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

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

Magnesium

(Mg)

53 atoms

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-Kasugamycin Complex (pdb code 9fco). 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-Kasugamycin Complex, PDB code: 9fco:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1655 b:71.9 occ:1.00 O B:HOH2748 2.9 31.8 1.0 O B:HOH1983 2.9 32.6 1.0 O6 B:G645 2.9 30.9 1.0 O4 B:U644 2.9 39.5 1.0 O B:HOH1752 3.0 35.2 1.0 O4 B:U594 3.0 42.7 1.0 O B:HOH3266 3.6 35.8 1.0 C4 B:U644 3.7 32.6 1.0 C2 B:A595 3.9 35.5 1.0 C6 B:G645 3.9 26.6 1.0 C4 B:U594 3.9 37.6 1.0 N1 B:A595 3.9 38.1 1.0 MG B:MG1618 3.9 67.2 1.0 N3 B:U594 3.9 31.8 1.0 N7 B:G645 4.1 31.1 1.0 C5 B:U644 4.1 32.4 1.0 O B:HOH2716 4.2 42.2 1.0 C5 B:G645 4.3 30.0 1.0 O4 B:U593 4.3 43.7 1.0 N6 B:A596 4.5 36.4 1.0 O B:HOH2138 4.6 33.0 1.0 N4 B:C643 4.6 31.8 1.0 N3 B:A595 4.8 41.4 1.0 C5 B:C643 4.9 34.0 1.0 O B:HOH2895 4.9 31.9 1.0 N3 B:U644 4.9 29.0 1.0 O6 B:G646 4.9 42.9 1.0 C6 B:A595 5.0 33.2 1.0 C4 B:C643 5.0 31.6 1.0

Potassium binding site 2 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1656 b:100.0 occ:1.00 O B:HOH2112 2.6 41.1 1.0 O6 B:G584 3.0 30.5 1.0 N7 B:A583 3.0 30.1 1.0 N3 B:C758 3.3 25.8 1.0 OP2 B:A583 3.4 55.0 1.0 N7 B:G584 3.4 34.8 1.0 O2 B:C758 3.4 36.3 1.0 C6 B:G584 3.5 29.9 1.0 C8 B:A583 3.7 33.9 1.0 C2 B:C758 3.7 29.5 1.0 OP2 B:C582 3.7 43.5 1.0 C5 B:G584 3.7 31.2 1.0 C5 B:C582 3.8 34.3 1.0 C6 B:C582 4.1 34.2 1.0 C5 B:A583 4.2 29.4 1.0 O5' B:C582 4.2 35.8 1.0 C4 B:C758 4.2 27.1 1.0 O4 B:U757 4.4 35.2 1.0 C8 B:G584 4.5 35.6 1.0 N4 B:C758 4.5 27.9 1.0 C4 B:C582 4.5 33.5 1.0 N6 B:A583 4.6 30.4 1.0 P B:C582 4.6 39.1 1.0 P B:A583 4.6 53.1 1.0 O5' B:A583 4.7 43.7 1.0 N3 B:U757 4.7 28.1 1.0 O B:HOH1744 4.7 44.9 1.0 N1 B:G584 4.7 29.6 1.0 C3' B:C582 4.7 41.6 1.0 C6 B:A583 4.9 28.6 1.0 N4 B:C582 4.9 37.2 1.0 C4 B:G584 4.9 31.2 1.0 N1 B:C758 4.9 28.9 1.0 N9 B:A583 5.0 33.6 1.0 N1 B:C582 5.0 33.7 1.0

Potassium binding site 3 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1657 b:44.3 occ:1.00 OP1 B:A1508 2.6 37.9 1.0 OP1 B:A1500 2.8 27.3 1.0 OP1 B:C1521 2.8 29.3 1.0 O B:HOH3074 2.9 35.3 1.0 O B:HOH2197 3.0 23.0 1.0 O3' B:A1499 3.0 29.4 1.0 O B:HOH2760 3.1 34.0 1.0 O B:HOH3119 3.2 34.3 1.0 MG B:MG1640 3.4 17.9 1.0 P B:A1500 3.4 29.3 1.0 P B:A1508 3.7 32.0 1.0 O B:HOH2318 3.8 48.4 1.0 P B:C1521 4.0 31.1 1.0 C5' B:A1500 4.1 32.2 1.0 OP2 B:A1508 4.1 40.1 1.0 OP2 B:C1521 4.2 40.1 1.0 C3' B:A1499 4.3 32.6 1.0 O B:HOH2026 4.3 44.8 1.0 O5' B:A1508 4.3 35.7 1.0 O5' B:A1500 4.3 30.3 1.0 O B:HOH1780 4.4 58.8 1.0 O2' B:A1499 4.4 39.6 1.0 C4' B:A1499 4.6 33.2 1.0 C5' B:A1508 4.7 35.2 1.0 OP2 B:A1500 4.8 34.1 1.0 OP1 B:G1505 4.8 31.9 1.0 O3' B:C1520 4.8 37.6 1.0 C2' B:A1499 4.9 34.7 1.0 O B:HOH1955 5.0 19.0 1.0

Potassium binding site 4 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1658 b:63.7 occ:1.00 O B:HOH2470 2.2 28.2 1.0 O6 B:G326 2.8 24.2 1.0 N7 B:A325 2.9 29.6 1.0 OP2 B:G107 2.9 30.5 1.0 O2' B:G324 3.0 31.4 1.0 OP1 B:G107 3.4 29.3 1.0 C8 B:A325 3.6 28.8 1.0 P B:G107 3.6 24.0 1.0 C6 B:G326 3.7 23.1 1.0 O B:HOH1773 3.8 21.7 1.0 O3' B:G324 4.0 37.8 1.0 K B:K1659 4.1 63.0 1.0 C5 B:A325 4.1 30.1 1.0 N7 B:G326 4.2 30.8 1.0 C2' B:G324 4.2 31.5 1.0 C5 B:G326 4.2 28.7 1.0 N6 B:A325 4.4 25.9 1.0 C3' B:G324 4.6 32.6 1.0 O3' B:C106 4.6 27.5 1.0 C6 B:A325 4.7 28.2 1.0 N1 B:G326 4.7 23.3 1.0 C4' B:G324 4.8 31.5 1.0 O B:HOH2278 4.9 30.2 1.0 N9 B:A325 4.9 29.7 1.0 O5' B:G107 4.9 27.1 1.0 OP1 B:A325 5.0 51.1 1.0 P B:A325 5.0 41.6 1.0

Potassium binding site 5 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1659 b:63.0 occ:1.00 O6 B:G326 2.8 24.2 1.0 O B:HOH2278 2.8 30.2 1.0 OP2 B:G107 2.8 30.5 1.0 OP2 B:G108 2.9 29.6 1.0 N7 B:G108 3.1 26.3 1.0 O5' B:G107 3.3 27.1 1.0 O B:HOH2470 3.5 28.2 1.0 P B:G107 3.5 24.0 1.0 N1 B:A109 3.6 22.9 1.0 C8 B:G108 3.7 26.5 1.0 C6 B:G326 3.7 23.1 1.0 C2 B:A109 3.8 20.0 1.0 N1 B:G326 3.8 23.3 1.0 C8 B:G107 4.0 25.7 1.0 OP1 B:G107 4.0 29.3 1.0 NH2 T:ARG10 4.1 32.3 1.0 K B:K1658 4.1 63.7 1.0 C3' B:G107 4.1 26.1 1.0 P B:G108 4.1 24.9 1.0 N7 B:G107 4.1 29.0 1.0 O B:HOH1773 4.2 21.7 1.0 C5 B:G108 4.4 25.8 1.0 C5' B:G107 4.4 27.5 1.0 O5' B:G108 4.4 25.2 1.0 O3' B:G107 4.5 24.6 1.0 C6 B:A109 4.6 22.3 1.0 CZ T:ARG10 4.7 31.9 1.0 C4' B:G107 4.8 28.0 1.0 N9 B:G107 4.8 24.6 1.0 O6 B:G108 4.9 31.9 1.0 N3 B:A109 4.9 23.4 1.0 O3' B:C106 5.0 27.5 1.0

Potassium binding site 6 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1660 b:86.7 occ:1.00 O B:HOH3214 2.6 41.5 1.0 OP2 B:A802 2.8 53.5 1.0 N1 B:A780 2.9 45.6 1.0 O6 B:G803 3.3 49.4 1.0 N2 B:G776 3.3 46.5 1.0 OP2 B:U801 3.5 63.6 1.0 N4 B:C779 3.6 31.8 1.0 C2 B:A780 3.6 43.7 1.0 O5' B:U801 3.7 52.9 1.0 C6 B:A780 3.8 37.2 1.0 N6 B:A780 3.9 40.4 1.0 C6 B:G803 4.1 38.9 1.0 P B:U801 4.1 53.8 1.0 C2 B:G776 4.1 47.2 1.0 P B:A802 4.2 56.6 1.0 C3' B:U801 4.4 52.8 1.0 O B:HOH3123 4.5 45.6 1.0 C5' B:U801 4.6 56.1 1.0 O B:HOH1948 4.6 31.4 1.0 O3' B:U801 4.7 52.3 1.0 C5 B:G803 4.8 37.3 1.0 N1 B:G776 4.8 41.3 1.0 N3 B:G776 4.8 48.8 1.0 OP1 B:U801 4.8 74.1 1.0 N7 B:G803 4.8 41.4 1.0 C4 B:C779 4.9 30.2 1.0 C6 B:U801 4.9 46.3 1.0 N3 B:A780 4.9 41.0 1.0

Potassium binding site 7 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1661 b:78.2 occ:1.00 OP2 B:G567 2.6 47.0 1.0 OP2 B:C564 2.6 34.0 1.0 O2' B:A563 2.9 23.6 1.0 OP2 B:U565 3.1 52.1 1.0 O B:HOH2795 3.4 36.9 1.0 O L:HOH201 3.7 39.3 1.0 P B:G567 3.7 35.9 1.0 O3' B:G566 3.7 37.8 1.0 P B:C564 3.8 30.7 1.0 O3' B:A563 3.8 29.0 1.0 C2' B:A563 3.9 24.3 1.0 O2' B:G566 4.1 29.5 1.0 O5' B:G567 4.1 35.4 1.0 C8 B:G567 4.3 25.2 1.0 O5' B:C564 4.3 33.9 1.0 P B:U565 4.3 41.4 1.0 N7 B:G567 4.4 24.2 1.0 NH2 L:ARG12 4.4 29.3 1.0 C3' B:A563 4.4 25.6 1.0 C5' B:C564 4.4 36.1 1.0 C3' B:G566 4.6 31.9 1.0 OP1 B:U565 4.6 53.9 1.0 C2' B:G566 4.9 33.5 1.0

Potassium binding site 8 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1662 b:53.4 occ:1.00 O6 B:G22 2.7 24.1 1.0 O B:HOH2364 2.8 28.1 1.0 O4 B:U12 2.8 31.9 1.0 O B:HOH2219 3.0 41.2 1.0 O6 B:G11 3.0 31.6 1.0 O6 B:G21 3.0 26.6 1.0 O B:HOH3197 3.4 35.2 1.0 C6 B:G21 3.5 21.7 1.0 N4 B:C23 3.6 21.2 1.0 C4 B:U12 3.7 27.0 1.0 C6 B:G22 3.7 23.1 1.0 N3 B:U12 3.8 23.5 1.0 N1 B:G21 3.9 21.0 1.0 N7 B:G22 3.9 25.4 1.0 C6 B:G11 4.0 26.1 1.0 C5 B:G22 4.2 23.1 1.0 C5 B:G21 4.4 21.1 1.0 C4 B:C23 4.5 22.8 1.0 N1 B:G11 4.8 30.8 1.0 C5 B:G11 4.9 27.8 1.0 C2 B:G21 4.9 21.5 1.0 N7 B:G21 4.9 25.4 1.0 N3 B:C23 5.0 26.5 1.0 N1 B:G22 5.0 22.1 1.0

Potassium binding site 9 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1663 b:32.5 occ:1.00 O4 B:U375 2.6 26.0 1.0 O4 B:U387 2.7 33.5 1.0 O2' B:C372 2.8 39.3 1.0 O2 B:C372 2.8 25.8 1.0 O6 B:G376 3.0 30.6 1.0 O B:HOH2702 3.1 30.5 1.0 O B:HOH1803 3.2 25.3 1.0 O B:HOH2566 3.3 29.0 1.0 O B:HOH1856 3.5 34.9 1.0 C2 B:C372 3.6 26.5 1.0 C4 B:U375 3.7 22.4 1.0 C4 B:U387 3.7 27.0 1.0 N6 B:A389 3.9 20.7 1.0 C6 B:G376 3.9 25.6 1.0 C2' B:C372 3.9 35.8 1.0 N3 B:U387 3.9 28.1 1.0 C5 B:U375 4.3 21.1 1.0 N3 B:C372 4.3 26.8 1.0 N7 B:G376 4.4 26.5 1.0 N1 B:C372 4.4 26.5 1.0 O B:HOH2264 4.4 28.9 1.0 C1' B:C372 4.4 33.1 1.0 C5 B:G376 4.5 23.6 1.0 N6 B:A374 4.5 22.4 1.0 N7 B:A374 4.6 28.2 1.0 O B:HOH1857 4.8 37.4 1.0 N3 B:U375 4.8 20.3 1.0 C6 B:A389 5.0 21.6 1.0

Potassium binding site 10 out of 25 in the Structure of E. Coli 30S-IF1-IF3-Mrna-Kasugamycin 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-Kasugamycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K1664 b:213.9 occ:1.00 O B:HOH2283 2.8 47.3 1.0 OP1 B:G413 3.0 76.9 1.0 O4 B:U427 3.1 65.9 1.0 O6 B:G428 3.5 55.1 1.0 O B:HOH2971 3.5 50.6 1.0 O4 B:U426 3.6 51.9 1.0 OP2 B:A414 3.7 91.1 1.0 N1 B:G428 3.7 46.4 1.0 O B:HOH1768 3.7 30.6 1.0 N6 B:A415 3.8 53.6 1.0 C6 B:G428 3.9 52.8 1.0 C4 B:U427 4.0 46.2 1.0 MG B:MG1643 4.0 88.2 1.0 N7 B:A414 4.0 55.3 1.0 P B:G413 4.0 78.4 1.0 N3 B:U427 4.1 42.5 1.0 O5' B:G413 4.1 68.5 1.0 C4 B:U426 4.5 42.0 1.0 OP2 B:G413 4.6 101.1 1.0 C8 B:A414 4.7 55.8 1.0 C2 B:G428 4.7 48.2 1.0 N7 B:A415 4.8 54.5 1.0 C6 B:A415 4.9 50.6 1.0 O6 B:G416 4.9 44.0 1.0 N3 B:U426 5.0 43.0 1.0 N2 B:G428 5.0 55.4 1.0

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