Potassium in PDB 8s1p: Ylmh Bound to Ptrna-50S

The structure of Ylmh Bound to Ptrna-50S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	158 atoms

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 - 47;

Binding sites:

The binding sites of Potassium atom in the Ylmh Bound to Ptrna-50S (pdb code 8s1p). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 47 binding sites of Potassium where determined in the Ylmh Bound to Ptrna-50S, PDB code: 8s1p:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3001 b:60.6 occ:1.00 OP2 A:U1681 2.5 38.8 1.0 OP1 A:A1680 2.8 40.5 1.0 O A:HOH4824 2.9 51.5 1.0 O3' A:A1339 3.8 48.9 1.0 P A:U1681 3.9 34.2 1.0 OP1 A:A1339 4.0 36.4 1.0 P A:A1680 4.0 34.4 1.0 O A:HOH5542 4.1 42.6 1.0 OP2 A:A1680 4.4 36.2 1.0 OP1 A:G1338 4.4 30.7 1.0 OP1 A:U1681 4.5 39.0 1.0 C3' A:A1339 4.5 41.8 1.0 O5' A:A1339 4.5 35.8 1.0 O5' A:U1681 4.6 33.0 1.0 O5' A:A1680 4.7 33.5 1.0 OP1 A:A1340 4.8 57.3 1.0 P A:A1339 4.8 32.0 1.0 P A:A1340 4.9 53.1 1.0

Potassium binding site 2 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3002 b:31.3 occ:1.00 OP1 A:C2580 2.6 27.9 1.0 O A:HOH3485 2.8 31.2 1.0 O A:HOH4268 2.9 32.6 1.0 O A:HOH3458 2.9 32.8 1.0 O A:HOH5098 2.9 27.1 1.0 O A:HOH4524 2.9 28.3 1.0 OP1 A:G2015 3.0 29.6 1.0 N2 A:G1983 3.5 26.9 1.0 P A:C2580 3.9 24.5 1.0 P A:G2015 4.0 27.8 1.0 O A:HOH3686 4.1 34.0 1.0 OP2 A:G2015 4.3 30.8 1.0 C2 A:G1983 4.3 27.3 1.0 OP2 A:C2580 4.4 25.8 1.0 O A:HOH4631 4.4 17.7 1.0 OP2 A:U2581 4.4 31.3 1.0 N1 A:G1983 4.5 26.9 1.0 OP1 A:G1718 4.5 26.6 1.0 O5' A:C2580 4.6 25.3 1.0 MG A:MG3108 4.6 33.6 1.0 O3' A:G2014 4.6 28.0 1.0 C5' A:C2580 4.7 26.0 1.0 OP1 A:U2581 4.7 31.0 1.0 OP2 A:G1719 4.9 26.1 1.0 O A:HOH5131 5.0 31.7 1.0

Potassium binding site 3 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3003 b:25.5 occ:1.00 O6 A:G603 2.6 25.7 1.0 O6 A:G579 2.8 22.7 1.0 O4 A:U580 2.8 22.3 1.0 O A:HOH4787 2.8 24.6 1.0 O6 A:G602 3.0 24.1 1.0 C6 A:G603 3.7 24.7 1.0 C4 A:U580 3.7 21.2 1.0 C6 A:G579 3.8 21.3 1.0 N3 A:U580 3.8 21.4 1.0 C6 A:G602 3.8 23.8 1.0 N4 A:C604 3.9 22.0 1.0 N7 A:G603 4.2 24.3 1.0 N4 A:C581 4.2 23.9 1.0 C5 A:G603 4.3 24.5 1.0 C5 A:G602 4.5 24.0 1.0 C5 A:G579 4.6 20.9 1.0 N7 A:G602 4.6 24.3 1.0 N1 A:G579 4.7 21.1 1.0 C4 A:C604 4.7 21.8 1.0 N1 A:G602 4.7 24.5 1.0 N7 A:G579 4.7 21.6 1.0 N1 A:G603 4.9 24.0 1.0

Potassium binding site 4 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3004 b:23.8 occ:1.00 O A:HOH3941 2.7 21.6 1.0 OP2 A:C195 2.7 21.2 1.0 O4 A:U196 2.7 22.5 1.0 O A:HOH4367 3.0 23.2 1.0 O4 A:U205 3.2 21.1 1.0 O A:HOH5496 3.3 33.0 1.0 O A:HOH5619 3.6 25.0 1.0 C4 A:U196 3.7 20.8 1.0 P A:C195 3.9 20.9 1.0 C5 A:U196 4.1 20.8 1.0 C4 A:U205 4.1 20.2 1.0 N3 A:U205 4.1 20.4 1.0 C2 A:A206 4.2 21.9 1.0 N1 A:A206 4.2 22.6 1.0 OP1 A:C195 4.3 21.1 1.0 OP2 A:A202 4.3 23.5 1.0 MG A:MG3148 4.4 23.8 1.0 O6 A:G197 4.4 19.1 1.0 N4 A:C204 4.6 20.9 1.0 O A:HOH4395 4.7 42.9 1.0 OP1 A:A202 4.8 25.0 1.0 N3 A:U196 4.9 20.1 1.0 O3' A:A194 4.9 20.7 1.0

Potassium binding site 5 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3005 b:24.1 occ:1.00 O6 A:G832 2.7 19.3 1.0 O6 A:G825 2.7 18.6 1.0 O4 A:U826 2.8 20.2 1.0 O A:HOH4931 2.9 28.1 1.0 O A:HOH4732 3.2 36.2 1.0 C4 A:U826 3.7 18.5 1.0 N4 A:C833 3.7 17.4 1.0 N1 A:G827 3.7 18.4 1.0 N3 A:U826 3.8 18.5 1.0 C6 A:G825 3.8 16.5 1.0 C6 A:G832 3.8 18.0 1.0 C2 A:G827 4.1 18.0 1.0 C6 A:G827 4.1 18.7 1.0 O A:HOH3676 4.2 31.6 1.0 N2 A:G827 4.3 18.0 1.0 O6 A:G827 4.3 19.8 1.0 OD1 C:ASP229 4.4 32.7 1.0 ND2 C:ASN228 4.5 36.5 1.0 N7 A:G832 4.5 18.3 1.0 C5 A:G832 4.6 18.2 1.0 C5 A:G825 4.6 17.1 1.0 N7 A:G825 4.6 17.4 1.0 C4 A:C833 4.7 17.2 1.0 N1 A:G825 4.7 16.1 1.0 C5 A:G827 4.8 18.7 1.0 N3 A:G827 4.8 18.4 1.0 N1 A:G832 4.9 17.7 1.0

Potassium binding site 6 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3006 b:26.9 occ:1.00 O4 A:U1436 2.7 28.5 1.0 O2' A:U1647 2.8 25.1 1.0 O2' A:U1433 2.9 28.2 1.0 O5' A:A1434 2.9 29.4 1.0 O3' A:U1647 2.9 26.1 1.0 O3' A:U1433 3.0 27.9 1.0 OP1 A:A1648 3.2 27.7 1.0 OP1 A:A1434 3.2 28.3 1.0 P A:A1434 3.3 27.4 1.0 P A:A1648 3.6 26.1 1.0 C5' A:A1648 3.6 25.8 1.0 C4 A:U1436 3.8 26.5 1.0 C2' A:U1647 3.8 25.0 1.0 C2' A:U1433 3.8 29.1 1.0 C3' A:U1647 3.9 25.8 1.0 C3' A:U1433 4.0 28.8 1.0 O5' A:A1648 4.1 26.2 1.0 C5' A:A1434 4.2 31.7 1.0 C1' A:U1647 4.2 24.7 1.0 MG A:MG3159 4.3 28.8 1.0 N3 A:U1436 4.3 25.1 1.0 OP1 A:U1380 4.4 24.8 1.0 O A:HOH3698 4.4 30.9 1.0 C4' A:A1434 4.6 32.5 1.0 OP2 A:U1380 4.6 25.0 1.0 O2 A:U1647 4.7 24.2 1.0 C4' A:U1433 4.8 29.4 1.0 OP2 A:A1434 4.8 29.7 1.0 OP2 A:C1649 4.9 27.4 1.0 C5 A:U1436 4.9 27.0 1.0 P A:U1380 4.9 23.8 1.0 OP2 A:A1648 5.0 28.9 1.0 C4' A:A1648 5.0 24.5 1.0

Potassium binding site 7 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3007 b:32.4 occ:1.00 O A:HOH4622 2.6 35.1 1.0 O6 A:G424 2.7 30.8 1.0 O4 A:U444 2.8 27.9 1.0 O6 A:G443 2.9 27.8 1.0 O6 A:G423 2.9 29.9 1.0 N4 A:C425 3.5 28.6 1.0 C6 A:G423 3.7 31.0 1.0 C4 A:U444 3.7 25.7 1.0 N3 A:U444 3.8 25.5 1.0 C6 A:G424 3.8 31.3 1.0 C6 A:G443 3.9 25.7 1.0 N7 A:G424 4.3 32.5 1.0 N4 A:C445 4.3 26.7 1.0 C5 A:G423 4.4 33.1 1.0 C5 A:G424 4.4 32.9 1.0 O A:HOH3482 4.5 31.0 1.0 C4 A:C425 4.5 28.6 1.0 N1 A:G423 4.5 30.4 1.0 N7 A:G423 4.5 33.4 1.0 C5 A:G443 4.7 25.8 1.0 N4 A:C442 4.7 27.4 1.0 N7 A:G443 4.8 25.4 1.0 N1 A:G443 4.8 25.4 1.0 N3 A:C425 4.9 29.9 1.0 C4 A:C445 5.0 26.1 1.0

Potassium binding site 8 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3008 b:34.9 occ:1.00 O2' A:A437 2.6 38.5 1.0 O A:HOH4033 2.7 30.7 1.0 O4 A:U439 2.9 32.5 1.0 OP2 A:A438 2.9 41.5 1.0 O6 A:G435 2.9 31.9 1.0 O4 A:U434 3.2 60.0 1.0 C4 A:U439 3.8 32.0 1.0 C4 A:U434 3.8 56.7 1.0 C2' A:A437 3.9 39.6 1.0 O3' A:A437 4.0 40.0 1.0 P A:A438 4.0 38.2 1.0 C6 A:G435 4.0 30.6 1.0 O A:HOH4670 4.2 44.1 1.0 N3 A:U434 4.2 54.9 1.0 N6 A:A429 4.2 30.7 1.0 C5 A:U439 4.3 32.2 1.0 N7 A:A438 4.3 29.7 1.0 N4 A:C430 4.3 27.2 1.0 N3 A:A437 4.5 37.7 1.0 C3' A:A437 4.5 40.2 1.0 N7 A:G435 4.5 35.0 1.0 C1' A:A437 4.5 39.2 1.0 C5 A:G435 4.7 33.0 1.0 C8 A:A438 4.8 29.6 1.0 C5 A:U434 4.8 55.4 1.0 N3 A:U439 5.0 32.5 1.0

Potassium binding site 9 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3009 b:30.2 occ:1.00 O6 A:G644 2.6 27.9 1.0 O6 A:G703 2.7 29.0 1.0 O A:HOH4964 2.7 31.3 1.0 O4 A:U643 2.7 29.4 1.0 O4 A:U704 2.8 29.7 1.0 C4 A:U643 3.7 28.4 1.0 C4 A:U704 3.7 27.7 1.0 C6 A:G644 3.7 27.1 1.0 N4 A:C645 3.7 30.2 1.0 C6 A:G703 3.7 28.9 1.0 N3 A:U704 3.8 27.5 1.0 N6 A:A705 3.9 26.2 1.0 O A:HOH5704 4.1 46.4 1.0 N7 A:G644 4.2 28.1 1.0 C5 A:G644 4.4 28.2 1.0 N3 A:U643 4.5 28.4 1.0 C5 A:U643 4.5 29.1 1.0 C5 A:G703 4.6 30.4 1.0 N1 A:G703 4.7 28.7 1.0 C6 A:A705 4.7 25.6 1.0 C4 A:C645 4.7 29.7 1.0 N7 A:G703 4.7 31.7 1.0 N1 A:G644 4.9 26.9 1.0 N1 A:A705 4.9 25.9 1.0

Potassium binding site 10 out of 47 in the Ylmh Bound to Ptrna-50S


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 Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:K3010 b:28.5 occ:1.00 O3' A:G1068 2.7 30.2 1.0 N7 A:G1070 2.7 26.3 1.0 OP2 A:U1069 2.8 30.3 1.0 O2' A:G1068 2.9 30.1 1.0 O6 A:G1070 3.0 25.9 1.0 N3 A:G1071 3.0 26.4 1.0 O2' A:G1071 3.0 30.9 1.0 P A:U1069 3.3 29.8 1.0 C2 A:G1071 3.4 26.7 1.0 C5 A:G1070 3.5 25.4 1.0 C4 A:G1071 3.5 26.6 1.0 C6 A:G1070 3.5 24.5 1.0 N2 A:G1071 3.7 27.5 1.0 C2' A:G1068 3.8 30.2 1.0 C3' A:G1068 3.8 30.6 1.0 MG A:MG3167 3.8 31.1 1.0 C8 A:G1070 3.9 26.8 1.0 O A:HOH3333 3.9 29.3 1.0 C2' A:G1071 4.0 33.0 1.0 N9 A:G1071 4.1 27.9 1.0 N1 A:G1071 4.2 26.3 1.0 C1' A:G1068 4.2 29.0 1.0 OP2 A:C1181 4.2 47.6 1.0 C1' A:G1071 4.3 31.1 1.0 C5 A:G1071 4.4 27.2 1.0 O5' A:U1069 4.4 31.0 1.0 OP1 A:U1069 4.5 32.0 1.0 C6 A:G1071 4.7 26.7 1.0 C4 A:G1070 4.8 25.5 1.0 N1 A:G1070 4.9 24.2 1.0 OP2 A:G1070 4.9 32.7 1.0 C4' A:G1068 4.9 31.1 1.0 N9 A:G1070 5.0 27.2 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