Atomistry » Potassium » PDB 9dkf-9gef » 9fda
Atomistry »
  Potassium »
    PDB 9dkf-9gef »
      9fda »

Potassium in PDB 9fda: Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex

Other elements in 9fda:

The structure of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex also contains other interesting chemical elements:

Magnesium (Mg) 53 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Potassium atom in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex (pdb code 9fda). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 25 binding sites of Potassium where determined in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex, PDB code: 9fda:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 1 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:80.5
occ:1.00
 O D:LEU82 2.7 77.6 1.0
O D:ALA80 3.0 57.8 1.0
OG1 D:THR86 3.1 50.3 1.0
O D:GLY84 3.1 61.8 1.0
O D:ALA79 3.2 56.9 1.0
C D:ALA80 3.6 57.9 1.0
O2 B:U5 3.6 116.0 1.0
N D:THR86 3.8 56.6 1.0
CA D:ALA80 3.9 53.1 1.0
C D:LEU82 3.9 72.0 1.0
CA D:THR86 4.0 54.7 1.0
C D:GLY84 4.0 69.7 1.0
ND2 D:ASN89 4.1 59.6 1.0
CB D:THR86 4.2 54.9 1.0
C D:ALA79 4.2 52.2 1.0
C D:ASN85 4.4 58.6 1.0
N D:GLY84 4.5 72.6 1.0
N D:ALA80 4.5 50.1 1.0
N D:LEU82 4.6 62.7 1.0
C D:LYS83 4.6 75.0 1.0
N D:ARG81 4.7 58.7 1.0
CA D:LYS83 4.7 80.8 1.0
O2' B:U5 4.7 100.2 1.0
C D:ARG81 4.8 61.9 1.0
N D:LYS83 4.8 76.2 1.0
C2 B:U5 4.8 120.5 1.0
N D:ASN85 4.8 65.1 1.0
CA D:LEU82 4.9 67.7 1.0
CA D:GLY84 4.9 72.9 1.0
CA D:ASN85 4.9 64.4 1.0
CG2 D:THR86 4.9 56.8 1.0
O D:ARG81 5.0 65.7 1.0

Potassium binding site 2 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 2 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K201

b:235.4
occ:1.00
 O F:VAL84 2.8 88.1 1.0
O F:ARG79 3.9 136.1 1.0
C F:VAL84 4.0 91.3 1.0
O F:ASN81 4.3 132.0 1.0
O F:ILE85 4.3 88.9 1.0
O F:PHE78 4.3 119.1 1.0
C F:ILE85 4.6 86.0 1.0
CA F:ILE85 4.6 88.4 1.0
CA F:ASP82 4.8 126.5 1.0
N F:ILE85 4.8 87.9 1.0
C F:ARG79 4.8 133.4 1.0
OD1 F:ASP82 4.9 141.0 1.0

Potassium binding site 3 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 3 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1654

b:74.0
occ:1.00
 O B:HOH3086 2.8 64.5 1.0
O B:HOH2570 2.8 78.0 1.0
O4 B:U644 2.9 36.4 1.0
O6 B:G645 2.9 36.9 1.0
O4 B:U594 3.1 35.2 1.0
C4 B:U644 3.7 34.3 1.0
N1 B:A595 3.8 41.5 1.0
C2 B:A595 3.8 37.3 1.0
C6 B:G645 3.9 34.7 1.0
C4 B:U594 4.0 38.8 1.0
MG B:MG1617 4.0 66.9 1.0
N3 B:U594 4.1 33.3 1.0
C5 B:U644 4.1 37.2 1.0
N7 B:G645 4.1 36.9 1.0
O B:HOH2401 4.3 62.0 1.0
C5 B:G645 4.4 35.8 1.0
N4 B:C643 4.4 34.2 1.0
O B:HOH3221 4.5 53.0 1.0
N6 B:A596 4.6 36.6 1.0
O4 B:U593 4.6 42.3 1.0
C5 B:C643 4.7 36.3 1.0
N3 B:A595 4.8 40.1 1.0
C4 B:C643 4.8 36.5 1.0
C6 B:A595 4.9 38.9 1.0
N3 B:U644 4.9 34.1 1.0

Potassium binding site 4 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 4 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1655

b:66.1
occ:1.00
 O B:HOH2265 2.4 30.4 1.0
N7 B:A583 2.9 45.8 1.0
O B:HOH2014 2.9 40.6 1.0
O6 B:G584 3.1 31.6 1.0
N3 B:C758 3.2 36.9 1.0
O2 B:C758 3.3 32.8 1.0
N7 B:G584 3.3 39.5 1.0
C5 B:C582 3.5 47.6 1.0
OP2 B:A583 3.5 51.5 1.0
C8 B:A583 3.6 46.5 1.0
C6 B:G584 3.6 35.9 1.0
C2 B:C758 3.6 37.5 1.0
C5 B:G584 3.7 39.1 1.0
C6 B:C582 3.9 46.2 1.0
OP2 B:C582 3.9 43.0 1.0
C5 B:A583 4.1 47.7 1.0
C4 B:C582 4.2 44.8 1.0
C4 B:C758 4.3 40.5 1.0
C8 B:G584 4.4 40.9 1.0
O5' B:C582 4.4 39.9 1.0
N6 B:A583 4.4 41.8 1.0
N4 B:C582 4.5 45.4 1.0
N4 B:C758 4.5 39.7 1.0
O4 B:U757 4.6 40.2 1.0
C6 B:A583 4.7 45.3 1.0
P B:A583 4.7 52.0 1.0
N1 B:C582 4.8 46.3 1.0
C3' B:C582 4.8 44.7 1.0
O5' B:A583 4.8 46.8 1.0
N1 B:G584 4.8 38.5 1.0
P B:C582 4.8 39.7 1.0
C4 B:G584 4.9 38.6 1.0
N9 B:A583 4.9 45.1 1.0
N3 B:U757 4.9 34.2 1.0
N1 B:C758 4.9 36.1 1.0
N3 B:C582 5.0 45.3 1.0

Potassium binding site 5 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 5 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1656

b:72.6
occ:1.00
 OP1 B:A1508 2.8 55.5 1.0
OP1 B:C1521 2.8 43.0 1.0
O B:HOH2873 2.9 30.1 1.0
OP1 B:A1500 3.0 43.1 1.0
O B:HOH2513 3.1 64.7 1.0
O3' B:A1499 3.1 44.1 1.0
O B:HOH2477 3.3 72.3 1.0
O B:HOH2214 3.4 98.4 1.0
P B:A1500 3.6 41.1 1.0
MG B:MG1639 3.7 34.2 1.0
P B:C1521 3.8 45.5 1.0
O B:HOH1909 3.9 60.2 1.0
OP2 B:C1521 3.9 48.2 1.0
P B:A1508 4.0 49.5 1.0
O B:HOH2228 4.1 83.3 1.0
O B:HOH2364 4.2 55.3 1.0
C3' B:A1499 4.3 48.0 1.0
OP2 B:A1508 4.3 55.0 1.0
C5' B:A1500 4.4 43.4 1.0
O2' B:A1499 4.5 53.2 1.0
O5' B:A1500 4.5 44.7 1.0
C4' B:A1499 4.5 48.0 1.0
O3' B:C1520 4.6 45.3 1.0
O5' B:A1508 4.8 52.1 1.0
OP2 B:A1500 4.9 48.9 1.0
C5' B:A1508 4.9 51.5 1.0

Potassium binding site 6 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 6 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1657

b:66.0
occ:1.00
 O B:HOH2031 2.2 27.7 1.0
O B:HOH2916 2.6 59.9 1.0
OP2 B:G107 3.7 22.5 1.0
O3' B:G324 3.8 35.8 1.0
N7 B:A325 3.8 32.6 1.0
OP1 B:C106 3.9 39.1 1.0
O2' B:G324 4.0 32.5 1.0
O B:HOH3180 4.1 40.1 1.0
C8 B:A325 4.2 35.1 1.0
OP1 B:A325 4.2 38.2 1.0
OP1 B:G107 4.2 28.8 1.0
P B:G107 4.3 25.1 1.0
O5' B:C106 4.6 28.8 1.0
P B:A325 4.6 38.2 1.0
P B:C106 4.6 29.8 1.0
C3' B:G324 4.8 31.4 1.0
O T:HOH119 4.8 49.7 1.0
OP2 B:C106 4.8 28.9 1.0
O3' B:C106 4.8 25.4 1.0
O6 B:G326 4.9 26.4 1.0
C5' B:C106 4.9 28.8 1.0
O2' B:G134 4.9 37.7 1.0
C2' B:G324 5.0 31.2 1.0

Potassium binding site 7 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 7 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1658

b:48.1
occ:1.00
 O6 B:G326 2.8 26.4 1.0
O B:HOH1953 2.8 29.5 1.0
OP2 B:G108 2.8 25.4 1.0
N7 B:G108 3.1 25.5 1.0
OP2 B:G107 3.1 22.5 1.0
N1 B:A109 3.5 32.2 1.0
O5' B:G107 3.5 27.3 1.0
O B:HOH3180 3.6 40.1 1.0
C2 B:A109 3.7 30.1 1.0
C8 B:G108 3.7 26.1 1.0
C6 B:G326 3.8 31.3 1.0
P B:G107 3.8 25.1 1.0
O B:HOH2031 4.0 27.7 1.0
N1 B:G326 4.0 30.3 1.0
NH2 T:ARG10 4.1 28.8 1.0
C8 B:G107 4.1 24.6 1.0
P B:G108 4.2 23.0 1.0
N7 B:G107 4.2 22.6 1.0
C5 B:G108 4.3 25.8 1.0
C3' B:G107 4.4 25.2 1.0
OP1 B:G107 4.4 28.8 1.0
C6 B:A109 4.6 32.9 1.0
O5' B:G108 4.6 24.8 1.0
O6 B:G108 4.6 34.7 1.0
C5' B:G107 4.7 26.6 1.0
CZ T:ARG10 4.8 33.0 1.0
O3' B:G107 4.8 24.9 1.0
N3 B:A109 4.8 27.8 1.0
C6 B:G108 4.9 29.5 1.0
N6 B:A109 5.0 31.3 1.0

Potassium binding site 8 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 8 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1659

b:168.6
occ:1.00
 O B:HOH2430 2.7 46.8 1.0
O B:HOH3101 2.8 72.8 1.0
O B:HOH3222 2.8 98.3 1.0
OP2 B:U801 2.8 60.4 1.0
O B:HOH3126 3.2 62.9 1.0
P B:U801 3.5 65.5 1.0
OP1 B:U801 3.6 72.1 1.0
O5' B:U801 3.8 62.5 1.0
O B:HOH3146 4.0 121.1 1.0
OP2 B:A802 4.3 59.6 1.0
C5' B:U801 4.6 62.5 1.0
N2 B:G776 4.6 55.7 1.0
N6 B:A780 4.6 41.4 1.0
N1 B:A780 4.7 40.7 1.0
N4 B:C779 4.8 39.8 1.0
O B:HOH3001 4.8 73.1 1.0
C2 B:G776 4.8 55.9 1.0
O B:HOH2566 4.9 75.4 1.0

Potassium binding site 9 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 9 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1660

b:65.7
occ:1.00
 OP2 B:G567 2.6 44.8 1.0
OP2 B:C564 2.6 38.2 1.0
OP2 B:U565 2.9 43.2 1.0
O2' B:A563 3.0 28.9 1.0
O L:HOH234 3.3 75.8 1.0
O B:HOH2746 3.3 48.8 1.0
O3' B:A563 3.7 35.0 1.0
P B:C564 3.7 34.3 1.0
P B:G567 3.7 39.0 1.0
O3' B:G566 3.8 39.6 1.0
C2' B:A563 4.0 30.5 1.0
O2' B:G566 4.0 33.7 1.0
P B:U565 4.1 42.4 1.0
C5' B:C564 4.2 40.8 1.0
O5' B:G567 4.3 38.0 1.0
O5' B:C564 4.3 39.3 1.0
C3' B:A563 4.4 34.2 1.0
OP1 B:U565 4.5 44.5 1.0
C3' B:G566 4.5 37.6 1.0
C8 B:G567 4.7 25.2 1.0
NH2 L:ARG12 4.7 29.8 1.0
N7 B:G567 4.7 25.7 1.0
O3' B:C564 4.9 39.5 1.0
C2' B:G566 4.9 36.0 1.0

Potassium binding site 10 out of 25 in 9fda

Go back to Potassium Binding Sites List in 9fda
Potassium binding site 10 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of E. Coli 30S-IF1-IF3-Mrna-Edeine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1661

b:55.1
occ:1.00
 O6 B:G22 2.7 24.9 1.0
O4 B:U12 2.9 32.6 1.0
O B:HOH2076 3.0 54.9 1.0
O B:HOH1789 3.0 45.2 1.0
O6 B:G21 3.2 32.1 1.0
O6 B:G11 3.3 34.2 1.0
O B:HOH3026 3.3 44.4 1.0
C6 B:G21 3.6 31.4 1.0
N4 B:C23 3.6 23.8 1.0
C6 B:G22 3.7 25.5 1.0
C4 B:U12 3.8 32.5 1.0
N1 B:G21 3.8 26.1 1.0
N3 B:U12 3.9 28.9 1.0
N7 B:G22 4.0 26.4 1.0
C5 B:G22 4.3 26.3 1.0
C6 B:G11 4.3 30.5 1.0
C5 B:G21 4.6 30.9 1.0
C4 B:C23 4.6 25.1 1.0
C2 B:G21 4.8 26.9 1.0
N1 B:G22 4.9 23.8 1.0

Reference:

H.A.Safdari, M.Morici, A.Sanchez-Castro, A.Dallape, H.Paternoga, A.M.Giuliodori, A.Fabbretti, P.Milon, D.N.Wilson. The Translation Inhibitors Kasugamycin, Edeine and GE81112 Target Distinct Steps During 30S Initiation Complex Formation. Nat Commun V. 16 2470 2025.
ISSN: ESSN 2041-1723
PubMed: 40075065
DOI: 10.1038/S41467-025-57731-8
Page generated: Sat Aug 9 18:57:53 2025

Last articles

Mg in 1R2Q
Mg in 1R2C
Mg in 1R10
Mg in 1R0Z
Mg in 1R0X
Mg in 1R0A
Mg in 1R03
Mg in 1QZR
Mg in 1QU2
Mg in 1QYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy