Magnesium in PDB 1ibk: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin, PDB code: 1ibk was solved by J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	316.23 / 3.31
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.160, 401.160, 176.360, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.2

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin 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 - 110; Page 12, Binding sites: 111 - 113;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin (pdb code 1ibk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 113 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin, PDB code: 1ibk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:24.1 occ:1.33 OP2 A:G945 2.4 50.1 1.0 OP1 A:G944 2.4 39.7 1.0 P A:G944 3.4 43.1 1.0 OP2 A:G944 3.6 39.7 1.0 P A:G945 3.6 31.1 1.0 O5' A:G944 4.0 43.1 1.0 O5' A:G945 4.1 31.1 1.0 N7 A:A946 4.1 41.9 1.0 OP1 A:G945 4.3 50.1 1.0 O6 A:G947 4.3 41.5 1.0 OP2 A:A946 4.4 41.9 1.0 C5' A:G944 4.6 43.1 1.0 O6 A:G1233 4.6 64.2 1.0 C8 A:A946 4.7 41.9 1.0 O3' A:U943 4.8 33.9 1.0 O3' A:G944 4.9 43.1 1.0 C5 A:A946 4.9 41.9 1.0 N6 A:A946 5.0 41.9 1.0

Magnesium binding site 2 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1547 b:24.1 occ:1.43 OP1 A:G1224 2.0 79.7 1.0 P A:G1224 3.3 55.3 1.0 OP2 A:G1224 3.7 79.7 1.0 O2' A:C1223 3.9 47.1 1.0 C2' A:C1223 4.2 47.1 1.0 O3' A:C1223 4.2 47.1 1.0 O5' A:G1224 4.3 55.3 1.0 N7 A:A977 4.4 86.1 1.0 C3' A:C1223 4.7 47.1 1.0 C2 A:A974 4.7 36.2 1.0 OP2 A:U952 4.8 50.0 1.0 N6 A:A977 4.8 86.1 1.0 OP1 A:G951 4.8 51.8 1.0

Magnesium binding site 3 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:24.1 occ:1.22 O6 A:G22 3.0 28.3 1.0 O4 A:U12 3.0 39.8 1.0 O6 A:G21 3.4 37.8 1.0 O6 A:G11 3.5 38.3 1.0 N4 A:C23 3.5 29.9 1.0 C6 A:G21 3.7 37.8 1.0 C4 A:U12 4.0 39.8 1.0 C6 A:G22 4.0 28.3 1.0 N1 A:G21 4.1 37.8 1.0 N3 A:U12 4.1 39.8 1.0 N7 A:G22 4.2 28.3 1.0 C5 A:G22 4.5 28.3 1.0 C5 A:G21 4.5 37.8 1.0 C6 A:G11 4.6 38.3 1.0 C4 A:C23 4.6 29.9 1.0 C2 A:G21 5.0 37.8 1.0

Magnesium binding site 4 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1549 b:24.1 occ:1.44 O6 A:G377 3.2 64.7 1.0 O6 A:G376 3.9 55.0 1.0 N7 A:G377 4.1 64.7 1.0 MG A:MG1595 4.1 24.1 1.0 N7 A:G376 4.2 55.0 1.0 C6 A:G377 4.2 64.7 1.0 C6 A:G376 4.4 55.0 1.0 C5 A:G377 4.5 64.7 1.0 C5 A:G376 4.5 55.0 1.0

Magnesium binding site 5 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1550 b:24.1 occ:0.89 OP2 A:C749 1.8 71.3 1.0 OP2 A:G750 2.1 52.2 1.0 P A:C749 3.0 47.8 1.0 OP1 A:C749 3.4 71.3 1.0 P A:G750 3.5 53.8 1.0 O2' A:C748 4.0 0.4 1.0 O3' A:C748 4.1 0.4 1.0 O3' A:C749 4.1 47.8 1.0 O5' A:C749 4.2 47.8 1.0 C3' A:C749 4.2 47.8 1.0 OP1 A:G750 4.4 52.2 1.0 O5' A:G750 4.5 53.8 1.0 C2' A:C748 4.7 0.4 1.0 C3' A:C748 4.9 0.4 1.0 C5' A:C749 5.0 47.8 1.0

Magnesium binding site 6 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1551 b:24.1 occ:1.51 OP2 A:A766 2.2 17.6 1.0 N4 A:C811 3.1 30.3 1.0 O2 A:C812 3.4 33.9 1.0 P A:A766 3.7 24.3 1.0 N3 A:C811 3.8 30.3 1.0 C4 A:C811 3.8 30.3 1.0 N3 A:C812 3.9 33.9 1.0 C2 A:C812 4.1 33.9 1.0 O4 A:U813 4.2 30.1 1.0 O3' A:G765 4.3 34.2 1.0 O5' A:A766 4.3 24.3 1.0 C3' A:G765 4.4 34.2 1.0 N7 A:A767 4.7 37.3 1.0 OP1 A:A766 4.8 17.6 1.0 C2' A:G765 4.8 34.2 1.0 N6 A:A768 4.8 32.8 1.0 C4 A:U813 4.9 30.1 1.0 C2 A:C811 5.0 30.3 1.0

Magnesium binding site 7 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1552 b:24.1 occ:1.47 OP2 A:A768 2.5 32.8 1.0 P A:A768 3.9 21.6 1.0 N7 A:A768 4.3 32.8 1.0 OP2 A:A767 4.3 37.3 1.0 O5' A:A767 4.3 46.0 1.0 O5' A:A768 4.5 21.6 1.0 N7 A:G769 4.5 23.5 1.0 P A:A767 4.6 46.0 1.0 C8 A:A768 4.6 32.8 1.0 OP1 A:U804 4.6 53.5 1.0 C3' A:A767 4.7 46.0 1.0 OP1 A:A767 4.7 37.3 1.0 OP2 A:C805 4.7 27.1 1.0 O3' A:A767 4.8 46.0 1.0 OP1 A:A768 4.9 32.8 1.0

Magnesium binding site 8 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1553 b:24.1 occ:1.11 O4 A:U772 4.1 39.5 1.0 N7 A:G771 4.2 35.0 1.0 OP1 A:G803 4.2 38.2 1.0 N4 A:C770 4.4 28.5 1.0 C5 A:C770 4.5 28.5 1.0 C4 A:C770 4.5 28.5 1.0 O6 A:G771 4.7 35.0 1.0 OP2 A:U804 4.8 53.5 1.0

Magnesium binding site 9 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1554 b:24.1 occ:1.11 N7 A:G800 3.6 33.0 1.0 OP2 A:A780 3.8 61.0 1.0 OP2 A:C779 3.9 40.6 1.0 O6 A:G800 4.0 33.0 1.0 N7 A:A780 4.4 61.0 1.0 C5 A:G800 4.5 33.0 1.0 OP1 A:C779 4.5 40.6 1.0 P A:C779 4.6 35.6 1.0 C6 A:G800 4.6 33.0 1.0 C8 A:G800 4.6 33.0 1.0 OP2 A:G800 4.8 33.0 1.0 C8 A:A780 4.8 61.0 1.0 O5' A:C779 4.9 35.6 1.0 OP2 A:G799 5.0 41.7 1.0

Magnesium binding site 10 out of 113 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with the Antibiotic Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1555 b:24.1 occ:1.52 OP1 A:C578 2.4 19.9 1.0 OP2 A:G576 3.3 48.6 1.0 O3' A:G577 3.5 26.2 1.0 P A:C578 3.6 28.8 1.0 OP2 A:C817 3.6 19.3 1.0 OP1 A:U820 4.4 43.3 1.0 O2' A:G575 4.4 28.1 1.0 C5' A:C578 4.5 28.8 1.0 O5' A:C578 4.6 28.8 1.0 O5' A:C817 4.6 25.6 1.0 P A:C817 4.6 25.6 1.0 OP2 A:C578 4.7 19.9 1.0 P A:G576 4.7 24.6 1.0 C3' A:G577 4.9 26.2 1.0

J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan. Recognition of Cognate Transfer Rna By the 30S Ribosomal Subunit. Science V. 292 897 2001.
ISSN: ISSN 0036-8075
PubMed: 11340196
DOI: 10.1126/SCIENCE.1060612