Potassium in PDB 8s1u: Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna

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>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna (pdb code 8s1u). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna, PDB code: 8s1u:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3001 b:40.0 occ:1.00 O4' A:C2530 2.7 24.8 1.0 O6 A:G2090 2.7 34.3 1.0 O2 A:C2530 3.0 18.2 1.0 O6 A:G2476 3.0 23.6 1.0 N7 A:G2090 3.1 30.0 1.0 N7 A:G2476 3.1 21.7 1.0 O2 A:PSU2533 3.2 46.5 1.0 C6 A:G2090 3.4 30.4 1.0 C1' A:C2530 3.4 23.1 1.0 C5 A:G2090 3.5 28.9 1.0 C4' A:C2530 3.6 25.7 1.0 C2 A:C2530 3.6 18.7 1.0 C6 A:G2476 3.7 21.8 1.0 C5 A:G2476 3.7 21.5 1.0 N1 A:C2530 3.8 20.5 1.0 C2 A:PSU2533 3.9 43.9 1.0 N1 A:PSU2533 3.9 41.1 1.0 C5' A:C2530 4.0 26.3 1.0 N6 A:A2480 4.1 32.7 1.0 C8 A:G2476 4.2 22.1 1.0 C8 A:G2090 4.2 28.4 1.0 N3 A:C2530 4.5 17.2 1.0 O5' A:C2530 4.7 26.5 1.0 N1 A:G2090 4.7 29.5 1.0 OP1 A:PSU2533 4.8 43.4 1.0 C4 A:G2090 4.8 27.6 1.0 C2' A:C2530 4.8 24.7 1.0 C6 A:C2530 4.9 19.1 1.0 C3' A:C2530 4.9 25.9 1.0 C4 A:G2476 5.0 21.4 1.0

Potassium binding site 2 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3002 b:105.3 occ:1.00 O2 A:U2051 2.7 38.2 1.0 O2 A:C2645 3.0 34.4 1.0 O2' A:C2645 3.4 30.0 1.0 C2 A:U2051 3.7 35.0 1.0 N2 A:G2082 3.7 21.4 1.0 C2' A:C2645 3.9 30.9 1.0 C1' A:C2645 4.1 30.3 1.0 C2 A:C2645 4.1 28.6 1.0 N3 A:U2051 4.1 34.0 1.0 O2' A:U2051 4.2 30.6 1.0 O4' A:C2646 4.2 25.6 1.0 C5 A:U2063 4.2 41.8 1.0 C4 A:U2063 4.3 42.3 1.0 C6 A:U2063 4.4 40.0 1.0 N3 A:U2063 4.5 41.7 1.0 N3 A:A2083 4.5 16.6 1.0 C1' A:C2646 4.5 23.6 1.0 N1 A:U2063 4.7 35.9 1.0 O4 A:U2063 4.7 51.0 1.0 N1 A:C2645 4.7 28.3 1.0 C2 A:U2063 4.7 39.7 1.0 N1 A:U2051 4.7 33.8 1.0 C2 A:A2083 4.9 17.4 1.0 C1' A:U2051 5.0 31.5 1.0

Potassium binding site 3 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3003 b:29.0 occ:1.00 N7 A:G2082 2.8 20.4 1.0 N7 A:G2081 2.8 26.8 1.0 O2' A:A2080 2.9 28.3 1.0 N3 A:A2080 3.0 28.5 1.0 C5 A:G2081 3.1 25.7 1.0 N1 A:A2643 3.1 19.8 1.0 O6 A:G2081 3.2 29.6 1.0 C6 A:G2081 3.3 26.4 1.0 O6 A:G2082 3.4 24.5 1.0 C8 A:G2081 3.6 26.4 1.0 C5 A:G2082 3.6 21.2 1.0 C2 A:A2080 3.7 30.8 1.0 C2 A:A2643 3.7 19.3 1.0 C8 A:G2082 3.8 20.7 1.0 C6 A:G2082 3.9 23.3 1.0 C1' A:A2080 3.9 24.0 1.0 C2' A:A2080 3.9 24.8 1.0 C4 A:A2080 4.0 27.3 1.0 C6 A:A2643 4.1 19.6 1.0 C4 A:G2081 4.1 24.4 1.0 N6 A:A2643 4.2 19.1 1.0 N9 A:A2080 4.3 25.2 1.0 N6 A:A2606 4.3 20.2 1.0 N9 A:G2081 4.4 22.9 1.0 N1 A:G2081 4.4 23.9 1.0 C6 A:A2606 4.6 19.4 1.0 O3' A:A2080 4.7 25.8 1.0 C4 A:G2082 4.9 19.7 1.0 C5 A:A2606 4.9 20.6 1.0 C3' A:A2080 4.9 24.6 1.0 N3 A:A2643 5.0 19.8 1.0 N9 A:G2082 5.0 20.1 1.0 N1 A:A2080 5.0 31.6 1.0

Potassium binding site 4 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3004 b:86.4 occ:1.00 O2' A:G2605 2.8 26.7 1.0 O6 A:G2534 3.1 64.3 1.0 O6 A:G2610 3.2 42.8 1.0 O2 A:C2639 3.6 58.5 1.0 C2' A:G2605 3.7 27.9 1.0 C1' A:G2605 3.9 28.8 1.0 OP2 A:U2609 4.0 30.2 1.0 OP2 A:C2608 4.0 33.5 1.0 O2' A:C2639 4.0 52.1 1.0 C6 A:G2610 4.0 40.7 1.0 N1 A:G2610 4.1 40.9 1.0 C6 A:G2534 4.1 52.5 1.0 OP2 A:C2640 4.2 47.8 1.0 C2 A:C2639 4.4 54.6 1.0 N9 A:G2605 4.4 30.5 1.0 N1 A:G2534 4.4 47.1 1.0 C8 A:G2605 4.5 33.9 1.0 C1' A:C2639 4.6 57.8 1.0 OP1 A:C2608 4.7 36.5 1.0 P A:C2608 4.7 36.9 1.0 O3' A:C2639 4.8 52.9 1.0 N1 A:C2639 4.9 51.2 1.0 C2' A:C2639 4.9 55.9 1.0

Potassium binding site 5 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3005 b:84.5 occ:1.00 OP2 A:OMG2280 2.5 45.9 1.0 O2' A:G2279 2.5 41.0 1.0 OP2 A:C2525 3.0 30.4 1.0 N7 A:A2526 3.2 45.2 1.0 OP2 A:A2526 3.2 39.1 1.0 P A:OMG2280 3.4 45.2 1.0 O3' A:G2279 3.4 43.0 1.0 C8 A:A2526 3.6 42.5 1.0 C2' A:G2279 3.7 40.9 1.0 P A:C2525 3.8 27.8 1.0 O5' A:C2525 3.9 27.0 1.0 OP1 A:C2525 4.0 27.7 1.0 C3' A:G2279 4.1 41.4 1.0 OP1 A:OMG2280 4.1 40.9 1.0 NE M:ARG82 4.2 62.2 1.0 CD M:ARG82 4.2 49.1 1.0 C1' A:G2279 4.4 41.8 1.0 C5 A:A2526 4.5 42.5 1.0 P A:A2526 4.6 38.5 1.0 C3' A:C2525 4.7 27.0 1.0 O5' A:OMG2280 4.7 48.1 1.0 C5' A:C2525 4.8 27.1 1.0 N9 A:A2526 5.0 39.3 1.0

Potassium binding site 6 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3006 b:51.9 occ:1.00 OP1 A:C2456 2.9 32.6 1.0 O3' A:A2455 2.9 31.9 1.0 OP1 A:G2458 3.0 27.7 1.0 OP2 A:U874 3.4 29.2 1.0 P A:C2456 3.5 32.5 1.0 O2' A:A2455 3.5 36.4 1.0 OP2 A:G2458 3.6 27.4 1.0 P A:G2458 3.7 28.2 1.0 OP1 A:U874 3.7 30.6 1.0 P A:U874 4.1 28.3 1.0 C3' A:A2455 4.1 33.2 1.0 C5' A:G2458 4.2 25.7 1.0 C2' A:A2455 4.3 34.5 1.0 C5' A:C2456 4.4 34.7 1.0 O5' A:G2458 4.5 26.5 1.0 O5' A:C2456 4.5 31.9 1.0 C1' A:A2455 4.5 37.1 1.0 OP2 A:C2456 4.6 33.5 1.0 OP2 A:A2459 4.8 50.9 1.0 OP1 A:U873 4.8 21.9 1.0 O4 A:U875 4.8 47.6 1.0

Potassium binding site 7 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3007 b:99.1 occ:1.00 O6 A:G709 2.9 44.2 1.0 O6 A:G710 3.3 28.6 1.0 O4 A:U711 3.5 33.8 1.0 C6 A:G709 3.6 41.1 1.0 N6 A:A637 3.7 41.2 1.0 N7 A:G710 3.8 35.3 1.0 N7 A:G709 3.9 36.4 1.0 O4 A:U638 3.9 43.3 1.0 C5 A:G709 4.0 36.7 1.0 C6 A:G710 4.1 29.7 1.0 C5 A:G710 4.4 31.2 1.0 C4 A:U711 4.4 34.3 1.0 N1 A:G709 4.6 42.1 1.0 N4 A:C639 4.7 38.4 1.0 C4 A:U638 4.8 40.8 1.0 C6 A:A637 4.9 38.7 1.0 N3 A:U638 4.9 40.9 1.0

Potassium binding site 8 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3008 b:67.4 occ:1.00 O L:GLY32 2.6 38.6 1.0 OP1 A:G1232 2.7 29.6 1.0 O2' A:A987 2.8 28.7 1.0 O3' A:A987 2.9 32.5 1.0 O3' A:G1231 3.4 27.4 1.0 P A:G1232 3.6 28.5 1.0 C3' A:A987 3.7 29.9 1.0 C L:GLY32 3.7 39.1 1.0 C2' A:A987 3.8 28.6 1.0 C4' A:A987 3.8 33.1 1.0 OP1 A:G988 4.1 43.4 1.0 P A:G988 4.1 39.5 1.0 CA L:GLY32 4.4 35.0 1.0 C5' A:G1232 4.6 27.2 1.0 O4' A:A987 4.6 31.0 1.0 C3' A:G1231 4.6 26.5 1.0 O5' A:G1232 4.7 26.2 1.0 C1' A:A987 4.7 28.2 1.0 OP2 A:G1232 4.7 31.5 1.0 O5' A:A987 4.7 47.0 1.0 C5' A:G988 4.8 32.6 1.0 O3' A:G986 4.8 45.0 1.0 O2' A:G986 4.8 44.8 1.0 N L:LYS33 4.8 44.1 1.0 C4' A:G1231 4.9 25.4 1.0 O5' A:G988 4.9 35.8 1.0 C5' A:A987 4.9 38.0 1.0 C5' A:G1231 5.0 25.5 1.0

Potassium binding site 9 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3009 b:66.3 occ:1.00 O6 A:G1255 2.6 28.9 1.0 N2 A:G1275 3.4 37.8 1.0 N4 A:C1256 3.4 43.1 1.0 O4 A:U1274 3.5 50.1 1.0 C6 A:G1255 3.6 27.8 1.0 C2 A:G1275 3.6 38.5 1.0 O6 A:G1273 3.6 36.8 1.0 N7 A:G1255 3.7 35.9 1.0 N1 A:G1275 3.8 39.8 1.0 OP2 A:A1254 4.0 50.6 1.0 C5 A:G1255 4.0 31.0 1.0 N3 A:U1274 4.3 43.9 1.0 C4 A:C1256 4.3 41.1 1.0 C4 A:U1274 4.3 47.1 1.0 N3 A:G1275 4.3 38.5 1.0 OP2 A:A1253 4.3 61.0 1.0 C6 A:G1273 4.7 34.0 1.0 C6 A:G1275 4.7 38.6 1.0 N3 A:C1256 4.8 43.1 1.0 N1 A:G1255 4.9 28.1 1.0 N7 A:A1254 4.9 41.1 1.0 C8 A:G1255 5.0 36.2 1.0

Potassium binding site 10 out of 15 in the Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Ylmh Bound to Stalled 50S Subunits with Rqch and Ptrna within 5.0Å range: probe atom residue distance (Å) B Occ A:K3010 b:59.9 occ:1.00 O6 A:G695 3.1 36.1 1.0 O6 A:G684 3.2 60.5 1.0 O4 A:U685 3.3 35.8 1.0 O6 A:G694 3.4 56.9 1.0 N4 A:C696 3.7 46.5 1.0 C6 A:G694 4.0 51.0 1.0 C6 A:G695 4.1 37.4 1.0 N7 A:G695 4.2 40.9 1.0 C4 A:U685 4.2 36.9 1.0 C6 A:G684 4.3 52.4 1.0 N3 A:U685 4.3 37.5 1.0 N7 A:G694 4.4 50.6 1.0 C5 A:G694 4.4 49.7 1.0 C5 A:G695 4.5 40.0 1.0 N4 A:C686 4.7 35.9 1.0 C4 A:C696 4.8 40.6 1.0 O6 A:G697 4.9 67.3 1.0 N1 A:G694 4.9 48.5 1.0

H.Takada, H.Paternoga, K.Fujiwara, J.A.Nakamoto, E.N.Park, L.Dimitrova-Paternoga, B.Beckert, M.Saarma, T.Tenson, A.R.Buskirk, G.C.Atkinson, S.Chiba, D.N.Wilson, V.Hauryliuk. A Role For the S4-Domain Containing Protein Ylmh in Ribosome-Associated Quality Control in Bacillus Subtilis. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38811035
DOI: 10.1093/NAR/GKAE399