.8 1.0 CA C:CYS37 3.8 89.7 1.0 CA C:CYS34 3.8 89.1 1.0 N C:GLY38 3.9 93.3 1.0 C C:CYS34 4.3 89.5 1.0 C C:CYS37 4.3 95.8 1.0 N C:CYS60 4.4 88.8 1.0 CB C:ASN36 4.5 90.8 1.0 C C:ASN36 4.5 90.7 1.0 N C:ASN36 4.5 88.3 1.0 CA C:CYS60 4.5 87.0 1.0 O C:CYS34 4.5 89.5 1.0 CG2 C:VAL40 4.6 79.9 1.0 N C:CYS34 4.7 90.7 1.0 CA C:CYS57 4.7 73.1 1.0 CA C:ASN36 4.7 90.4 1.0 N C:GLU39 4.8 85.2 1.0 CB C:PHE62 4.9 74.9 1.0 CA C:GLY38 5.0 93.0 1.0 N C:PRO35 5.0 84.6 1.0

Zinc binding site 2 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:129.0 occ:1.00 OD1 C:ASP45 2.0 77.6 1.0 CB C:CYS19 2.1 79.7 1.0 SG C:CYS48 2.1 88.6 1.0 SG C:CYS19 2.2 91.1 1.0 SG C:CYS16 2.3 85.2 1.0 CG C:ASP45 2.8 74.8 1.0 CB C:CYS48 3.1 66.1 1.0 CB C:CYS16 3.1 73.5 1.0 OD2 C:ASP45 3.2 77.4 1.0 CA C:CYS19 3.3 75.8 1.0 N C:CYS19 3.3 80.4 1.0 OG C:SER18 3.8 74.3 1.0 CB C:ASP45 3.9 69.4 1.0 N C:ASP45 4.2 71.5 1.0 CA C:CYS48 4.2 57.7 1.0 N C:CYS48 4.2 62.8 1.0 NZ C:LYS21 4.3 75.2 1.0 C C:CYS19 4.3 71.0 1.0 N C:GLY20 4.5 65.2 1.0 NE I:ARG21 4.5 108.5 1.0 CA C:CYS16 4.6 70.1 1.0 CA C:ASP45 4.6 63.8 1.0 C C:SER18 4.6 73.1 1.0 CE C:LYS21 4.9 75.2 1.0

Zinc binding site 3 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:180.8 occ:1.00 CB F:CYS128 1.2 125.5 1.0 NE2 F:HIS132 2.1 90.9 1.0 SG F:CYS128 2.1 129.7 1.0 SG F:CYS121 2.3 113.6 1.0 SG F:CYS126 2.4 102.0 1.0 CD2 F:HIS132 2.4 90.7 1.0 CA F:CYS128 2.5 121.0 1.0 N F:CYS128 3.0 121.7 1.0 CB F:CYS121 3.1 104.7 1.0 C F:CYS128 3.3 119.2 1.0 CE1 F:HIS132 3.3 89.3 1.0 N F:GLY129 3.5 114.4 1.0 CG F:HIS132 3.7 86.0 1.0 CB F:CYS126 3.9 103.9 1.0 CD F:LYS154 4.1 75.5 1.0 ND1 F:HIS132 4.1 87.3 1.0 O F:CYS128 4.2 117.5 1.0 CA F:CYS121 4.3 104.1 1.0 O F:GLU130 4.3 116.1 1.0 C F:THR127 4.4 109.4 1.0 N F:GLU130 4.4 116.2 1.0 CG F:LYS154 4.6 77.0 1.0 CA F:GLY129 4.7 114.0 1.0 C F:GLY129 4.9 116.9 1.0 C F:CYS126 4.9 106.0 1.0 CA F:CYS126 5.0 103.9 1.0 CB F:HIS132 5.0 84.6 1.0 N F:LYS154 5.0 70.6 1.0

Zinc binding site 4 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:175.1 occ:1.00 SG W:CYS24 1.4 130.2 1.0 CB W:CYS24 2.1 121.8 1.0 SG W:CYS43 2.3 126.3 1.0 SG W:CYS21 2.3 107.0 1.0 SG W:CYS40 2.4 113.2 1.0 CA W:CYS24 2.9 120.2 1.0 N W:CYS24 3.0 121.2 1.0 OG W:SER42 3.4 111.9 1.0 CB W:CYS43 3.4 118.4 1.0 CB W:CYS21 3.4 102.2 1.0 C W:CYS24 3.4 124.1 1.0 N W:GLY25 3.7 122.9 1.0 CB W:CYS40 3.8 100.9 1.0 N W:ASN26 4.0 111.2 1.0 CB W:ASN26 4.0 102.8 1.0 N W:CYS43 4.1 116.5 1.0 O W:CYS24 4.2 122.4 1.0 C W:ASN23 4.3 113.8 1.0 CA W:CYS43 4.4 115.9 1.0 CB W:SER42 4.6 110.5 1.0 ND2 W:ASN23 4.7 116.4 1.0 CA W:ASN26 4.7 103.0 1.0 CG W:ASN23 4.7 117.2 1.0 CB W:ASN23 4.8 112.6 1.0 CA W:CYS21 4.8 100.5 1.0 CA W:GLY25 4.8 118.9 1.0 O W:CYS21 4.9 106.6 1.0 C W:GLY25 4.9 118.2 1.0 CA W:ASN23 4.9 112.6 1.0 N W:ASN23 5.0 113.1 1.0

Zinc binding site 5 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn101 b:177.9 occ:1.00 SG a:CYS61 2.3 106.4 1.0 SG a:CYS38 2.3 117.5 1.0 SG a:CYS41 2.3 136.6 1.0 CB a:CYS61 2.4 101.4 1.0 NZ a:LYS40 2.7 123.4 1.0 SG a:CYS64 2.8 112.7 1.0 CB a:CYS38 3.0 110.2 1.0 OG1 a:THR66 3.1 101.4 1.0 CE a:LYS40 3.6 124.1 1.0 CA a:CYS61 3.9 99.7 1.0 CB a:CYS41 4.0 123.3 1.0 CD a:LYS40 4.1 126.1 1.0 CB a:CYS64 4.3 102.8 1.0 N a:CYS64 4.4 104.1 1.0 CA a:CYS38 4.4 107.8 1.0 CB a:THR66 4.5 92.7 1.0 N a:THR66 4.5 94.8 1.0 N a:CYS61 4.6 98.6 1.0 C a:CYS61 4.7 100.6 1.0 N a:GLY65 4.7 103.9 1.0 N a:CYS41 4.8 126.3 1.0 CB a:TYR63 4.8 94.2 1.0 CA a:CYS64 4.9 103.9 1.0 C a:CYS38 5.0 108.2 1.0

Zinc binding site 6 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn102 b:144.9 occ:1.00 CB a:CYS24 1.5 109.9 1.0 SG a:CYS50 2.3 80.9 1.0 SG a:CYS21 2.3 105.7 1.0 SG a:CYS24 2.3 119.0 1.0 OD2 a:ASP53 2.4 109.5 1.0 CA a:CYS24 2.8 104.4 1.0 OD1 a:ASP53 3.1 106.7 1.0 CG a:ASP53 3.1 108.1 1.0 CB a:CYS21 3.1 98.0 1.0 N a:CYS24 3.3 105.7 1.0 C a:CYS24 3.5 103.8 1.0 CB a:ARG26 3.8 95.5 1.0 CB a:CYS50 3.9 91.2 1.0 N a:ASN25 4.0 95.8 1.0 O a:CYS24 4.2 105.0 1.0 N a:ARG26 4.4 98.8 1.0 CB a:ASP53 4.5 108.3 1.0 CA a:CYS21 4.6 96.2 1.0 C a:ILE23 4.6 102.0 1.0 N a:CYS50 4.6 81.7 1.0 CA a:ARG26 4.8 91.9 1.0 CG a:ARG26 4.9 95.7 1.0 CA a:CYS50 4.9 83.7 1.0

Zinc binding site 7 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd 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 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 O2' 2:G1165 4.3 82.7 1.0 CB P:ARG21 4.6 23.2 1.0 CB P:SER24 4.7 27.1 1.0 O P:CYS37 4.7 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 C P:CYS22 4.9 26.1 1.0

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

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