Magnesium in PDB 8p6p: Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells

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

Zinc

(Zn)

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 - 103;

Binding sites:

The binding sites of Magnesium atom in the Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells (pdb code 8p6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 103 binding sites of Magnesium where determined in the Mycoplasma Pneumoniae Small Ribosomal Subunit in Chloramphenicol- Treated Cells, PDB code: 8p6p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1606 b:30.0 occ:1.00 O2 5:C1372 3.0 73.6 1.0 C5' 5:C1372 3.5 73.6 1.0 O5' 5:C1372 3.9 73.6 1.0 C2 5:C1372 4.1 73.6 1.0 C2' 5:C1372 4.2 73.6 1.0 C4' 5:C1372 4.4 73.6 1.0 C3' 5:C1372 4.5 73.6 1.0 O4' 5:C1372 4.7 73.6 1.0 N3 5:C1372 4.9 73.6 1.0 C1' 5:C1372 4.9 73.6 1.0 N1 5:C1372 4.9 73.6 1.0

Magnesium binding site 2 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1607 b:30.0 occ:1.00 OP1 5:G881 4.4 74.3 1.0 C5' 5:G881 4.4 74.3 1.0 O5' 5:C910 4.7 82.0 1.0 O3' 5:G881 4.9 74.3 1.0

Magnesium binding site 3 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1608 b:30.0 occ:1.00 OP2 5:A581 2.4 72.2 1.0 P 5:A581 3.7 72.2 1.0 N7 5:G582 4.0 70.2 1.0 O5' 5:A581 4.2 72.2 1.0 O6 5:G582 4.5 70.2 1.0 O5' 5:C580 4.6 71.8 1.0 OP1 5:A581 4.6 72.2 1.0 OP2 5:C580 4.6 71.8 1.0 OP1 5:C580 4.6 71.8 1.0 NZ N:LYS65 4.7 74.7 1.0 O4 5:U754 4.8 67.5 1.0 O6 5:G583 4.8 68.5 1.0 P 5:C580 4.8 71.8 1.0 N7 5:A581 4.8 72.2 1.0 O3' 5:C580 4.9 71.8 1.0 C8 5:A581 4.9 72.2 1.0 C5 5:G582 4.9 70.2 1.0 C8 5:G582 4.9 70.2 1.0

Magnesium binding site 4 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1609 b:30.0 occ:1.00 OP1 5:G22 2.0 64.3 1.0 P 5:G22 3.2 64.3 1.0 O3' 5:U21 3.7 64.9 1.0 OP2 5:G22 3.8 64.3 1.0 N6 5:A571 4.1 67.0 1.0 O2' 5:G565 4.3 70.0 1.0 N1 5:A571 4.4 67.0 1.0 N3 5:G565 4.4 70.0 1.0 O5' 5:G22 4.4 64.3 1.0 N2 5:G565 4.6 70.0 1.0 C6 5:A571 4.8 67.0 1.0 C5' 5:G22 4.8 64.3 1.0 OP2 5:U559 4.9 69.4 1.0

Magnesium binding site 5 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1610 b:30.0 occ:1.00 OP2 5:U558 2.8 73.2 1.0 OP1 5:U560 2.9 74.5 1.0 P 5:U560 4.0 74.5 1.0 P 5:U558 4.1 73.2 1.0 O3' 5:A557 4.2 68.0 1.0 N2 5:G564 4.2 77.3 1.0 OP2 5:U560 4.4 74.5 1.0 O5' 5:U560 4.5 74.5 1.0 OP1 5:A561 4.6 72.9 1.0 C5' 5:U558 4.6 73.2 1.0 N1 5:G564 4.7 77.3 1.0 OP1 5:G555 4.7 69.0 1.0 OP2 5:G556 4.7 69.2 1.0 O5' 5:U558 4.8 73.2 1.0 O2' 5:A557 4.9 68.0 1.0

Magnesium binding site 6 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1611 b:30.0 occ:1.00 OP1 5:G556 2.0 69.2 1.0 O6 5:G295 2.5 80.5 1.0 O3' 5:G555 2.8 69.0 1.0 P 5:G556 3.0 69.2 1.0 O2' 5:G293 3.5 73.9 1.0 C6 5:G295 3.7 80.5 1.0 OP2 5:G556 4.1 69.2 1.0 O5' 5:G556 4.1 69.2 1.0 C3' 5:G555 4.2 69.0 1.0 C5' 5:G556 4.2 69.2 1.0 N1 5:G295 4.5 80.5 1.0 OP1 5:U558 4.5 73.2 1.0 C4' 5:G555 4.5 69.0 1.0 C5 5:G295 4.7 80.5 1.0 N7 5:A294 4.8 80.2 1.0 O2' 5:G555 4.8 69.0 1.0 N6 5:A296 4.8 79.0 1.0 C5' 5:G555 4.9 69.0 1.0 C2' 5:G293 4.9 73.9 1.0

Magnesium binding site 7 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1612 b:30.0 occ:1.00 OP2 5:A572 2.0 66.3 1.0 OP2 5:A571 2.8 67.0 1.0 P 5:A572 3.1 66.3 1.0 OP1 5:A572 3.4 66.3 1.0 OP2 5:A570 3.6 63.6 1.0 P 5:A571 3.9 67.0 1.0 OP1 5:U569 3.9 62.4 1.0 O5' 5:A572 4.1 66.3 1.0 OP1 5:A571 4.1 67.0 1.0 O3' 5:A571 4.3 67.0 1.0 C5' 5:A570 4.5 63.6 1.0 C3' 5:A571 4.6 67.0 1.0 O5' 5:A571 4.7 67.0 1.0 C5' 5:A571 4.8 67.0 1.0 P 5:A570 4.8 63.6 1.0 P 5:U569 4.9 62.4 1.0 C8 5:A572 4.9 66.3 1.0 C2 5:A816 4.9 63.2 1.0 N7 5:A572 5.0 66.3 1.0

Magnesium binding site 8 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1613 b:30.0 occ:1.00 OP1 5:A576 3.0 61.3 1.0 OP2 5:C574 3.1 61.6 1.0 OP1 5:U817 3.8 64.4 1.0 OP2 5:C814 4.0 63.3 1.0 O3' 5:G573 4.1 64.5 1.0 P 5:C574 4.1 61.6 1.0 O3' 5:A575 4.1 61.8 1.0 P 5:A576 4.2 61.3 1.0 C5' 5:A818 4.5 63.0 1.0 O2' 5:G573 4.6 64.5 1.0 P 5:U817 4.8 64.4 1.0 OP1 5:C574 4.9 61.6 1.0 P 5:C814 4.9 63.3 1.0 OP2 5:U817 4.9 64.4 1.0 C4' 5:A818 5.0 63.0 1.0

Magnesium binding site 9 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1614 b:30.0 occ:1.00 OP2 5:A811 2.0 61.2 1.0 OP1 5:A811 2.3 61.2 1.0 P 5:A811 2.3 61.2 1.0 O5' 5:A811 3.0 61.2 1.0 C5' 5:A811 3.6 61.2 1.0 O3' 5:U810 3.9 63.8 1.0 OP2 5:A575 4.0 61.8 1.0 OP2 5:A812 4.1 61.7 1.0 N7 5:A813 4.3 62.4 1.0 OP1 5:A812 4.5 61.7 1.0 N6 5:A813 4.5 62.4 1.0 P 5:A812 4.7 61.7 1.0 C3' 5:U810 4.7 63.8 1.0 OP1 5:A575 4.8 61.8 1.0 C4' 5:A811 4.8 61.2 1.0 P 5:A575 4.9 61.8 1.0

Magnesium binding site 10 out of 103 in the Mycoplasma Pneumoniae Small 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 Small Ribosomal Subunit in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1615 b:30.0 occ:1.00 OP2 5:C862 2.6 65.6 1.0 P 5:C862 3.7 65.6 1.0 N7 5:A863 3.8 67.6 1.0 OP2 5:U851 3.9 81.1 1.0 OP1 5:C862 4.1 65.6 1.0 OP2 5:A863 4.1 67.6 1.0 N7 5:G852 4.2 77.0 1.0 OP2 5:G852 4.3 77.0 1.0 O5' 5:C862 4.3 65.6 1.0 C8 5:A863 4.5 67.6 1.0 P 5:U851 4.9 81.1 1.0 O5' 5:U851 5.0 81.1 1.0 C8 5:G852 5.0 77.0 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