Zinc in PDB 9fy0: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna

Other elements in 9fy0:

The structure of Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna also contains other interesting chemical elements:

Magnesium (Mg) 47 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless Mrna (pdb code 9fy0). 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, PDB code: 9fy0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9fy0

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Zinc binding site 1 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:153.4
occ:1.00
 CB C:CYS60 1.5 94.4 1.0
SG C:CYS34 2.3 80.1 1.0
SG C:CYS37 2.3 89.0 1.0
SG C:CYS60 2.3 101.7 1.0
SG C:CYS57 2.3 90.4 1.0
CA C:CYS60 3.0 89.2 1.0
CB C:CYS37 3.1 81.8 1.0
CB C:CYS57 3.2 85.1 1.0
N C:CYS60 3.5 87.1 1.0
N C:CYS37 3.5 81.7 1.0
CB C:CYS34 3.5 75.7 1.0
C C:CYS60 3.8 88.4 1.0
CA C:CYS37 3.9 80.7 1.0
OD1 C:ASN59 4.1 90.6 1.0
N C:GLY61 4.2 81.3 1.0
CB C:PHE62 4.2 76.6 1.0
CB C:ASN36 4.3 76.7 1.0
N C:PHE62 4.3 78.4 1.0
C C:ASN36 4.6 80.1 1.0
O C:CYS60 4.6 87.4 1.0
N C:GLY38 4.7 84.8 1.0
CA C:CYS57 4.7 78.1 1.0
C C:ASN59 4.8 87.2 1.0
CA C:ASN36 4.8 78.2 1.0
CG1 C:VAL40 4.9 79.7 1.0
C C:CYS37 4.9 81.0 1.0
CA C:CYS34 4.9 73.0 1.0
N C:ASN36 4.9 77.5 1.0
CA C:PHE62 4.9 76.8 1.0

Zinc binding site 2 out of 9 in 9fy0

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Zinc binding site 2 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:118.2
occ:1.00
 OD1 C:ASP45 2.0 66.0 1.0
SG C:CYS19 2.1 84.7 1.0
CB C:CYS19 2.1 63.1 1.0
SG C:CYS48 2.1 81.0 1.0
SG C:CYS16 2.3 64.7 1.0
N C:CYS19 2.5 67.6 1.0
OG C:SER18 2.8 66.6 1.0
CA C:CYS19 2.8 63.1 1.0
CG C:ASP45 2.9 64.1 1.0
CB C:CYS48 3.0 60.0 1.0
OD2 C:ASP45 3.2 67.0 1.0
CB C:CYS16 3.3 54.1 1.0
C C:SER18 3.7 60.9 1.0
CB C:SER18 4.0 63.0 1.0
C C:CYS19 4.1 64.3 1.0
CA C:CYS48 4.2 51.0 1.0
NE I:ARG21 4.2 87.8 1.0
CA C:SER18 4.3 63.7 1.0
CB C:ASP45 4.3 55.7 1.0
N C:GLY20 4.3 57.5 1.0
N C:SER18 4.4 65.5 1.0
N C:CYS48 4.5 47.5 1.0
N C:ASP45 4.5 55.2 1.0
CA C:CYS16 4.7 57.0 1.0
O C:SER18 4.7 58.8 1.0
NH2 I:ARG21 4.8 83.0 1.0
CA C:ASP45 5.0 50.5 1.0

Zinc binding site 3 out of 9 in 9fy0

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Zinc binding site 3 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:152.7
occ:1.00
 CB F:CYS128 1.2 110.0 1.0
NE2 F:HIS132 2.1 75.0 1.0
SG F:CYS128 2.3 118.9 1.0
SG F:CYS121 2.3 92.2 1.0
CA F:CYS128 2.4 107.0 1.0
SG F:CYS126 2.4 87.3 1.0
CB F:CYS121 2.7 81.7 1.0
CD2 F:HIS132 2.8 73.1 1.0
N F:CYS128 2.8 106.4 1.0
C F:CYS128 3.1 107.4 1.0
CE1 F:HIS132 3.2 71.2 1.0
N F:GLY129 3.3 97.0 1.0
CB F:CYS126 3.9 85.7 1.0
CA F:CYS121 4.0 80.3 1.0
CG F:HIS132 4.1 66.0 1.0
O F:CYS128 4.1 106.8 1.0
C F:THR127 4.2 98.4 1.0
ND1 F:HIS132 4.2 65.9 1.0
CD F:LYS154 4.3 62.0 1.0
O F:GLU130 4.4 96.8 1.0
CG F:LYS154 4.4 62.0 1.0
N F:GLU130 4.4 95.5 1.0
CA F:GLY129 4.5 94.0 1.0
C F:CYS126 4.7 85.7 1.0
CA F:CYS126 4.8 82.1 1.0
O F:CYS126 4.8 86.6 1.0
C F:GLY129 4.9 94.2 1.0
N F:THR127 4.9 95.2 1.0
O F:THR127 4.9 98.0 1.0
N F:CYS121 4.9 80.2 1.0

Zinc binding site 4 out of 9 in 9fy0

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Zinc binding site 4 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:113.1
occ:1.00
 SG P:CYS40 2.1 78.0 1.0
CB P:CYS40 2.1 67.1 1.0
SG P:CYS37 2.2 101.5 1.0
SG P:CYS19 2.3 65.9 1.0
SG P:CYS22 2.3 73.9 1.0
CB P:CYS37 3.0 66.1 1.0
CB P:CYS22 3.2 62.0 1.0
CB P:CYS19 3.3 61.7 1.0
N P:CYS37 3.3 68.0 1.0
CA P:CYS40 3.6 44.5 1.0
CA P:CYS37 3.7 62.5 1.0
N P:CYS40 4.0 55.5 1.0
N P:CYS22 4.1 61.5 1.0
CA P:CYS22 4.2 65.7 1.0
CB P:ARG21 4.3 62.0 1.0
O P:CYS37 4.4 66.6 1.0
C P:CYS37 4.4 66.9 1.0
C P:LEU36 4.5 67.5 1.0
O2' 2:G1165 4.5 66.3 1.0
C P:CYS40 4.6 41.9 1.0
N2 2:G1165 4.7 69.0 1.0
CA P:CYS19 4.7 60.1 1.0
CA P:LEU36 4.8 67.4 1.0
C P:ARG21 4.8 63.6 1.0
N3 2:G1165 4.9 71.6 1.0
CA P:ARG21 4.9 61.2 1.0
N P:ARG21 5.0 65.8 1.0
C P:CYS22 5.0 67.1 1.0
CB P:LEU36 5.0 59.5 1.0

Zinc binding site 5 out of 9 in 9fy0

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Zinc binding site 5 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:138.1
occ:1.00
 ND1 R:HIS31 2.0 86.0 1.0
SG R:CYS28 2.3 100.5 1.0
SG R:CYS23 2.3 104.8 1.0
SG R:CYS84 2.3 107.5 1.0
CE1 R:HIS31 2.6 86.3 1.0
CB R:CYS84 2.7 91.8 1.0
CB R:CYS28 3.2 85.5 1.0
CG R:HIS31 3.3 82.6 1.0
CB R:CYS23 3.7 101.2 1.0
NE2 R:HIS31 3.9 85.5 1.0
CB R:HIS31 3.9 80.7 1.0
N R:HIS31 4.1 75.1 1.0
CA R:CYS84 4.1 89.1 1.0
CD2 R:HIS31 4.2 82.9 1.0
N R:CYS23 4.3 99.6 1.0
N R:CYS84 4.3 87.9 1.0
CB R:PRO82 4.3 71.1 1.0
CB R:TYR30 4.3 71.8 1.0
CD2 R:TYR30 4.4 78.1 1.0
CA R:CYS23 4.6 99.6 1.0
CA R:HIS31 4.6 79.4 1.0
CA R:CYS28 4.6 80.5 1.0
OD1 R:ASP25 4.7 103.8 1.0
N R:TYR30 4.8 79.3 1.0
CG R:PRO19 4.8 96.0 1.0
CG R:TYR30 4.8 77.0 1.0
C R:TYR30 4.9 74.2 1.0
CA R:TYR30 4.9 74.5 1.0
CG R:PRO82 4.9 71.8 1.0

Zinc binding site 6 out of 9 in 9fy0

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Zinc binding site 6 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn101

b:166.3
occ:1.00
 CB W:CYS24 2.0 111.5 1.0
SG W:CYS40 2.2 119.1 1.0
SG W:CYS21 2.2 107.3 1.0
SG W:CYS43 2.3 120.4 1.0
SG W:CYS24 3.0 112.5 1.0
OG W:SER42 3.1 122.4 1.0
CB W:CYS21 3.2 104.4 1.0
CB W:CYS40 3.3 103.6 1.0
CA W:CYS24 3.4 106.9 1.0
N W:CYS24 3.6 107.5 1.0
CB W:CYS43 3.8 114.6 1.0
OD1 W:ASN23 4.0 106.3 1.0
CG2 W:THR45 4.1 97.0 1.0
C W:CYS24 4.2 109.0 1.0
N W:CYS43 4.3 112.4 1.0
CB W:ASN26 4.3 99.2 1.0
N W:GLY25 4.4 106.8 1.0
CB W:SER42 4.5 114.3 1.0
CA W:CYS21 4.6 98.6 1.0
N W:ASN26 4.6 103.0 1.0
CA W:CYS43 4.6 115.5 1.0
CA W:CYS40 4.8 101.1 1.0
CG W:ASN23 4.9 109.0 1.0
C W:ASN23 4.9 109.1 1.0

Zinc binding site 7 out of 9 in 9fy0

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Zinc binding site 7 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn101

b:127.6
occ:1.00
 CB a:CYS64 1.9 93.5 1.0
CB a:CYS61 2.2 83.7 1.0
SG a:CYS61 2.2 79.2 1.0
SG a:CYS38 2.4 110.6 1.0
CB a:CYS41 2.4 101.7 1.0
SG a:CYS64 2.5 92.0 1.0
SG a:CYS41 2.6 108.7 1.0
CB a:CYS38 2.8 96.9 1.0
CA a:CYS64 3.4 89.9 1.0
OG1 a:THR66 3.4 93.2 1.0
CA a:CYS61 3.7 80.8 1.0
N a:CYS64 3.8 85.5 1.0
CA a:CYS41 3.9 98.3 1.0
CA a:CYS38 4.3 92.7 1.0
C a:CYS64 4.3 96.2 1.0
C a:CYS61 4.4 84.9 1.0
N a:CYS41 4.5 103.2 1.0
N a:CYS61 4.5 84.6 1.0
O a:CYS41 4.5 98.5 1.0
C a:CYS41 4.5 97.0 1.0
O a:CYS61 4.6 92.3 1.0
C a:TYR63 4.6 72.7 1.0
N a:GLY65 4.6 95.4 1.0
CB a:THR66 4.8 90.0 1.0
N a:THR66 4.8 88.4 1.0

Zinc binding site 8 out of 9 in 9fy0

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Zinc binding site 8 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn102

b:109.9
occ:1.00
 OD1 a:ASP53 1.8 102.1 1.0
CG a:ASP53 1.8 97.9 1.0
CB a:CYS50 2.0 78.8 1.0
CB a:CYS24 2.0 84.1 1.0
OD2 a:ASP53 2.1 97.0 1.0
SG a:CYS21 2.3 84.0 1.0
SG a:CYS50 2.7 78.1 1.0
CB a:ASP53 2.7 95.2 1.0
SG a:CYS24 2.9 89.9 1.0
CA a:CYS24 3.2 80.0 1.0
CA a:CYS50 3.3 74.8 1.0
N a:CYS24 3.4 81.0 1.0
N a:ASP53 3.6 92.4 1.0
CB a:CYS21 3.7 81.0 1.0
CA a:ASP53 3.7 90.7 1.0
N a:CYS50 3.7 79.5 1.0
C a:CYS50 4.0 75.8 1.0
O a:CYS50 4.3 84.0 1.0
C a:CYS24 4.5 81.3 1.0
C a:ILE23 4.6 75.2 1.0
C a:ALA52 4.7 88.1 1.0
N a:GLU51 4.8 85.7 1.0
CA a:CYS21 5.0 80.8 1.0
C a:PHE49 5.0 77.8 1.0

Zinc binding site 9 out of 9 in 9fy0

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Zinc binding site 9 out of 9 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Ss-AIF2BETA Leaderless 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-AIF2BETA Leaderless Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn101

b:112.3
occ:1.00
 SG b:CYS73 2.3 69.9 1.0
SG b:CYS23 2.3 61.3 1.0
CB b:CYS26 2.4 58.5 1.0
CB b:CYS73 3.0 56.6 1.0
N b:CYS26 3.2 70.5 1.0
CB b:CYS70 3.2 52.9 1.0
CA b:CYS26 3.3 56.3 1.0
N b:CYS70 3.4 53.1 1.0
CB b:CYS23 3.4 50.5 1.0
SG b:CYS70 3.5 81.1 1.0
SG b:CYS26 3.8 83.5 1.0
CA b:CYS70 3.9 56.3 1.0
N b:CYS73 3.9 38.7 1.0
CA b:CYS73 4.1 42.7 1.0
C b:GLN25 4.4 65.8 1.0
C b:TYR69 4.5 49.8 1.0
C b:CYS26 4.5 56.6 1.0
CA b:TYR69 4.6 45.4 1.0
C b:CYS70 4.6 54.8 1.0
CB b:GLN25 4.7 60.3 1.0
O b:CYS70 4.8 63.3 1.0
CB b:TYR69 4.8 45.5 1.0
N b:GLY27 4.8 50.9 1.0
CA b:CYS23 4.8 51.6 1.0
CA b:GLN25 4.9 65.1 1.0
CD1 b:TYR69 5.0 54.0 1.0

Reference:

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
Page generated: Sun Feb 9 01:07:32 2025

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