Magnesium in PDB 7ood: Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells

The structure of Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	3 atoms
Potassium	(K)	1 atom

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Magnesium atom in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells (pdb code 7ood). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 25 binding sites of Magnesium where determined in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells, PDB code: 7ood:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3002 b:70.0 occ:1.00 O6 3:G2408 3.7 69.2 1.0 O4 3:U2409 3.8 70.4 1.0 O6 3:G2423 4.3 65.8 1.0 N4 3:C2424 4.4 64.6 1.0 C6 3:G2408 4.8 69.2 1.0 C4 3:U2409 4.9 70.4 1.0

Magnesium binding site 2 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3003 b:44.5 occ:1.00 O6 3:G2017 3.9 52.6 1.0 N7 3:G2017 4.1 52.6 1.0 OP2 3:U1297 4.2 51.5 1.0 N7 3:G2016 4.3 53.1 1.0 O6 3:G2016 4.7 53.1 1.0 C6 3:G2017 4.7 52.6 1.0 C5 3:G2017 4.7 52.6 1.0 O4 3:U2018 4.8 52.5 1.0 C5 3:G2016 4.8 53.1 1.0

Magnesium binding site 3 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3004 b:40.1 occ:1.00 OP1 3:U600 1.8 47.8 1.0 P 3:U600 3.3 47.8 1.0 O3' 3:U599 3.8 48.1 1.0 C5' 3:U600 4.0 47.8 1.0 OP2 3:G844 4.1 45.9 1.0 OP2 3:G843 4.1 45.8 1.0 OE1 k:GLN36 4.2 48.0 1.0 O5' 3:U600 4.2 47.8 1.0 CE k:LYS30 4.2 47.2 1.0 OP2 3:U600 4.3 47.8 1.0 NE2 k:GLN36 4.5 48.0 1.0 N7 3:G844 4.6 45.9 1.0 CD k:GLN36 4.7 48.0 1.0

Magnesium binding site 4 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3005 b:48.7 occ:1.00 OP1 3:A1298 2.2 51.3 1.0 OP1 3:C2013 2.2 51.2 1.0 P 3:A1298 3.6 51.3 1.0 P 3:C2013 3.6 51.2 1.0 OP2 3:A2056 3.9 50.6 1.0 OP1 3:A2055 4.0 51.2 1.0 O2' 3:U1297 4.1 51.5 1.0 C5' 3:A1298 4.2 51.3 1.0 O3' 3:A2012 4.3 50.6 1.0 O5' 3:A1298 4.4 51.3 1.0 OP2 3:A1298 4.4 51.3 1.0 OP2 3:C2013 4.5 51.2 1.0 O5' 3:C2013 4.6 51.2 1.0 O3' 3:U1297 4.7 51.5 1.0 C5' 3:C2013 4.8 51.2 1.0 OP1 3:A2622 4.9 49.8 1.0 P 3:A2056 4.9 50.6 1.0 OP1 3:A2056 5.0 50.6 1.0

Magnesium binding site 5 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3006 b:41.9 occ:1.00 N7 3:A1283 4.1 45.4 1.0 N6 3:A1283 4.2 45.4 1.0 OP1 3:U846 4.4 48.3 1.0 OP1 3:U845 4.5 46.0 1.0 CE1 k:HIS24 4.6 48.7 1.0 O3' 3:G598 4.6 46.2 1.0 ND1 k:HIS24 4.7 48.7 1.0 C5' 3:U846 4.7 48.3 1.0 C4' 3:G598 4.8 46.2 1.0 C5 3:A1283 4.9 45.4 1.0

Magnesium binding site 6 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3007 b:60.7 occ:1.00 OP2 3:A1656 2.3 61.6 1.0 P 3:A1656 3.7 61.6 1.0 N7 3:A1656 4.0 61.6 1.0 O5' 3:A1656 4.2 61.6 1.0 C8 3:A1656 4.3 61.6 1.0 OP2 3:G1657 4.3 62.6 1.0 OP1 3:A1656 4.4 61.6 1.0 N7 3:G1657 4.5 62.6 1.0 O3' 3:U1655 4.8 57.1 1.0

Magnesium binding site 7 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3008 b:48.3 occ:1.00 OP2 3:G1642 2.2 55.6 1.0 OP2 3:C1653 3.5 53.3 1.0 P 3:G1642 3.5 55.6 1.0 N7 3:G1654 3.9 54.6 1.0 OP1 3:G1642 4.0 55.6 1.0 O5' 3:G1642 4.2 55.6 1.0 O4 3:U1655 4.4 57.1 1.0 C5 3:C1653 4.7 53.3 1.0 C8 3:G1654 4.7 54.6 1.0 O6 3:G1654 4.7 54.6 1.0 O3' 3:A1641 4.7 55.0 1.0 C3' 3:A1641 4.8 55.0 1.0 C5 3:G1654 4.9 54.6 1.0 OP2 3:G1654 4.9 54.6 1.0 C5' 3:G1642 4.9 55.6 1.0 P 3:C1653 4.9 53.3 1.0

Magnesium binding site 8 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3009 b:45.5 occ:1.00 O4 3:U781 1.9 51.4 1.0 C4 3:U781 3.1 51.4 1.0 OP1 3:C2619 3.2 54.1 1.0 C5 3:U781 3.9 51.4 1.0 OP1 3:C2618 4.1 56.0 1.0 N3 3:U781 4.1 51.4 1.0 P 3:C2619 4.7 54.1 1.0 OP2 3:C779 4.8 50.4 1.0 OP1 3:U2588 4.8 55.1 1.0 O5' 3:C2618 5.0 56.0 1.0

Magnesium binding site 9 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3010 b:59.8 occ:1.00 OP2 3:A898 2.0 70.3 1.0 P 3:A898 3.2 70.3 1.0 O5' 3:A898 3.5 70.3 1.0 OP1 3:A898 4.0 70.3 1.0 C8 3:A898 4.1 70.3 1.0 N7 3:A899 4.2 69.9 1.0 N7 3:A898 4.2 70.3 1.0 OP2 3:A897 4.3 69.1 1.0 O3' 3:A897 4.5 69.1 1.0 N6 3:A899 4.5 69.9 1.0 OP2 3:A947 4.5 56.8 1.0 OP1 3:A897 4.6 69.1 1.0 O5' 3:A897 4.6 69.1 1.0 P 3:A897 4.7 69.1 1.0 C3' 3:A897 4.8 69.1 1.0 OP1 3:A947 4.8 56.8 1.0 C5' 3:A898 4.9 70.3 1.0

Magnesium binding site 10 out of 25 in the Mycoplasma Pneumoniae 50S Subunit of Ribosomes 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 50S Subunit of Ribosomes in Chloramphenicol- Treated Cells within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg3011 b:50.4 occ:1.00 OP2 3:A1299 2.2 51.0 1.0 OP1 3:A2012 2.2 50.6 1.0 OP2 3:A1298 3.0 51.3 1.0 P 3:A2012 3.6 50.6 1.0 P 3:A1299 3.7 51.0 1.0 OP2 3:C2013 3.9 51.2 1.0 C5' 3:A2012 4.1 50.6 1.0 N7 3:A1299 4.2 51.0 1.0 O5' 3:A2012 4.2 50.6 1.0 P 3:A1298 4.2 51.3 1.0 O5' 3:A1298 4.3 51.3 1.0 O5' 3:A1299 4.4 51.0 1.0 O3' 3:A1298 4.4 51.3 1.0 C3' 3:A1298 4.5 51.3 1.0 C8 3:A1299 4.5 51.0 1.0 OP2 3:A2012 4.5 50.6 1.0 C5' 3:A1298 4.6 51.3 1.0 O3' 3:G2011 4.7 51.1 1.0 OP1 3:A1299 4.7 51.0 1.0

L.Xue, S.Lenz, M.Zimmermann-Kogadeeva, D.Tegunov, P.Cramer, P.Bork, J.Rappsilber, J.Mahamid. Visualizing Translation Dynamics at Atomic Detail Inside A Bacterial Cell. Nature V. 610 205 2022.
ISSN: ESSN 1476-4687
PubMed: 36171285
DOI: 10.1038/S41586-022-05255-2