Magnesium in PDB 2f4v: 30S Ribosome + Designer Antibiotic

The structure of 30S Ribosome + Designer Antibiotic, PDB code: 2f4v was solved by J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	403.323, 403.323, 176.685, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 31.5

The structure of 30S Ribosome + Designer Antibiotic also contains other interesting chemical elements:

Potassium	(K)	12 atoms
Chlorine	(Cl)	1 atom
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 - 101;

Binding sites:

The binding sites of Magnesium atom in the 30S Ribosome + Designer Antibiotic (pdb code 2f4v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 101 binding sites of Magnesium where determined in the 30S Ribosome + Designer Antibiotic, PDB code: 2f4v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1535 b:16.1 occ:1.00 OP2 A:G945 2.0 44.0 1.0 OP1 A:G944 2.8 46.7 1.0 P A:G945 3.2 44.5 1.0 P A:G944 3.4 46.2 1.0 OP2 A:G944 3.4 46.2 1.0 O5' A:G945 3.6 46.1 1.0 O5' A:G944 3.8 43.9 1.0 OP1 A:G945 3.9 44.5 1.0 OP2 A:A946 4.2 50.6 1.0 C5' A:G944 4.4 43.1 1.0 N7 A:A946 4.4 42.2 1.0 O3' A:G944 4.5 43.7 1.0 O6 A:G1233 4.6 60.6 1.0 C8 A:A946 4.9 42.2 1.0 O3' A:U943 4.9 44.5 1.0 O6 A:G947 4.9 47.3 1.0 C3' A:G944 5.0 42.4 1.0

Magnesium binding site 2 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1536 b:34.9 occ:1.00 OP1 A:G1224 1.8 75.3 1.0 P A:G1224 2.9 75.3 1.0 OP2 A:G1224 3.0 75.8 1.0 N6 A:A977 3.7 88.3 1.0 O5' A:G1224 3.9 76.1 1.0 O3' A:C1223 4.0 75.3 1.0 OP1 A:G951 4.1 60.0 1.0 N7 A:A977 4.4 88.5 1.0 C2' A:C1223 4.5 76.4 1.0 C3' A:C1223 4.6 76.1 1.0 C6 A:A977 4.7 88.5 1.0 OP2 A:U952 4.7 64.8 1.0 O2' A:C1223 4.7 76.2 1.0 C2 A:A974 4.7 72.2 1.0 OP1 A:U952 4.9 64.7 1.0 C5 A:A977 4.9 88.7 1.0

Magnesium binding site 3 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1537 b:28.6 occ:1.00 O4 A:U12 2.3 58.7 1.0 O6 A:G11 2.5 55.7 1.0 O6 A:G22 2.9 36.6 1.0 O6 A:G21 3.2 35.9 1.0 C4 A:U12 3.3 59.5 1.0 N4 A:C23 3.3 32.5 1.0 C6 A:G11 3.6 55.0 1.0 N3 A:U12 3.6 59.2 1.0 C6 A:G21 3.7 34.4 1.0 C6 A:G22 3.9 36.0 1.0 N1 A:G21 4.1 34.7 1.0 N1 A:G11 4.4 55.0 1.0 N7 A:G22 4.4 35.6 1.0 C5 A:G11 4.5 55.0 1.0 C5 A:G22 4.5 35.5 1.0 C4 A:C23 4.5 32.6 1.0 C5 A:U12 4.6 59.9 1.0 C5 A:G21 4.6 32.6 1.0 N7 A:G11 4.7 55.7 1.0 N1 A:G22 5.0 36.5 1.0 C2 A:U12 5.0 58.5 1.0 N3 A:C23 5.0 33.0 1.0

Magnesium binding site 4 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1538 b:14.0 occ:1.00 O6 A:G377 3.1 55.7 1.0 O6 A:G376 3.3 41.5 1.0 C6 A:G376 3.9 42.4 1.0 N7 A:G376 4.0 43.2 1.0 C6 A:G377 4.2 55.4 1.0 C5 A:G376 4.2 42.8 1.0 N7 A:G377 4.6 56.5 1.0 O4 A:U387 4.7 68.8 1.0 C5 A:G377 4.8 55.9 1.0 C8 A:G376 5.0 43.9 1.0

Magnesium binding site 5 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1541 b:14.9 occ:1.00 O6 A:G771 3.4 56.9 1.0 OP2 A:U804 4.2 44.6 1.0 O4 A:U772 4.3 56.0 1.0 C6 A:G771 4.4 55.3 1.0 MG A:MG1635 4.5 91.9 1.0 OP1 A:G803 4.5 38.0 1.0 C5 A:C770 4.7 32.1 1.0 N7 A:G771 4.7 53.3 1.0 N4 A:C770 4.7 31.4 1.0 O6 A:G773 4.8 60.2 1.0 C5 A:G771 4.9 53.7 1.0 N6 A:A807 4.9 65.4 1.0 C4 A:C770 5.0 31.8 1.0

Magnesium binding site 6 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1542 b:15.9 occ:1.00 OP2 A:C779 3.3 36.9 1.0 OP2 A:A780 3.6 40.0 1.0 OP1 A:C779 3.9 36.9 1.0 P A:C779 4.0 37.5 1.0 N7 A:G800 4.4 51.0 1.0 O5' A:C779 4.4 38.2 1.0 O6 A:G800 4.4 52.3 1.0 N7 A:A780 4.8 41.1 1.0 C5' A:C779 4.9 38.6 1.0 C8 A:A780 5.0 41.3 1.0

Magnesium binding site 7 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1543 b:8.2 occ:1.00 OP1 A:C578 2.2 29.1 1.0 OP2 A:G576 3.5 33.7 1.0 P A:C578 3.7 28.2 1.0 O3' A:G575 3.9 37.4 1.0 O3' A:G577 4.1 27.6 1.0 OP1 A:U820 4.1 36.1 1.0 P A:G576 4.4 35.0 1.0 O2' A:G575 4.4 39.2 1.0 OP2 A:C817 4.4 34.8 1.0 C5' A:G821 4.6 50.6 1.0 OP2 A:C578 4.6 27.2 1.0 OP1 A:C817 4.7 33.4 1.0 O5' A:C578 4.7 27.7 1.0 C5' A:C578 4.9 27.7 1.0 C4' A:G821 4.9 49.5 1.0 P A:C817 4.9 33.8 1.0

Magnesium binding site 8 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1544 b:14.5 occ:1.00 O6 A:G854 3.5 50.1 1.0 N7 A:G853 3.8 46.8 1.0 O6 A:G853 4.0 48.9 1.0 N7 A:G854 4.2 51.2 1.0 MG A:MG1595 4.2 41.0 1.0 OP1 A:U871 4.3 56.6 1.0 C5 A:G853 4.4 46.7 1.0 C6 A:G854 4.4 49.6 1.0 C6 A:G853 4.5 47.0 1.0 C8 A:G853 4.7 47.3 1.0 C5 A:G854 4.7 50.0 1.0 OP2 A:U871 4.8 56.7 1.0

Magnesium binding site 9 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1545 b:32.9 occ:1.00 OP2 A:A509 2.1 68.7 1.0 OP2 A:A510 3.0 69.6 1.0 O3' A:A509 3.0 69.5 1.0 P A:A509 3.4 68.5 1.0 OP1 A:G506 3.6 75.6 1.0 P A:A510 3.6 69.8 1.0 O3' A:C508 3.6 70.0 1.0 C3' A:A509 4.1 69.4 1.0 N7 A:A510 4.1 81.8 1.0 OP2 A:C507 4.2 72.2 1.0 O5' A:A509 4.3 67.7 1.0 O5' A:A510 4.3 71.3 1.0 C8 A:A510 4.4 81.7 1.0 OP1 A:A509 4.5 67.7 1.0 O2' A:C508 4.6 72.8 1.0 P A:G506 4.7 75.6 1.0 C5' A:A509 4.7 68.1 1.0 C3' A:C508 4.9 71.6 1.0 C4' A:A509 4.9 68.9 1.0 OP1 A:A510 4.9 69.4 1.0 O5' A:G506 5.0 75.9 1.0

Magnesium binding site 10 out of 101 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:23.3 occ:1.00 OP2 A:U560 2.0 44.2 1.0 P A:U560 3.4 43.8 1.0 OP1 A:C562 3.5 42.2 1.0 O2' A:A559 4.0 44.4 1.0 O3' A:A559 4.0 44.2 1.0 OP2 A:G558 4.3 33.9 1.0 N2 A:G566 4.4 46.3 1.0 OP1 A:U560 4.4 44.2 1.0 O5' A:U560 4.4 43.6 1.0 OP1 A:G557 4.5 35.5 1.0 C5' A:U560 4.6 44.6 1.0 O5' A:C562 4.7 43.2 1.0 P A:C562 4.7 43.2 1.0 OP1 A:A563 4.8 41.4 1.0 N1 A:G566 4.9 44.9 1.0

J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery. Interactions of Designer Antibiotics and the Bacterial Ribosome Aminoacyl-Trna Site Chem.Biol. V. 13 129 2006.
ISSN: ISSN 1074-5521
PubMed: 16492561
DOI: 10.1016/J.CHEMBIOL.2005.11.004