Zinc in PDB 9frk: Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd Mrna

Other elements in 9frk:

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

Magnesium (Mg) 59 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 9frk

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:153.4
occ:1.00
 SG C:CYS37 2.2 99.5 1.0
SG C:CYS60 2.2 85.8 1.0
SG C:CYS57 2.2 94.4 1.0
SG C:CYS34 2.4 86.9 1.0
CB C:CYS34 2.4 79.9 1.0
CB C:CYS37 3.1 85.7 1.0
CB C:CYS60 3.3 77.1 1.0
CB C:CYS57 3.3 79.9 1.0
N C:CYS37 3.4 85.8 1.0
CA C:CYS37 3.8 83.3 1.0
OD1 C:ASN59 3.9 84.0 1.0
CA C:CYS34 3.9 78.5 1.0
N C:GLY38 4.0 97.8 1.0
N C:CYS60 4.3 81.8 1.0
C C:CYS37 4.3 88.2 1.0
CA C:CYS60 4.4 78.2 1.0
C C:CYS34 4.4 75.3 1.0
CG2 C:VAL40 4.4 78.9 1.0
C C:ASN36 4.6 88.9 1.0
CA C:CYS57 4.7 74.0 1.0
O C:CYS34 4.7 75.4 1.0
N C:GLU39 4.7 92.6 1.0
N C:ASN36 4.7 82.8 1.0
CB C:ASN36 4.7 83.2 1.0
N C:CYS34 4.8 79.8 1.0
CB C:PHE62 4.9 77.5 1.0
CA C:ASN36 4.9 87.5 1.0
CG C:ASN59 4.9 81.0 1.0

Zinc binding site 2 out of 8 in 9frk

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:129.0
occ:1.00
 OD1 C:ASP45 2.0 72.1 1.0
CB C:CYS19 2.1 73.7 1.0
SG C:CYS48 2.1 83.2 1.0
SG C:CYS19 2.2 89.9 1.0
SG C:CYS16 2.3 86.3 1.0
CG C:ASP45 2.8 71.2 1.0
N C:CYS19 3.0 76.6 1.0
OD2 C:ASP45 3.0 72.7 1.0
CA C:CYS19 3.1 72.6 1.0
CB C:CYS16 3.1 66.8 1.0
CB C:CYS48 3.2 68.3 1.0
OG C:SER18 3.5 67.6 1.0
C C:CYS19 4.1 71.7 1.0
CB C:ASP45 4.1 63.6 1.0
NE I:ARG21 4.3 99.8 1.0
C C:SER18 4.3 65.4 1.0
N C:GLY20 4.3 64.0 1.0
CA C:CYS48 4.3 63.6 1.0
N C:ASP45 4.4 69.3 1.0
N C:CYS48 4.4 66.7 1.0
CA C:CYS16 4.5 58.0 1.0
CB C:SER18 4.7 61.1 1.0
CA C:ASP45 4.8 59.0 1.0
CD I:ARG21 4.9 96.2 1.0
CA C:SER18 4.9 57.7 1.0
N C:SER18 4.9 63.5 1.0
C C:CYS16 5.0 69.1 1.0

Zinc binding site 3 out of 8 in 9frk

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:195.4
occ:1.00
 CB F:CYS128 1.5 126.8 1.0
NE2 F:HIS132 2.0 89.6 1.0
SG F:CYS121 2.2 117.0 1.0
SG F:CYS128 2.3 137.7 1.0
CD2 F:HIS132 2.3 88.0 1.0
SG F:CYS126 2.4 108.7 1.0
CA F:CYS128 2.8 122.2 1.0
CB F:CYS121 3.1 105.1 1.0
N F:CYS128 3.2 123.6 1.0
CE1 F:HIS132 3.3 90.6 1.0
C F:CYS128 3.5 121.6 1.0
N F:GLY129 3.6 113.0 1.0
CG F:HIS132 3.6 78.2 1.0
CB F:CYS126 3.9 103.2 1.0
ND1 F:HIS132 4.0 85.8 1.0
CD F:LYS154 4.1 80.1 1.0
CA F:CYS121 4.2 100.0 1.0
O F:GLU130 4.3 115.1 1.0
O F:CYS128 4.4 122.2 1.0
N F:GLU130 4.5 115.5 1.0
CG F:LYS154 4.5 83.7 1.0
C F:THR127 4.6 110.4 1.0
CA F:GLY129 4.8 111.5 1.0
CB F:HIS132 4.9 80.6 1.0
N F:LYS154 4.9 76.7 1.0
CA F:CYS126 5.0 100.0 1.0
C F:GLY129 5.0 114.0 1.0
C F:CYS126 5.0 103.7 1.0

Zinc binding site 4 out of 8 in 9frk

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:170.4
occ:1.00
 CB P:CYS40 2.1 85.4 1.0
SG P:CYS19 2.2 99.4 1.0
SG P:CYS37 2.2 110.7 1.0
SG P:CYS22 2.3 82.1 1.0
SG P:CYS40 2.3 90.0 1.0
N P:CYS37 2.7 84.1 1.0
CB P:CYS37 2.9 83.3 1.0
CB P:CYS19 3.2 82.6 1.0
CA P:CYS37 3.3 79.8 1.0
CA P:CYS40 3.5 70.4 1.0
C P:LEU36 3.8 80.2 1.0
N P:CYS40 3.9 79.4 1.0
O P:CYS37 3.9 79.2 1.0
CB P:CYS22 3.9 77.1 1.0
C P:CYS37 4.0 76.4 1.0
CA P:LEU36 4.1 76.4 1.0
N P:CYS22 4.3 81.4 1.0
CB P:LEU36 4.3 71.3 1.0
CD2 P:LEU36 4.4 85.0 1.0
C P:CYS40 4.4 66.2 1.0
CA P:CYS19 4.5 81.3 1.0
CB P:ARG21 4.7 73.7 1.0
CA P:CYS22 4.7 85.5 1.0
N P:PHE41 4.7 62.5 1.0
O2' 2:G1165 4.8 76.8 1.0
O P:LEU36 4.9 82.6 1.0

Zinc binding site 5 out of 8 in 9frk

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:163.7
occ:1.00
 ND1 R:HIS31 2.0 94.2 1.0
SG R:CYS28 2.3 113.2 1.0
SG R:CYS23 2.3 117.2 1.0
SG R:CYS84 2.3 120.0 1.0
CE1 R:HIS31 2.7 95.6 1.0
CB R:CYS84 2.9 108.0 1.0
CB R:CYS28 3.2 100.5 1.0
CG R:HIS31 3.2 89.4 1.0
CB R:CYS23 3.5 110.2 1.0
CB R:HIS31 3.9 89.0 1.0
NE2 R:HIS31 3.9 95.1 1.0
N R:CYS23 3.9 111.0 1.0
N R:HIS31 4.1 86.7 1.0
CD2 R:HIS31 4.2 91.2 1.0
CA R:CYS84 4.2 106.9 1.0
CA R:CYS23 4.2 110.3 1.0
CB R:TYR30 4.3 84.1 1.0
N R:CYS84 4.3 102.5 1.0
CD2 R:TYR30 4.4 91.5 1.0
CB R:PRO82 4.4 83.3 1.0
CA R:CYS28 4.6 94.6 1.0
CA R:HIS31 4.6 87.3 1.0
C R:CYS23 4.8 110.1 1.0
CG R:TYR30 4.8 86.0 1.0
N R:TYR30 4.9 91.5 1.0
CG R:PRO19 4.9 101.3 1.0
C R:TYR30 4.9 92.4 1.0
CA R:TYR30 5.0 91.7 1.0
O R:CYS23 5.0 109.3 1.0

Zinc binding site 6 out of 8 in 9frk

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn101

b:201.5
occ:1.00
 SG W:CYS24 1.6 151.2 1.0
CB W:CYS24 2.1 136.5 1.0
SG W:CYS43 2.3 122.3 1.0
SG W:CYS21 2.3 110.8 1.0
SG W:CYS40 2.4 117.0 1.0
CA W:CYS24 3.0 132.4 1.0
N W:CYS24 3.0 133.7 1.0
CB W:CYS43 3.4 117.7 1.0
CB W:CYS21 3.4 107.7 1.0
OG W:SER42 3.4 125.4 1.0
C W:CYS24 3.6 131.5 1.0
CB W:CYS40 3.7 101.9 1.0
N W:GLY25 3.8 123.2 1.0
N W:ASN26 4.1 119.3 1.0
CB W:ASN26 4.1 114.9 1.0
N W:CYS43 4.1 119.6 1.0
C W:ASN23 4.2 117.8 1.0
O W:CYS24 4.3 127.7 1.0
CA W:CYS43 4.4 115.8 1.0
ND2 W:ASN23 4.6 124.1 1.0
CG W:ASN23 4.6 120.7 1.0
CB W:ASN23 4.6 119.5 1.0
CB W:SER42 4.7 119.9 1.0
CA W:CYS21 4.8 104.7 1.0
CA W:ASN26 4.8 116.2 1.0
OG1 W:THR45 4.8 110.3 1.0
CA W:ASN23 4.8 119.9 1.0
O W:CYS21 4.9 110.6 1.0
N W:ASN23 4.9 121.7 1.0
CA W:GLY25 5.0 118.0 1.0
C W:CYS21 5.0 107.2 1.0

Zinc binding site 7 out of 8 in 9frk

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Saccharolobus Solfataricus 30S Initiation Complex Bound to Sd 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 Sd Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn101

b:182.2
occ:1.00
 CB a:CYS61 2.1 113.5 1.0
SG a:CYS61 2.1 128.3 1.0
SG a:CYS64 2.2 119.3 1.0
SG a:CYS38 2.3 126.2 1.0
SG a:CYS41 2.4 134.4 1.0
CB a:CYS38 3.4 112.3 1.0
CA a:CYS61 3.6 114.4 1.0
N a:CYS64 3.8 109.0 1.0
CB a:CYS64 3.8 110.0 1.0
NZ a:LYS40 4.0 123.8 1.0
OG1 a:THR66 4.0 108.5 1.0
C a:CYS61 4.1 112.0 1.0
CB a:CYS41 4.1 119.4 1.0
O a:CYS61 4.1 110.2 1.0
N a:GLY65 4.2 97.3 1.0
CA a:CYS64 4.2 109.0 1.0
N a:THR66 4.3 104.3 1.0
N a:CYS61 4.4 117.4 1.0
CB a:THR66 4.5 110.0 1.0
CB a:TYR63 4.5 95.9 1.0
C a:CYS64 4.6 109.8 1.0
CG a:LYS40 4.7 122.8 1.0
CD2 a:TYR63 4.7 98.2 1.0
CA a:CYS38 4.7 108.9 1.0
C a:TYR63 4.8 98.2 1.0
N a:TYR63 4.8 96.7 1.0
N a:CYS41 4.8 120.4 1.0
CA a:TYR63 4.9 95.0 1.0
CA a:THR66 5.0 109.2 1.0
CG a:TYR63 5.0 99.9 1.0

Zinc binding site 8 out of 8 in 9frk

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

b:154.4
occ:1.00
 CB a:CYS24 2.0 99.9 1.0
SG a:CYS21 2.2 111.1 1.0
OD2 a:ASP53 2.3 112.4 1.0
SG a:CYS24 2.5 110.6 1.0
CB a:CYS21 2.8 95.8 1.0
CA a:CYS24 3.0 92.4 1.0
CG a:ASP53 3.1 112.1 1.0
N a:CYS24 3.2 96.7 1.0
C a:CYS24 3.6 94.6 1.0
CB a:CYS50 3.7 93.8 1.0
OD1 a:ASP53 3.7 111.3 1.0
SG a:CYS50 3.8 84.8 1.0
N a:ASN25 3.9 93.5 1.0
CB a:ASP53 4.0 109.2 1.0
N a:ARG26 4.3 96.2 1.0
CB a:ARG26 4.3 98.9 1.0
CA a:CYS21 4.3 95.8 1.0
O a:CYS24 4.4 95.6 1.0
N a:CYS50 4.5 89.1 1.0
C a:ILE23 4.5 98.9 1.0
CA a:CYS50 4.7 91.4 1.0
C a:CYS21 4.9 93.0 1.0
CA a:ARG26 5.0 93.3 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 01:07:31 2025

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