Potassium in PDB 9d89: E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)

The structure of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) also contains other interesting chemical elements:

Magnesium	(Mg)	204 atoms
Zinc	(Zn)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 93;

Binding sites:

The binding sites of Potassium atom in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) (pdb code 9d89). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 93 binding sites of Potassium where determined in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement), PDB code: 9d89:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3198 b:62.9 occ:1.00 O D:HOH6389 2.7 61.5 1.0 O6 D:G871 2.8 55.0 1.0 O D:HOH3402 2.8 67.0 1.0 O2 D:C867 2.8 52.0 1.0 O4 D:U870 2.8 57.7 1.0 O2' D:C867 3.0 63.7 1.0 O D:HOH3698 3.6 68.5 1.0 C2 D:C867 3.6 50.9 1.0 C6 D:G871 3.8 55.4 1.0 C4 D:U870 3.9 59.1 1.0 N4 D:C910 4.1 52.4 1.0 C1' D:C867 4.1 57.2 1.0 N6 D:A911 4.1 46.9 1.0 C2' D:C867 4.1 62.1 1.0 N7 D:G871 4.2 58.1 1.0 N1 D:C867 4.3 51.9 1.0 C5 D:C869 4.3 59.5 1.0 O4 D:U872 4.3 65.1 1.0 C5 D:G871 4.4 54.3 1.0 N3 D:C867 4.4 53.8 1.0 C5 D:U870 4.4 61.0 1.0 N4 D:C869 4.5 56.2 1.0 O3' D:C867 4.8 71.5 1.0 C4 D:C869 4.8 58.5 1.0 O D:HOH5815 4.8 78.8 1.0 N1 D:G871 5.0 52.6 1.0

Potassium binding site 2 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3199 b:61.8 occ:1.00 OD1 t:ASN69 2.6 60.9 1.0 OG t:SER68 2.7 59.3 1.0 O2 D:U328 2.8 57.3 1.0 O D:HOH6787 2.8 65.1 1.0 O2 D:C335 3.0 61.7 1.0 O2' D:U328 3.0 60.2 1.0 O t:SER68 3.2 61.7 1.0 N6 D:A332 3.4 55.2 1.0 C t:SER68 3.5 53.6 1.0 CB t:SER68 3.6 57.2 1.0 C2' D:U328 3.7 59.6 1.0 C1' D:U328 3.8 55.7 1.0 CG t:ASN69 3.8 58.9 1.0 C2 D:U328 3.9 49.8 1.0 N2 D:G327 4.0 53.3 1.0 C2 D:C335 4.0 53.7 1.0 N t:ASN69 4.0 55.0 1.0 CA t:ASN69 4.2 56.1 1.0 CA t:SER68 4.2 55.9 1.0 N1 D:U328 4.4 54.8 1.0 CG2 t:THR15 4.4 80.3 1.0 C1' D:C335 4.6 56.4 1.0 CB t:ASN69 4.7 57.6 1.0 C6 D:A332 4.7 56.0 1.0 N3 D:C335 4.7 55.1 1.0 N1 D:C335 4.8 56.1 1.0 OP1 D:G329 4.8 56.1 1.0 ND2 t:ASN69 4.8 58.9 1.0 C2 D:G327 4.8 50.2 1.0 O D:HOH4661 5.0 55.9 1.0

Potassium binding site 3 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3200 b:69.5 occ:1.00 O5' D:U1975 2.7 55.2 1.0 OP2 D:U1975 2.9 61.1 1.0 O D:HOH5708 2.9 70.4 1.0 O2' D:G1828 3.0 48.7 1.0 O4' D:U1975 3.0 64.0 1.0 OP1 D:C1906 3.0 64.0 1.0 P D:U1975 3.3 52.2 1.0 C4' D:U1975 3.7 62.0 1.0 C5' D:U1975 3.8 58.1 1.0 O3' D:G1828 3.9 44.6 1.0 C1' D:U1975 4.0 67.7 1.0 C4' D:G1828 4.1 44.5 1.0 C2' D:G1828 4.2 47.0 1.0 OP1 D:U1975 4.3 57.7 1.0 C3' D:G1828 4.3 46.4 1.0 P D:C1906 4.4 56.2 1.0 O3' D:A1974 4.5 50.7 1.0 O D:HOH5571 4.6 57.3 1.0 O D:HOH3504 4.6 65.8 1.0 N1 D:U1975 4.7 75.4 1.0 O D:HOH3781 4.7 74.7 1.0 O D:HOH3571 4.8 58.5 1.0 C6 D:U1975 4.8 82.0 1.0 O4' D:G1828 4.9 45.2 1.0 OP2 D:C1906 4.9 53.4 1.0 C1' D:G1828 5.0 44.7 1.0

Potassium binding site 4 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3201 b:84.3 occ:1.00 O D:HOH5143 2.8 65.9 1.0 O6 D:G1220 2.8 58.3 1.0 O D:HOH4599 2.9 83.2 1.0 O4 D:U1219 2.9 55.4 1.0 O4 D:U1233 3.0 67.2 1.0 O D:HOH3697 3.4 81.8 1.0 N6 D:A1232 3.8 59.7 1.0 C6 D:G1220 3.8 53.9 1.0 C4 D:U1233 3.9 60.8 1.0 C4 D:U1219 4.0 50.5 1.0 N3 D:U1233 4.0 55.4 1.0 N7 D:G1220 4.1 56.2 1.0 C5 D:G1220 4.3 53.8 1.0 O6 D:G1234 4.3 56.0 1.0 O4 D:U1221 4.4 61.7 1.0 N3 D:U1219 4.5 49.5 1.0 C6 D:A1232 4.7 56.3 1.0 O D:HOH3485 4.9 75.0 1.0

Potassium binding site 5 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3202 b:77.7 occ:1.00 O6 D:G1977 2.7 49.8 1.0 O6 D:G1833 2.9 51.8 1.0 O6 D:G1976 3.0 52.9 1.0 O D:HOH4314 3.3 68.2 1.0 O D:HOH3303 3.4 54.5 1.0 C6 D:G1976 3.6 46.2 1.0 N4 D:C1834 3.6 48.4 1.0 N4 D:C1978 3.8 45.7 1.0 C6 D:G1977 3.9 46.9 1.0 O D:HOH3941 3.9 55.9 1.0 C6 D:G1833 4.0 46.6 1.0 N4 D:C1832 4.1 46.9 1.0 N1 D:G1976 4.2 45.0 1.0 C5 D:G1976 4.3 46.5 1.0 OP1 D:A1831 4.4 52.9 1.0 N4 D:C1835 4.4 50.6 1.0 N7 D:G1977 4.5 46.0 1.0 C5 D:G1977 4.6 45.2 1.0 N7 D:G1976 4.7 44.7 1.0 O D:HOH6640 4.7 79.3 1.0 C5 D:G1833 4.8 48.9 1.0 N7 D:G1833 4.8 49.2 1.0 O D:HOH5395 4.8 72.6 1.0 C4 D:C1978 4.8 46.9 1.0 C4 D:C1832 4.8 45.9 1.0 C4 D:C1834 4.8 50.8 1.0 N3 D:C1835 4.9 48.9 1.0 C4 D:C1835 4.9 48.8 1.0 N1 D:G1977 5.0 48.1 1.0 O D:HOH6721 5.0 66.7 1.0

Potassium binding site 6 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3203 b:71.9 occ:1.00 O6 D:G658 2.8 60.2 1.0 O D:HOH4838 2.8 60.4 1.0 O6 D:G602 2.9 54.7 1.0 O4 D:U659 2.9 54.7 1.0 N6 D:A601 3.3 49.2 1.0 O D:HOH5334 3.3 94.7 1.0 O D:HOH4258 3.6 64.2 1.0 C4 D:U659 3.8 52.5 1.0 N4 D:C603 3.8 53.6 1.0 C6 D:G658 3.9 52.9 1.0 N3 D:U659 4.0 50.4 1.0 C6 D:G602 4.0 48.8 1.0 C6 D:A601 4.2 47.5 1.0 N7 D:G602 4.5 49.2 1.0 C5 D:G602 4.6 49.8 1.0 C5 D:G658 4.7 56.9 1.0 O4 D:U660 4.7 53.7 1.0 N7 D:G658 4.8 57.4 1.0 N1 D:G658 4.8 50.3 1.0 O D:HOH4191 4.8 62.0 1.0 C4 D:C603 4.9 49.6 1.0 C5 D:A601 4.9 51.2 1.0 N7 D:A601 4.9 56.2 1.0

Potassium binding site 7 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3204 b:62.3 occ:1.00 O D:HOH4191 2.6 62.0 1.0 O6 D:G661 2.8 51.6 1.0 O6 D:G599 2.8 48.1 1.0 O D:HOH5052 2.8 60.3 1.0 O D:HOH4532 2.9 72.4 1.0 O4 D:U600 3.0 49.7 1.0 O4 D:U660 3.4 53.7 1.0 C4 D:U600 3.9 50.5 1.0 C6 D:G661 3.9 47.6 1.0 C6 D:G599 3.9 47.5 1.0 N6 D:A601 3.9 49.2 1.0 N4 D:C662 3.9 47.4 1.0 N3 D:U600 4.0 49.5 1.0 N7 D:G661 4.2 49.0 1.0 C4 D:U660 4.4 50.4 1.0 C5 D:G661 4.4 50.1 1.0 C5 D:G599 4.6 46.8 1.0 N7 D:G599 4.7 53.4 1.0 C6 D:A601 4.7 47.5 1.0 O4 D:U598 4.8 54.4 1.0 N1 D:G599 4.9 46.0 1.0 C4 D:C662 4.9 46.0 1.0

Potassium binding site 8 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3205 b:59.2 occ:1.00 O D:HOH3359 2.8 56.5 1.0 OP1 D:A471 2.8 54.4 1.0 O D:HOH6895 2.9 57.3 1.0 OP1 D:A453 2.9 45.6 1.0 O3' D:G452 2.9 46.8 1.0 O D:HOH6176 3.0 40.9 1.0 O H:HOH404 3.0 50.0 1.0 OP2 D:A471 3.3 50.1 1.0 P D:A471 3.4 48.0 1.0 P D:A453 3.5 44.8 1.0 OG H:SER80 3.9 55.9 1.0 O2' D:G452 4.0 45.9 1.0 MG D:MG3054 4.0 41.0 1.0 C3' D:G452 4.1 46.9 1.0 C5' D:A453 4.2 44.2 1.0 O3' D:A470 4.2 50.5 1.0 O H:HOH423 4.3 63.3 1.0 C4' D:G452 4.3 51.0 1.0 O5' D:A453 4.4 45.8 1.0 O D:HOH4738 4.4 42.0 1.0 O D:HOH3837 4.5 50.0 1.0 NH1 H:ARG79 4.6 46.7 1.0 O D:HOH5910 4.6 38.9 1.0 C2' D:G452 4.6 48.4 1.0 CB H:SER80 4.6 51.8 1.0 OP2 D:A453 4.7 49.3 1.0 OP1 D:A470 4.8 54.4 1.0 NH2 H:ARG79 4.8 45.1 1.0 O D:HOH3309 4.8 58.5 1.0 C5' D:A470 4.9 49.8 1.0 O5' D:A471 4.9 48.9 1.0

Potassium binding site 9 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3206 b:75.3 occ:1.00 OP1 D:U2510 2.6 88.3 1.0 OP2 D:C2577 2.9 52.9 1.0 O2' D:A2576 3.0 43.0 1.0 N3 D:A2576 3.0 53.0 1.0 O D:HOH4404 3.4 57.0 1.0 O4' D:A2457 3.5 47.2 1.0 C2 D:A2576 3.7 58.8 1.0 O3' D:A2576 3.8 50.0 1.0 C1' D:A2576 3.9 41.9 1.0 P D:C2577 3.9 49.0 1.0 C2' D:A2576 3.9 46.1 1.0 C4 D:A2576 4.0 45.8 1.0 C4' D:A2457 4.1 44.7 1.0 P D:U2510 4.1 86.0 1.0 C1' D:A2457 4.1 43.6 1.0 C5' D:U2510 4.2 94.2 1.0 N9 D:A2576 4.3 45.1 1.0 O2' D:A2457 4.4 47.5 1.0 C3' D:A2576 4.5 43.7 1.0 O2' D:C2456 4.6 55.5 1.0 O D:HOH5908 4.6 72.2 1.0 O5' D:U2510 4.6 89.6 1.0 C2' D:A2457 4.8 45.2 1.0 OP1 D:C2577 4.8 50.1 1.0 C5' D:A2457 4.8 47.1 1.0 OP2 D:U2510 4.9 91.3 1.0 O D:HOH5871 4.9 51.4 1.0 N1 D:A2576 5.0 57.8 1.0

Potassium binding site 10 out of 93 in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement) within 5.0Å range: probe atom residue distance (Å) B Occ D:K3207 b:62.8 occ:1.00 O D:HOH3451 2.6 71.7 1.0 O6 D:G2713 2.7 45.6 1.0 O D:HOH3338 2.8 55.1 1.0 O4 D:U2702 2.9 45.2 1.0 O6 D:G2712 2.9 52.4 1.0 O6 D:G2701 3.4 45.9 1.0 C6 D:G2712 3.8 47.5 1.0 C4 D:U2702 3.8 44.9 1.0 C6 D:G2713 3.8 43.0 1.0 N4 D:C2714 3.8 40.7 1.0 N3 D:U2702 3.9 43.0 1.0 N4 D:C2703 4.1 47.5 1.0 N7 D:G2713 4.2 45.1 1.0 C5 D:G2713 4.4 44.4 1.0 C6 D:G2701 4.4 43.4 1.0 C5 D:G2712 4.5 47.7 1.0 N1 D:G2712 4.6 45.5 1.0 N7 D:G2712 4.7 49.9 1.0 C4 D:C2714 4.9 42.1 1.0 C4 D:C2703 5.0 45.8 1.0 N1 D:G2713 5.0 42.3 1.0

P.V.Panteleev, E.B.Pichkur, R.N.Kruglikov, A.Paleskava, O.V.Shulenina, I.A.Bolosov, I.V.Bogdanov, V.N.Safronova, S.V.Balandin, V.I.Marina, T.I.Kombarova, O.V.Korobova, O.V.Shamova, A.G.Myasnikov, A.I.Borzilov, I.A.Osterman, P.V.Sergiev, A.A.Bogdanov, O.A.Dontsova, A.L.Konevega, T.V.Ovchinnikova. Rumicidins Are A Family of Mammalian Host-Defense Peptides Plugging the 70S Ribosome Exit Tunnel. Nat Commun V. 15 8925 2024.
ISSN: ESSN 2041-1723
PubMed: 39414793
DOI: 10.1038/S41467-024-53309-Y