Magnesium in PDB 8p8b: Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells

All present enzymatic activity of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells:
5.2.1.8;

The structure of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	4 atoms
Chlorine	(Cl)	2 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 - 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 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 229;

Binding sites:

The binding sites of Magnesium atom in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells (pdb code 8p8b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 229 binding sites of Magnesium where determined in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells, PDB code: 8p8b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3003 b:9.3 occ:1.00 O6 3:G2017 3.8 38.9 1.0 OP2 3:U1297 4.2 32.1 1.0 O6 3:G2016 4.3 40.9 1.0 N7 3:G2016 4.5 30.6 1.0 O4 3:U2018 4.5 33.3 1.0 N7 3:G2017 4.6 28.9 1.0 C6 3:G2017 4.7 29.1 1.0 N4 3:C2015 4.9 38.1 1.0 C6 3:G2016 4.9 30.2 1.0 C5 3:G2016 5.0 25.2 1.0

Magnesium binding site 2 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3004 b:24.2 occ:1.00 OP1 3:U600 3.1 39.3 1.0 OP2 3:G843 3.8 39.2 1.0 N7 3:G844 4.1 28.1 1.0 O3' 3:U599 4.2 26.1 1.0 P 3:U600 4.2 39.0 1.0 OP2 3:G844 4.2 39.3 1.0 C5' 3:U600 4.4 26.9 1.0 CG k:LYS37 4.4 31.7 1.0 OE1 k:GLN36 4.5 47.0 1.0 O4 3:U845 4.6 40.5 1.0 O5' 3:U600 4.7 33.3 1.0 O5' 3:G843 4.7 46.3 1.0 C8 3:G844 4.7 27.3 1.0 P 3:G843 4.8 28.2 1.0 N7 3:G843 4.8 40.8 1.0 CD k:LYS37 4.8 41.6 1.0

Magnesium binding site 3 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3005 b:18.8 occ:1.00 OP1 3:C2013 2.1 37.1 1.0 OP1 3:A1298 2.8 45.0 1.0 P 3:C2013 3.5 43.2 1.0 O3' 3:U1297 3.6 32.0 1.0 P 3:A1298 3.8 37.8 1.0 OP1 3:A2055 3.9 44.3 1.0 OP2 3:C2013 4.2 33.8 1.0 O3' 3:A2012 4.2 27.0 1.0 C5' 3:A1298 4.4 28.0 1.0 O5' 3:C2013 4.5 38.6 1.0 O5' 3:A1298 4.6 22.4 1.0 C5' 3:C2013 4.7 33.8 1.0 C3' 3:U1297 4.9 33.7 1.0

Magnesium binding site 4 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3006 b:18.4 occ:1.00 N7 3:A1283 3.8 16.9 1.0 OP1 3:U845 3.8 34.9 1.0 OP1 3:U846 4.1 14.7 1.0 OP2 3:U845 4.1 21.9 1.0 O3' 3:G598 4.2 29.7 1.0 N6 3:A1283 4.3 24.8 1.0 CE1 k:HIS24 4.4 31.0 1.0 P 3:U845 4.5 37.4 1.0 O2' 3:G598 4.5 38.9 1.0 C4' 3:G598 4.5 25.1 1.0 C5 3:A1283 4.7 12.9 1.0 C8 3:A1283 4.7 23.3 1.0 ND1 k:HIS24 4.8 34.6 1.0 C3' 3:G598 4.9 25.5 1.0 C6 3:A1283 5.0 20.2 1.0

Magnesium binding site 5 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3007 b:45.0 occ:1.00 OP2 3:A1656 2.9 54.4 1.0 N7 3:A1656 3.1 46.6 1.0 C8 3:A1656 3.5 44.0 1.0 N7 3:G1657 4.1 41.2 1.0 P 3:A1656 4.1 57.2 1.0 C5 3:A1656 4.2 45.9 1.0 O5' 3:A1656 4.3 52.5 1.0 O3' 3:U1655 4.7 42.5 1.0 N9 3:A1656 4.7 45.7 1.0 N6 3:A1656 4.8 43.9 1.0 C2' 3:U1655 4.8 40.6 1.0 C8 3:G1657 4.9 42.7 1.0 C6 3:A1656 4.9 47.5 1.0 C3' 3:U1655 4.9 36.7 1.0 O6 3:G1657 5.0 50.0 1.0

Magnesium binding site 6 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3008 b:24.4 occ:1.00 OP2 3:G1642 2.2 45.4 1.0 P 3:G1642 3.3 56.2 1.0 O5' 3:G1642 3.5 38.0 1.0 OP2 3:C1653 3.8 34.1 1.0 N7 3:G1654 4.0 43.8 1.0 OP1 3:G1642 4.0 39.5 1.0 O4 3:U1655 4.2 44.9 1.0 O6 3:G1654 4.4 41.3 1.0 O3' 3:A1641 4.6 40.7 1.0 OP2 3:G1654 4.8 43.4 1.0 C5 3:G1654 4.8 33.1 1.0 C8 3:G1654 4.9 38.0 1.0 C5' 3:G1642 4.9 39.1 1.0 C6 3:G1654 4.9 34.5 1.0 P 3:C1653 5.0 51.6 1.0

Magnesium binding site 7 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3009 b:20.5 occ:1.00 O4 3:U781 2.1 46.3 1.0 C4 3:U781 3.2 42.7 1.0 C5 3:U781 3.9 33.4 1.0 OP2 3:C779 4.3 37.6 1.0 N3 3:U781 4.3 36.5 1.0 OP1 3:C2619 4.3 39.7 1.0 N7 3:G780 4.5 34.4 1.0 C2 3:SPD3228 5.0 20.0 1.0

Magnesium binding site 8 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3010 b:25.9 occ:1.00 OP2 3:A898 2.2 32.7 1.0 P 3:A898 3.5 43.7 1.0 O5' 3:A898 3.9 49.0 1.0 N7 3:A899 4.1 32.1 1.0 N7 3:A898 4.2 36.9 1.0 OP1 3:A897 4.3 40.3 1.0 N6 3:A899 4.3 30.3 1.0 OP1 3:A898 4.3 36.8 1.0 OP1 3:A947 4.3 29.6 1.0 C8 3:A898 4.4 35.6 1.0 OP2 3:A897 4.4 36.5 1.0 P 3:A897 4.6 44.0 1.0 O3' 3:A897 4.7 33.3 1.0 O5' 3:A897 4.7 33.8 1.0 OP2 3:A947 4.8 42.3 1.0 C5 3:A899 4.9 24.9 1.0

Magnesium binding site 9 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3011 b:53.0 occ:1.00 OP2 3:A1299 2.0 18.8 1.0 OP1 3:A2012 2.1 30.1 1.0 P 3:A1299 3.4 29.6 1.0 P 3:A2012 3.6 40.0 1.0 O5' 3:A1299 4.0 34.1 1.0 O5' 3:A2012 4.0 45.1 1.0 C5' 3:A2012 4.1 36.2 1.0 N7 3:A1299 4.1 30.2 1.0 OP2 3:C2013 4.2 33.8 1.0 C8 3:A1299 4.3 24.9 1.0 O3' 3:A1298 4.3 40.4 1.0 O5' 3:A1298 4.4 22.4 1.0 OP2 3:A1298 4.4 30.7 1.0 OP1 3:A1299 4.4 40.7 1.0 OP1 3:A1298 4.5 45.0 1.0 OP2 3:A2012 4.5 31.5 1.0 O3' 3:G2011 4.5 27.8 1.0 C3' 3:A1298 4.6 39.7 1.0 P 3:A1298 4.6 37.8 1.0 C5' 3:A1298 4.8 28.0 1.0

Magnesium binding site 10 out of 229 in the Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mycoplasma Pneumoniae Large Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3012 b:26.8 occ:1.00 OP1 3:U2623 2.0 25.7 1.0 OP2 3:A1295 2.5 26.1 1.0 P 3:U2623 3.3 42.0 1.0 OP2 3:U2623 3.7 31.3 1.0 P 3:A1295 3.8 41.9 1.0 O5' 3:U2623 4.2 24.8 1.0 OP1 3:A1295 4.3 41.8 1.0 O3' 3:A2622 4.4 32.1 1.0 C3' 3:A2622 4.4 23.4 1.0 C5' 3:U2623 4.5 24.0 1.0 OP1 3:A2622 4.6 40.5 1.0 O2' 3:U1297 4.6 34.9 1.0 C5' 3:A1295 4.8 22.8 1.0 O5' 3:A1295 4.8 36.2 1.0 O3' 3:G1294 4.8 18.5 1.0

L.Xue, C.M.T.Spahn, M.Schacherl, J.Mahamid. Structural Insights Into Context-Dependent Inhibitory Mechanisms of Chloramphenicol in Cells Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01441-0