Magnesium 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
Potassium	(K)	47 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 - 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 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 158;

Binding sites:

The binding sites of Magnesium atom in the Ylmh Bound to Ptrna-50S (pdb code 8s1p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 158 binding sites of Magnesium where determined in the Ylmh Bound to Ptrna-50S, PDB code: 8s1p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3047 b:19.3 occ:1.00 OP1 A:U1289 2.0 20.7 1.0 OP1 A:G1290 2.0 20.1 1.0 O A:HOH3370 2.1 20.2 1.0 O A:HOH5493 2.1 20.6 1.0 O A:HOH4967 2.1 19.4 1.0 O A:HOH4492 2.1 18.7 1.0 P A:G1290 3.3 18.3 1.0 P A:U1289 3.4 18.9 1.0 O3' A:U1289 3.5 19.8 1.0 OP2 A:A630 3.7 19.7 1.0 O A:HOH3628 3.8 32.9 1.0 K A:K3035 4.0 28.4 1.0 O3' A:G1288 4.0 20.9 1.0 O A:HOH3408 4.0 23.6 1.0 OP2 A:G1290 4.3 20.0 1.0 O5' A:U1289 4.3 19.5 1.0 OP2 A:G629 4.4 19.7 1.0 O5' A:G1290 4.4 19.7 1.0 OP2 A:U1289 4.4 22.2 1.0 N3 A:U858 4.4 16.6 1.0 C5' A:U1289 4.4 19.5 1.0 N1 A:A1291 4.4 16.8 1.0 O4 A:U858 4.4 17.7 1.0 C3' A:U1289 4.5 20.1 1.0 O A:HOH3449 4.5 33.0 1.0 OP1 A:G629 4.6 21.0 1.0 C5' A:G1290 4.6 19.5 1.0 P A:A630 4.9 18.9 1.0 C4' A:U1289 4.9 19.9 1.0 P A:G629 4.9 18.1 1.0 C4 A:U858 4.9 17.3 1.0

Magnesium binding site 2 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3048 b:29.0 occ:1.00 O A:HOH5023 2.0 28.7 1.0 O4 A:U2448 2.1 28.7 1.0 O 3:HOH101 2.1 27.3 1.0 O 3:HOH112 2.1 31.7 1.0 O A:HOH5196 2.1 26.9 1.0 O 3:HOH115 2.1 30.3 1.0 C4 A:U2448 3.2 28.5 1.0 C5 A:U2448 3.8 28.1 1.0 O A:HOH4201 3.9 35.0 1.0 O A:HOH3455 3.9 28.2 1.0 O 3:SER30 3.9 27.2 1.0 O 3:HOH105 4.0 31.3 1.0 O A:HOH5218 4.2 37.5 1.0 O 3:THR29 4.2 31.0 1.0 N6 A:A2447 4.3 26.2 1.0 N7 A:A2447 4.3 26.6 1.0 N3 A:U2448 4.3 27.2 1.0 O A:HOH4822 4.5 29.5 1.0 O A:HOH4878 4.6 31.1 1.0 C 3:SER30 4.8 26.0 1.0 CA 3:SER30 4.9 28.2 1.0 C5 A:A2447 4.9 26.8 1.0 C6 A:A2447 5.0 26.9 1.0

Magnesium binding site 3 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3049 b:25.3 occ:1.00 OP2 A:G909 2.0 27.5 1.0 O A:HOH5386 2.0 23.2 1.0 O A:HOH4427 2.1 25.9 1.0 O A:HOH4127 2.1 24.5 1.0 O A:HOH5185 2.1 26.0 1.0 O A:HOH4326 2.1 25.6 1.0 P A:G909 3.3 26.9 1.0 O5' A:G909 3.8 29.6 1.0 OP1 A:G909 4.0 29.2 1.0 OP1 A:A908 4.2 31.4 1.0 OP2 A:A908 4.2 31.8 1.0 O A:HOH4131 4.2 38.0 1.0 N7 A:G909 4.2 27.1 1.0 OP1 A:A957 4.2 31.2 1.0 N7 A:A910 4.3 29.6 1.0 C8 A:G909 4.3 27.2 1.0 OP2 A:A957 4.5 29.4 1.0 P A:A908 4.5 29.0 1.0 O3' A:A908 4.5 26.9 1.0 N6 A:A910 4.5 25.8 1.0 O5' A:A908 4.7 28.3 1.0 C3' A:A908 4.9 26.5 1.0 P A:A957 4.9 28.9 1.0

Magnesium binding site 4 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3050 b:23.1 occ:1.00 OP2 A:G2299 2.0 25.0 1.0 O A:HOH3887 2.0 22.5 1.0 O A:HOH5332 2.1 22.0 1.0 O A:HOH3677 2.1 23.1 1.0 O A:HOH4048 2.1 23.9 1.0 O A:HOH4788 2.1 22.4 1.0 P A:G2299 3.3 26.1 1.0 O5' A:G2299 3.7 26.9 1.0 OP2 A:A2296 4.0 25.7 1.0 N7 A:G2300 4.0 25.8 1.0 O A:HOH5368 4.1 24.3 1.0 OP1 A:G2299 4.3 28.8 1.0 C8 A:G2299 4.3 28.6 1.0 O A:HOH3593 4.3 40.4 1.0 N7 A:G2299 4.3 28.2 1.0 O6 A:G2300 4.4 29.0 1.0 O5' A:A2298 4.4 26.8 1.0 O4 A:U2301 4.4 26.1 1.0 O3' A:A2298 4.4 26.7 1.0 OP2 A:G2300 4.5 28.5 1.0 C3' A:A2298 4.6 27.5 1.0 OP1 A:A2298 4.6 24.6 1.0 O3' A:A2297 4.8 24.2 1.0 C5 A:G2300 4.9 26.9 1.0 C8 A:G2300 5.0 26.1 1.0

Magnesium binding site 5 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3051 b:66.2 occ:1.00 O A:HOH4807 2.1 51.3 1.0 OP1 A:U1013 2.9 34.5 1.0 O6 A:G2299 3.1 30.6 1.0 N2 A:G2300 3.2 26.6 1.0 N1 A:G2300 3.5 26.1 1.0 O3' A:G1012 3.5 27.6 1.0 C5' A:U1013 3.5 32.9 1.0 C2 A:G2300 3.6 25.9 1.0 P A:U1013 3.7 30.3 1.0 C6 A:G2299 4.0 30.3 1.0 O5' A:U1013 4.1 31.7 1.0 N1 A:G2299 4.2 30.9 1.0 O2' A:G1012 4.3 25.8 1.0 C6 A:G2300 4.5 26.8 1.0 O A:HOH4924 4.6 25.8 1.0 N3 A:G2300 4.7 27.2 1.0 C3' A:G1012 4.8 24.9 1.0 C4' A:U1013 4.8 32.8 1.0 O6 A:G2300 4.9 29.0 1.0 O A:HOH5526 4.9 28.1 1.0

Magnesium binding site 6 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3052 b:22.4 occ:1.00 OP2 A:A1305 1.9 22.2 1.0 O A:HOH4091 1.9 22.0 1.0 OP1 A:U2644 2.0 24.2 1.0 O A:HOH4064 2.1 24.2 1.0 O A:HOH3876 2.1 21.6 1.0 O A:HOH3701 2.1 23.8 1.0 P A:U2644 3.2 23.3 1.0 P A:A1305 3.2 21.0 1.0 OP2 A:U2644 3.5 25.7 1.0 OP1 A:A1305 3.6 21.2 1.0 O A:HOH4115 3.8 27.7 1.0 O2' A:U1307 4.1 25.0 1.0 O3' A:G1304 4.2 20.7 1.0 O3' A:A2643 4.3 22.9 1.0 O5' A:A1305 4.3 20.8 1.0 O5' A:U2644 4.3 23.7 1.0 C3' A:A2643 4.3 22.5 1.0 C5' A:A1305 4.3 20.9 1.0 C5' A:U2644 4.4 23.4 1.0 OP1 A:A2643 4.5 27.1 1.0 C4' A:A2643 4.9 22.3 1.0 C5' A:A2643 5.0 22.5 1.0

Magnesium binding site 7 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3053 b:30.1 occ:1.00 O A:HOH5714 2.0 29.1 1.0 O A:HOH3785 2.1 32.3 1.0 O A:HOH4457 2.1 27.4 1.0 O A:HOH3453 2.1 28.4 1.0 O A:HOH5239 2.1 25.8 1.0 O A:HOH5703 2.1 31.7 1.0 O4 A:U2040 3.9 21.2 1.0 O A:HOH4887 3.9 35.4 1.0 O A:HOH3398 4.0 26.9 1.0 O A:HOH4225 4.0 40.8 1.0 N7 A:G2038 4.1 20.3 1.0 O A:HOH4479 4.1 22.6 1.0 O6 A:G2039 4.1 18.9 1.0 O A:HOH5398 4.2 32.2 1.0 N7 A:G2039 4.2 19.0 1.0 O6 A:G2038 4.3 19.6 1.0 O A:HOH5657 4.4 24.0 1.0 OP2 A:U1307 4.4 27.4 1.0 N4 A:C2037 4.7 22.8 1.0 O A:HOH4320 4.7 48.1 1.0 C5 A:G2038 4.8 19.9 1.0 C6 A:G2038 4.9 19.0 1.0 C4 A:U2040 4.9 19.3 1.0 C4 A:C2037 4.9 23.2 1.0 C5 A:C2037 4.9 23.4 1.0 C6 A:G2039 4.9 19.2 1.0 C5 A:G2039 5.0 19.1 1.0 C8 A:G2038 5.0 19.9 1.0

Magnesium binding site 8 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3054 b:19.5 occ:1.00 O A:HOH4132 2.0 18.7 1.0 OP2 A:C1366 2.0 22.4 1.0 O A:HOH3545 2.1 19.8 1.0 O A:HOH4926 2.1 19.3 1.0 O A:HOH4277 2.1 19.2 1.0 O A:HOH5009 2.1 18.5 1.0 P A:C1366 3.3 22.7 1.0 O5' A:C1366 3.9 22.8 1.0 O A:HOH3977 4.0 36.0 1.0 OP1 A:C1366 4.0 23.7 1.0 OP1 A:U1365 4.1 25.6 1.0 O A:HOH5283 4.1 22.9 1.0 OP2 A:U1365 4.2 25.9 1.0 O A:HOH4232 4.2 20.0 1.0 O S:HOH211 4.2 39.8 1.0 N7 A:G1363 4.3 22.8 1.0 N7 A:G1367 4.3 23.3 1.0 O6 A:G1367 4.4 23.4 1.0 P A:U1365 4.5 24.1 1.0 O3' A:U1365 4.6 22.5 1.0 C8 A:G1363 4.6 22.5 1.0 OP2 A:G1367 4.8 26.1 1.0 C3' A:U1365 4.9 22.0 1.0

Magnesium binding site 9 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3055 b:17.9 occ:1.00 OP1 A:A1659 2.0 19.9 1.0 OP1 A:A798 2.0 19.4 1.0 O A:HOH5132 2.1 17.7 1.0 O A:HOH3590 2.1 16.7 1.0 O A:HOH4939 2.1 17.8 1.0 O A:HOH3775 2.1 18.3 1.0 P A:A1659 3.3 20.8 1.0 P A:A798 3.4 19.3 1.0 OP2 A:A1659 3.8 21.9 1.0 O3' A:A797 3.8 21.3 1.0 O A:HOH5304 4.0 33.2 1.0 O3' A:G1658 4.1 22.1 1.0 O2' A:G1658 4.1 23.0 1.0 O S:HOH204 4.1 21.9 1.0 N7 A:A1659 4.2 33.3 1.0 C2' A:G1658 4.2 22.1 1.0 O5' A:A798 4.2 21.4 1.0 N6 A:A836 4.3 29.3 1.0 N3 A:C1662 4.3 19.9 1.0 N1 A:A836 4.3 27.2 1.0 N7 A:A798 4.4 25.6 1.0 O5' A:A1659 4.4 23.4 1.0 OP2 A:A798 4.5 20.9 1.0 C8 A:A1659 4.5 32.2 1.0 N4 A:C1662 4.5 20.5 1.0 C3' A:G1658 4.6 22.3 1.0 C8 A:A798 4.6 25.5 1.0 N4 A:C1660 4.8 22.1 1.0 C6 A:A836 4.8 28.3 1.0 C4 A:C1662 5.0 20.6 1.0

Magnesium binding site 10 out of 158 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3056 b:46.0 occ:1.00 O A:HOH4404 2.1 41.8 1.0 O A:HOH4933 2.1 38.1 1.0 O A:HOH5299 2.1 44.7 1.0 O A:HOH4545 2.1 47.8 1.0 O A:HOH5296 2.1 46.6 1.0 O A:HOH5624 2.1 42.9 1.0 N7 A:G1664 3.9 24.1 1.0 O6 A:G1664 4.0 22.3 1.0 O6 A:G1658 4.1 25.0 1.0 OP2 A:G1664 4.5 32.0 1.0 O2' A:C1662 4.5 21.3 1.0 O2' A:A1653 4.6 36.0 1.0 OP1 A:C1662 4.7 26.2 1.0 C5 A:G1664 4.7 23.0 1.0 C6 A:G1664 4.7 22.3 1.0 C6 A:G1658 4.8 22.1 1.0 C2' A:C1662 4.8 22.4 1.0 N1 A:G1658 4.9 22.2 1.0 OP2 A:C1662 4.9 25.8 1.0 O6 A:G1665 5.0 25.0 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