Magnesium 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:

Potassium	(K)	93 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 - 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 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 204;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 204 binding sites of Magnesium where determined in the E. Coli 50S Ribosomal Subunit in Complex with Pramp Rumicidin-2 (Focused Refinement), PDB code: 9d89:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3001 b:67.0 occ:1.00 O D:HOH3529 2.0 71.0 1.0 O D:HOH4570 2.0 67.9 1.0 OP2 D:A1643 2.0 69.4 1.0 O D:HOH5438 2.0 70.1 1.0 O D:HOH3586 2.0 65.2 1.0 N7 D:G1644 2.2 54.0 1.0 C8 D:G1644 3.1 50.5 1.0 C5 D:G1644 3.3 53.0 1.0 P D:A1643 3.3 63.7 1.0 O6 D:G1644 3.6 53.3 1.0 O5' D:A1643 3.7 64.1 1.0 C6 D:G1644 3.8 51.0 1.0 OP1 D:A1643 4.1 74.9 1.0 N2 D:G1301 4.3 47.2 1.0 N9 D:G1644 4.3 52.8 1.0 OP2 D:G1644 4.4 78.8 1.0 C4 D:G1644 4.4 49.3 1.0 O3' D:A1642 4.5 62.6 1.0 C8 D:A1643 4.6 53.8 1.0 N7 D:A1643 4.7 52.8 1.0 C3' D:A1642 4.8 60.8 1.0 N7 D:G1645 4.8 50.3 1.0 OP2 D:A1642 4.8 60.5 1.0

Magnesium binding site 2 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3002 b:62.9 occ:1.00 OP2 D:G58 2.0 58.2 1.0 O D:HOH6329 2.0 58.4 1.0 O D:HOH6074 2.0 63.7 1.0 O D:HOH5285 2.0 62.4 1.0 O K:HOH107 2.0 59.7 1.0 O D:HOH5314 2.0 60.6 1.0 P D:G58 3.4 56.1 1.0 OP1 D:G58 4.0 63.1 1.0 O K:ARG76 4.1 62.5 1.0 O D:HOH3757 4.2 76.9 1.0 O D:HOH4693 4.2 62.6 1.0 O D:HOH3604 4.2 69.9 1.0 O D:HOH4985 4.2 62.3 1.0 OG K:SER78 4.2 74.4 1.0 O3' D:C57 4.3 60.8 1.0 O5' D:G58 4.4 60.8 1.0 OP1 D:U65 4.5 62.2 1.0 C5' D:G58 4.5 61.9 1.0 C3' D:C57 4.6 56.5 1.0

Magnesium binding site 3 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3003 b:81.8 occ:1.00 O D:HOH7006 2.0 78.5 1.0 O D:HOH6986 2.0 84.2 1.0 O D:HOH6989 2.0 79.9 1.0 O D:HOH5960 2.0 73.0 1.0 O D:HOH6923 2.0 79.1 1.0 O D:HOH3667 2.0 75.0 1.0 O D:HOH4985 4.1 62.3 1.0 O D:HOH5325 4.1 67.0 1.0 N4 D:C57 4.2 50.9 1.0 O6 D:G58 4.3 53.9 1.0 O D:HOH4080 4.4 67.8 1.0 K D:K3260 4.5 80.5 1.0 O D:HOH4132 4.6 79.1 1.0 OP2 D:C66 4.6 73.7 1.0

Magnesium binding site 4 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3004 b:72.1 occ:1.00 O D:HOH7038 2.0 73.3 1.0 O D:HOH3315 2.0 57.8 1.0 O D:HOH7051 2.0 71.8 1.0 O I:HOH237 2.0 71.1 1.0 O D:HOH6688 2.0 73.1 1.0 O D:HOH6374 2.0 74.7 1.0 OP1 D:A672 3.8 59.1 1.0 O D:HOH6768 3.8 70.6 1.0 O D:HOH4940 4.0 57.4 1.0 O D:HOH3743 4.0 56.8 1.0 OP2 D:A806 4.1 58.4 1.0 O D:HOH5580 4.2 50.1 1.0 O I:SER42 4.3 51.3 1.0 OG I:SER42 4.4 53.1 1.0 O D:HOH6899 4.6 74.7 1.0 CB I:SER42 4.7 48.6 1.0 O3' D:G671 4.9 53.2 1.0 P D:A672 5.0 51.2 1.0 C I:SER42 5.0 46.2 1.0

Magnesium binding site 5 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3005 b:62.1 occ:1.00 O D:HOH7063 2.0 65.4 1.0 O D:HOH6945 2.0 58.7 1.0 O D:HOH6967 2.0 62.0 1.0 O D:HOH5670 2.0 59.3 1.0 O D:HOH5835 2.0 54.4 1.0 O D:HOH4450 2.0 60.0 1.0 O D:HOH4306 3.7 62.1 1.0 O6 D:G2053 4.1 41.8 1.0 O D:HOH6832 4.1 60.4 1.0 N7 D:G2053 4.2 40.6 1.0 O D:HOH3367 4.2 57.5 1.0 N7 D:G2052 4.3 44.1 1.0 O6 D:G2052 4.5 44.4 1.0 O D:HOH6740 4.8 68.0 1.0 C6 D:G2053 4.9 41.3 1.0 C5 D:C2051 4.9 43.6 1.0 OP2 D:U2619 5.0 57.5 1.0 C5 D:G2053 5.0 41.5 1.0 N4 D:C2051 5.0 41.5 1.0

Magnesium binding site 6 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3006 b:75.4 occ:1.00 O D:HOH7027 2.0 80.0 1.0 O D:HOH5797 2.0 71.5 1.0 O D:HOH3688 2.0 81.0 1.0 O6 D:G1238 2.0 55.9 1.0 O D:HOH4133 2.0 66.5 1.0 O D:HOH5152 2.0 69.5 1.0 C6 D:G1238 3.1 48.9 1.0 N7 D:G1238 3.7 51.3 1.0 O D:HOH3535 3.7 60.9 1.0 C5 D:G1238 3.7 47.0 1.0 N7 D:G1237 3.7 45.1 1.0 N1 D:G1238 4.3 47.4 1.0 C8 D:G1237 4.4 47.7 1.0 OP2 D:G1237 4.4 52.8 1.0 OP2 D:U1236 4.5 60.5 1.0 C5 D:G1237 4.7 45.7 1.0 O6 D:G1237 4.9 47.4 1.0 C8 D:G1238 5.0 49.3 1.0

Magnesium binding site 7 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3007 b:71.9 occ:1.00 OP2 D:C1015 2.0 65.4 1.0 O D:HOH6698 2.0 76.5 1.0 OP2 D:A1016 2.0 71.7 1.0 O D:HOH3866 2.0 76.1 1.0 O D:HOH6335 2.0 73.3 1.0 O D:HOH4034 2.0 74.1 1.0 P D:A1016 3.3 72.4 1.0 P D:C1015 3.5 64.2 1.0 O3' D:C1015 3.9 71.2 1.0 OP1 D:A1016 4.0 89.6 1.0 C3' D:C1015 4.1 67.9 1.0 O3' D:U1014 4.3 66.1 1.0 OP1 D:C1015 4.3 73.0 1.0 O5' D:C1015 4.4 67.6 1.0 O5' D:A1016 4.4 75.7 1.0 C5' D:C1015 4.4 67.2 1.0 OP2 D:A1145 4.7 65.7 1.0 C4' D:C1015 4.9 68.8 1.0

Magnesium binding site 8 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3008 b:77.6 occ:1.00 O D:HOH4325 2.0 71.5 1.0 O D:HOH6983 2.0 80.5 1.0 O D:HOH4817 2.0 64.7 1.0 O D:HOH6649 2.0 80.8 1.0 O D:HOH6387 2.0 74.1 1.0 O D:HOH3939 2.0 75.1 1.0 OP1 D:U2711 3.7 72.0 1.0 O D:HOH5201 3.9 76.6 1.0 OP1 D:G2697 3.9 57.2 1.0 OP2 D:G2698 4.1 57.5 1.0 O D:HOH4058 4.1 59.9 1.0 O2' D:A2854 4.3 60.4 1.0 OP2 D:U2711 4.4 65.0 1.0 OP1 D:G2698 4.4 64.9 1.0 P D:U2711 4.6 64.7 1.0 P D:G2698 4.6 51.8 1.0 O5' D:G2697 4.8 50.0 1.0 O3' D:A2854 4.8 60.2 1.0 P D:G2697 4.9 51.6 1.0 O3' D:G2697 5.0 55.5 1.0 C5' D:G2697 5.0 50.5 1.0

Magnesium binding site 9 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3009 b:76.8 occ:1.00 O D:HOH5054 2.0 74.2 1.0 O D:HOH3473 2.0 75.3 1.0 O D:HOH4902 2.0 84.1 1.0 OP2 D:U2705 2.0 65.6 1.0 O D:HOH4562 2.0 78.6 1.0 OP1 D:C2707 2.0 73.8 1.0 P D:C2707 3.1 68.3 1.0 O3' D:G2706 3.1 64.2 1.0 P D:U2705 3.5 62.0 1.0 OP2 D:C2707 4.2 72.6 1.0 O5' D:C2707 4.2 67.0 1.0 O5' D:U2705 4.2 67.1 1.0 C5' D:C2707 4.2 66.7 1.0 OP1 D:U2705 4.3 75.0 1.0 O3' D:A2704 4.5 64.4 1.0 C3' D:A2704 4.5 61.8 1.0 C3' D:G2706 4.5 68.0 1.0 C5 D:U2705 4.5 51.3 1.0 C6 D:U2705 4.9 51.8 1.0 O2' D:G2706 4.9 70.1 1.0 OP1 D:C1465 5.0 95.3 1.0 C4' D:G2706 5.0 69.8 1.0 O5' D:A2704 5.0 63.6 1.0

Magnesium binding site 10 out of 204 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 Magnesium with other atoms in the Mg 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:Mg3010 b:77.3 occ:1.00 O D:HOH3310 2.0 72.5 1.0 OP1 D:G2243 2.0 67.1 1.0 O D:HOH6395 2.0 72.4 1.0 O F:HOH419 2.0 72.4 1.0 O D:HOH7029 2.0 92.1 1.0 O D:HOH3518 2.0 74.9 1.0 P D:G2243 3.4 58.2 1.0 OP1 D:G2242 3.8 65.4 1.0 OP2 D:G2243 4.1 63.0 1.0 O5' D:G2243 4.2 55.8 1.0 O F:GLY249 4.3 56.4 1.0 C5' D:G2242 4.4 56.9 1.0 C3' D:G2242 4.4 53.7 1.0 C4' D:G2242 4.4 53.0 1.0 O3' D:G2242 4.4 58.6 1.0 P D:G2242 4.9 64.2 1.0 C5' D:G2243 4.9 58.9 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