Magnesium in PDB 5iwa: Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic, PDB code: 5iwa was solved by A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Chieko, K.Masahito, C.Takemoto, S.Yokoyama, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.03 / 3.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	413.140, 413.140, 173.630, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.8

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

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 - 204;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic (pdb code 5iwa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 204 binding sites of Magnesium where determined in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic, PDB code: 5iwa:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:0.9 occ:1.00 OD2 B:ASP166 2.3 0.7 1.0 OD2 B:ASP191 2.8 1.0 1.0 CE1 B:HIS19 2.9 0.3 1.0 OD2 B:ASP205 3.3 0.1 1.0 CG B:ASP166 3.3 0.7 1.0 NE2 B:HIS19 3.5 0.9 1.0 OD1 B:ASP205 3.6 0.0 1.0 OD1 B:ASP166 3.7 0.1 1.0 CG B:ASP191 3.7 0.6 1.0 CG B:ASP205 3.8 0.3 1.0 OD1 B:ASP191 4.0 0.7 1.0 ND1 B:HIS19 4.0 0.8 1.0 NZ B:LYS74 4.4 0.1 1.0 OD1 B:ASP206 4.6 0.0 1.0 CB B:ASP166 4.7 0.6 1.0 CD2 B:HIS19 4.8 0.6 1.0 OD2 B:ASP206 4.8 0.2 1.0 OG1 B:THR168 4.9 0.5 1.0 CB B:ASP191 5.0 0.8 1.0

Magnesium binding site 2 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:67.3 occ:1.00 OD2 E:ASP147 3.5 0.1 1.0 O E:GLU68 4.2 0.9 1.0 O E:LEU142 4.4 0.5 1.0 CG E:PRO70 4.5 0.0 1.0 CD E:PRO70 4.5 0.7 1.0 CG E:ASP147 4.5 0.7 1.0 OD1 E:ASP147 4.8 0.7 1.0 CB E:PRO70 4.8 0.6 1.0

Magnesium binding site 3 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:69.2 occ:1.00 NH1 H:ARG105 4.0 0.8 1.0 CZ H:ARG105 4.5 0.8 1.0 O E:ALA94 4.8 0.3 1.0 NH2 H:ARG105 4.9 0.6 1.0

Magnesium binding site 4 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg201 b:83.4 occ:1.00 NZ K:LYS122 3.4 0.0 1.0 OP2 A:A780 3.7 0.7 1.0 O6 A:G800 3.8 0.3 1.0 N7 A:G800 3.8 0.9 1.0 OP2 A:C779 4.1 0.0 1.0 OP1 A:C779 4.3 1.0 1.0 N7 A:A780 4.4 0.9 1.0 P A:C779 4.4 0.2 1.0 OP2 A:G799 4.4 0.7 1.0 O5' A:C779 4.5 0.9 1.0 CE K:LYS122 4.5 0.2 1.0 C6 A:G800 4.6 0.5 1.0 C5 A:G800 4.6 0.8 1.0 OP2 A:G800 4.6 0.8 1.0 C8 A:G800 4.9 0.7 1.0 C8 A:A780 4.9 1.0 1.0

Magnesium binding site 5 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg101 b:92.6 occ:1.00 NH2 O:ARG68 2.8 0.5 1.0 OP2 A:A583 3.7 0.4 1.0 N2 A:G758 4.0 0.7 1.0 N7 A:G584 4.1 0.2 1.0 O6 A:G584 4.1 0.2 1.0 CZ O:ARG68 4.1 0.3 1.0 O6 A:G585 4.4 0.5 1.0 N4 A:C756 4.4 0.9 1.0 O4 A:U757 4.7 0.3 1.0 NH1 O:ARG68 4.8 0.5 1.0 C6 A:G584 4.8 0.3 1.0 C5 A:G584 4.8 1.0 1.0 C2 A:G758 4.9 0.8 1.0 P A:A583 5.0 0.6 1.0

Magnesium binding site 6 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg101 b:0.1 occ:1.00 OE2 S:GLU17 3.7 0.3 1.0 CB S:HIS14 3.8 0.4 1.0 OP1 A:A1015 3.9 0.3 1.0 OD2 S:ASP13 4.4 0.7 1.0 CA S:HIS14 4.6 0.2 1.0 O6 A:G1013 4.7 0.8 1.0 CG S:HIS14 4.8 0.3 1.0 CD S:GLU17 4.8 0.6 1.0 N7 A:G1013 4.8 0.5 1.0

Magnesium binding site 7 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3401 b:0.1 occ:1.00 OP2 A:C651 3.2 0.0 1.0 OP2 A:G752 3.5 0.6 1.0 MG A:MG3402 3.8 93.9 1.0 O5' A:G752 4.1 0.8 1.0 P A:G752 4.1 0.8 1.0 C2' A:G752 4.4 0.7 1.0 C8 A:G752 4.5 0.7 1.0 OP1 A:G752 4.5 1.0 1.0 P A:C651 4.5 0.4 1.0 O2' A:G752 4.5 0.4 1.0 OP1 A:C651 5.0 0.5 1.0

Magnesium binding site 8 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3402 b:93.9 occ:1.00 MG A:MG3401 3.8 0.1 1.0 N7 A:G752 3.9 0.8 1.0 C8 A:G752 4.3 0.7 1.0 OP2 A:U652 4.3 0.7 1.0 OP2 A:U751 4.4 0.4 1.0 OP1 A:C651 4.4 0.5 1.0 OP2 A:G752 4.6 0.6 1.0 OP2 A:C651 4.6 0.0 1.0 OP1 A:U751 4.7 0.2 1.0 P A:U751 4.9 0.2 1.0 P A:C651 4.9 0.4 1.0

Magnesium binding site 9 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3403 b:83.5 occ:1.00 O6 A:G650 3.7 1.0 1.0 O6 A:G649 4.2 0.6 1.0 N7 A:G650 4.3 1.0 1.0 N7 A:G649 4.3 0.4 1.0 OP2 A:A753 4.4 0.2 1.0 C6 A:G650 4.6 0.2 1.0 C6 A:G649 4.9 0.2 1.0 C5 A:G650 4.9 0.0 1.0 C5 A:G649 4.9 0.7 1.0

Magnesium binding site 10 out of 204 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the GE81112 Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3404 b:0.4 occ:1.00 OP2 A:C749 2.6 0.7 1.0 OP2 A:G750 3.0 0.9 1.0 O3' A:C748 3.6 0.3 1.0 P A:C749 3.7 0.0 1.0 O5' A:C749 4.4 0.4 1.0 O2' A:C748 4.4 0.9 1.0 P A:G750 4.5 0.7 1.0 N7 A:G750 4.5 0.4 1.0 C3' A:C749 4.7 0.9 1.0 C3' A:C748 4.9 0.9 1.0 C6 A:C749 4.9 0.7 1.0 OP1 A:C749 5.0 0.9 1.0

A.Fabbretti, A.Schedlbauer, L.Brandi, T.Kaminishi, A.M.Giuliodori, R.Garofalo, B.Ochoa-Lizarralde, C.Takemoto, S.Yokoyama, S.R.Connell, C.O.Gualerzi, P.Fucini. Inhibition of Translation Initiation Complex Formation By GE81112 Unravels A 16S Rrna Structural Switch Involved in P-Site Decoding. Proc.Natl.Acad.Sci.Usa V. 113 E2286 2016.
ISSN: ESSN 1091-6490
PubMed: 27071098
DOI: 10.1073/PNAS.1521156113