Zinc in PDB 9fs6: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna with H44 in Up Position

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna with H44 in Up Position 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-AIF2BETA Leaderless Mrna with H44 in Up Position (pdb code 9fs6). 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-AIF2BETA Leaderless Mrna with H44 in Up Position, PDB code: 9fs6:
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-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:153.8 occ:1.00 CB C:CYS60 1.6 98.2 1.0 SG C:CYS57 2.3 104.7 1.0 SG C:CYS34 2.3 93.8 1.0 SG C:CYS60 2.3 100.5 1.0 SG C:CYS37 2.3 103.4 1.0 CA C:CYS60 3.0 96.5 1.0 CB C:CYS37 3.1 95.4 1.0 CB C:CYS57 3.1 94.4 1.0 N C:CYS60 3.6 95.5 1.0 N C:CYS37 3.6 90.2 1.0 CB C:CYS34 3.7 88.5 1.0 OD1 C:ASN36 3.8 97.2 1.0 CB C:PHE62 3.8 87.0 1.0 C C:CYS60 3.9 96.9 1.0 CA C:CYS37 4.0 91.9 1.0 OD1 C:ASN59 4.0 100.1 1.0 N C:PHE62 4.1 88.5 1.0 N C:GLY61 4.2 93.0 1.0 CB C:ASN36 4.2 91.9 1.0 CG C:ASN36 4.4 94.3 1.0 CA C:PHE62 4.6 87.5 1.0 CA C:CYS57 4.6 92.0 1.0 O C:CYS60 4.7 94.2 1.0 C C:ASN36 4.7 91.6 1.0 CA C:ASN36 4.8 92.4 1.0 N C:GLY38 4.9 97.6 1.0 C C:ASN59 4.9 95.3 1.0 N C:ASN36 4.9 93.3 1.0

Zinc binding site 2 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:120.8 occ:1.00 OD1 C:ASP45 2.0 66.4 1.0 CB C:CYS19 2.1 72.7 1.0 SG C:CYS19 2.2 81.4 1.0 SG C:CYS48 2.2 66.6 1.0 SG C:CYS16 2.3 72.3 1.0 CG C:ASP45 2.8 62.8 1.0 N C:CYS19 2.9 76.4 1.0 OD2 C:ASP45 3.0 64.3 1.0 CA C:CYS19 3.0 71.2 1.0 CB C:CYS48 3.0 61.0 1.0 CB C:CYS16 3.1 63.5 1.0 OG C:SER18 3.6 62.0 1.0 C C:CYS19 4.0 70.5 1.0 CB C:ASP45 4.1 54.6 1.0 C C:SER18 4.2 67.7 1.0 N C:GLY20 4.2 63.3 1.0 CA C:CYS48 4.3 57.0 1.0 N C:ASP45 4.4 54.4 1.0 NE I:ARG21 4.4 82.8 1.0 N C:CYS48 4.5 57.6 1.0 CA C:CYS16 4.5 61.1 1.0 CB C:SER18 4.7 60.3 1.0 N C:SER18 4.8 58.7 1.0 CA C:SER18 4.8 61.8 1.0 C C:CYS16 4.9 65.0 1.0 CA C:ASP45 4.9 47.4 1.0 CD I:ARG21 5.0 76.9 1.0

Zinc binding site 3 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:161.3 occ:1.00 CB F:CYS128 1.1 109.5 1.0 NE2 F:HIS132 2.1 78.8 1.0 SG F:CYS128 2.2 119.7 1.0 CA F:CYS128 2.3 107.0 1.0 SG F:CYS121 2.3 84.9 1.0 SG F:CYS126 2.5 87.8 1.0 CD2 F:HIS132 2.7 78.4 1.0 N F:CYS128 2.8 110.2 1.0 CB F:CYS121 2.8 82.8 1.0 C F:CYS128 3.0 108.0 1.0 CE1 F:HIS132 3.2 72.1 1.0 N F:GLY129 3.2 99.4 1.0 CG F:HIS132 3.8 69.2 1.0 CB F:CYS126 3.9 85.3 1.0 O F:CYS128 4.0 108.1 1.0 ND1 F:HIS132 4.0 67.9 1.0 C F:THR127 4.1 100.8 1.0 CA F:CYS121 4.1 82.1 1.0 CD F:LYS154 4.3 67.0 1.0 N F:GLU130 4.3 94.6 1.0 O F:GLU130 4.3 91.0 1.0 CG F:LYS154 4.4 66.4 1.0 CA F:GLY129 4.4 94.5 1.0 C F:GLY129 4.7 97.0 1.0 C F:CYS126 4.7 80.7 1.0 N F:THR127 4.8 91.6 1.0 O F:THR127 4.8 96.8 1.0 CA F:CYS126 4.8 83.3 1.0

Zinc binding site 4 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:128.9 occ:1.00 ND1 R:HIS31 2.0 81.5 1.0 SG R:CYS28 2.3 102.7 1.0 SG R:CYS84 2.3 99.9 1.0 SG R:CYS23 2.3 96.2 1.0 CE1 R:HIS31 2.7 79.3 1.0 CB R:CYS84 2.7 91.8 1.0 CB R:CYS28 3.1 82.9 1.0 CG R:HIS31 3.3 74.2 1.0 CB R:CYS23 3.6 97.3 1.0 CB R:HIS31 3.9 71.3 1.0 NE2 R:HIS31 3.9 75.1 1.0 CA R:CYS84 4.1 88.3 1.0 N R:HIS31 4.1 68.1 1.0 N R:CYS23 4.2 98.0 1.0 CD2 R:HIS31 4.2 74.1 1.0 N R:CYS84 4.3 88.7 1.0 CB R:PRO82 4.3 74.5 1.0 CB R:TYR30 4.3 66.7 1.0 CD2 R:TYR30 4.4 72.2 1.0 CA R:CYS23 4.5 96.1 1.0 CA R:CYS28 4.6 77.4 1.0 CA R:HIS31 4.6 71.8 1.0 N R:TYR30 4.8 73.6 1.0 CG R:TYR30 4.8 72.2 1.0 OD1 R:ASP25 4.8 96.7 1.0 CG R:PRO19 4.9 93.2 1.0 C R:TYR30 4.9 71.0 1.0 CA R:TYR30 4.9 68.1 1.0

Zinc binding site 5 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:176.3 occ:1.00 CB W:CYS24 2.0 110.6 1.0 SG W:CYS40 2.2 99.9 1.0 SG W:CYS43 2.2 117.6 1.0 SG W:CYS21 2.3 105.7 1.0 CB W:CYS21 3.0 94.4 1.0 SG W:CYS24 3.0 110.5 1.0 CA W:CYS24 3.0 105.4 1.0 N W:CYS24 3.1 106.1 1.0 CB W:CYS43 3.2 107.5 1.0 CB W:CYS40 3.5 94.4 1.0 OG W:SER42 3.7 104.1 1.0 C W:CYS24 3.7 105.1 1.0 N W:GLY25 3.9 105.6 1.0 CB W:ASN26 3.9 95.2 1.0 N W:ASN26 4.0 98.1 1.0 N W:CYS43 4.0 106.7 1.0 CA W:CYS43 4.2 107.8 1.0 C W:ASN23 4.3 103.8 1.0 CA W:CYS21 4.4 90.6 1.0 OD1 W:ASN23 4.6 106.5 1.0 CA W:ASN26 4.6 98.2 1.0 O W:CYS24 4.6 102.0 1.0 C W:CYS21 4.8 95.6 1.0 O W:CYS21 4.8 100.5 1.0 CA W:CYS40 4.8 88.1 1.0 N W:ASN23 4.9 98.9 1.0 CB W:ASN23 4.9 101.9 1.0 CA W:ASN23 4.9 101.7 1.0 CB W:SER42 4.9 102.2 1.0 C W:GLY25 5.0 102.9 1.0

Zinc binding site 6 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn101 b:171.7 occ:1.00 SG a:CYS38 2.3 102.7 1.0 SG a:CYS41 2.4 107.8 1.0 SG a:CYS64 2.4 104.6 1.0 SG a:CYS61 2.4 99.3 1.0 CB a:CYS61 3.0 93.1 1.0 CB a:CYS38 3.4 90.1 1.0 CB a:CYS64 3.5 88.3 1.0 CB a:CYS41 3.9 100.5 1.0 N a:CYS41 4.0 97.9 1.0 N a:CYS64 4.1 91.5 1.0 OG1 a:THR66 4.3 94.7 1.0 CA a:CYS64 4.4 89.2 1.0 CA a:CYS61 4.5 92.3 1.0 CA a:CYS41 4.5 100.5 1.0 CB a:LYS40 4.6 99.5 1.0 N a:LYS40 4.8 100.7 1.0 CB a:TYR63 4.8 78.8 1.0 CA a:CYS38 4.8 86.8 1.0 CB a:THR66 4.9 91.5 1.0 C a:TYR63 4.9 82.0 1.0 N a:GLY65 4.9 88.1 1.0 CD2 a:TYR63 4.9 79.9 1.0 C a:LYS40 5.0 98.9 1.0

Zinc binding site 7 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn102 b:137.4 occ:1.00 CB a:CYS24 1.9 87.8 1.0 SG a:CYS21 2.2 93.2 1.0 SG a:CYS50 2.2 71.6 1.0 OD1 a:ASP53 2.6 97.3 1.0 SG a:CYS24 2.6 98.3 1.0 CB a:CYS21 2.7 83.6 1.0 OD2 a:ASP53 2.9 99.5 1.0 CG a:ASP53 2.9 97.3 1.0 CA a:CYS24 3.0 81.5 1.0 N a:CYS24 3.2 84.5 1.0 CB a:CYS50 3.7 83.0 1.0 C a:CYS24 3.7 76.0 1.0 N a:CYS50 4.1 78.3 1.0 CA a:CYS21 4.1 82.3 1.0 N a:ASN25 4.1 72.2 1.0 CB a:ASP53 4.2 96.2 1.0 CB a:ARG26 4.3 77.2 1.0 N a:ASP53 4.4 93.7 1.0 C a:CYS21 4.4 79.1 1.0 CA a:CYS50 4.5 81.1 1.0 O a:CYS24 4.5 73.8 1.0 N a:ARG26 4.5 84.1 1.0 C a:ILE23 4.5 71.8 1.0 CB a:ALA52 4.8 91.7 1.0 CA a:ASP53 4.8 95.3 1.0 N a:ARG22 4.8 70.9 1.0 O a:CYS21 4.9 75.9 1.0 N a:ILE23 4.9 71.3 1.0

Zinc binding site 8 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:129.9 occ:1.00 CB P:CYS40 2.1 62.2 1.0 SG P:CYS37 2.2 86.1 1.0 SG P:CYS40 2.3 70.3 1.0 SG P:CYS19 2.3 62.6 1.0 SG P:CYS22 2.3 72.0 1.0 N P:CYS37 3.0 56.4 1.0 CB P:CYS37 3.1 58.5 1.0 CB P:CYS19 3.3 65.2 1.0 CA P:CYS40 3.5 42.7 1.0 CA P:CYS37 3.5 56.0 1.0 CB P:CYS22 3.7 55.2 1.0 N P:CYS40 3.8 48.8 1.0 O P:CYS37 3.9 64.7 1.0 C P:CYS37 4.1 60.3 1.0 C P:LEU36 4.2 62.2 1.0 O2' 2:G1165 4.4 70.8 1.0 N P:CYS22 4.5 49.5 1.0 C P:CYS40 4.5 33.6 1.0 CA P:LEU36 4.6 61.9 1.0 CA P:CYS19 4.7 62.0 1.0 CA P:CYS22 4.7 62.2 1.0 CB P:ARG21 4.9 65.5 1.0 N2 2:G1165 4.9 70.1 1.0 N P:PHE41 5.0 36.4 1.0 N3 2:G1165 5.0 71.9 1.0

Zinc binding site 9 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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 9 of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna with H44 in Up Position within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn101 b:94.5 occ:1.00 SG b:CYS23 2.3 53.3 1.0 SG b:CYS73 2.3 63.4 1.0 CB b:CYS26 2.4 48.2 1.0 SG b:CYS70 3.0 80.0 1.0 CB b:CYS73 3.1 49.9 1.0 CB b:CYS70 3.1 44.7 1.0 N b:CYS26 3.2 60.8 1.0 CB b:CYS23 3.3 40.8 1.0 CA b:CYS26 3.3 46.4 1.0 N b:CYS70 3.5 53.0 1.0 SG b:CYS26 3.8 80.5 1.0 CA b:CYS70 3.9 51.2 1.0 N b:CYS73 4.1 47.6 1.0 CA b:CYS73 4.2 47.1 1.0 C b:GLN25 4.2 56.5 1.0 C b:CYS26 4.4 50.2 1.0 CB b:GLN25 4.4 51.7 1.0 N b:GLY27 4.5 49.3 1.0 CB b:TYR69 4.6 39.3 1.0 C b:TYR69 4.6 44.7 1.0 CA b:CYS23 4.6 36.2 1.0 C b:CYS70 4.7 50.7 1.0 CA b:GLN25 4.7 53.1 1.0 CA b:TYR69 4.8 42.4 1.0 C b:CYS23 4.9 47.8 1.0 N b:GLN25 4.9 52.7 1.0 O b:CYS23 4.9 58.6 1.0 O b:CYS70 4.9 51.3 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