Magnesium in PDB 4dr7: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound, PDB code: 4dr7 was solved by H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 3.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.490, 402.490, 174.790, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 20.1

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound 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 - 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 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 344;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound (pdb code 4dr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 344 binding sites of Magnesium where determined in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound, PDB code: 4dr7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:66.5 occ:0.62 O A:HOH2001 2.1 57.7 0.6 O A:HOH2002 2.1 0.6 0.6 O2' A:G61 2.9 0.9 1.0 O2 A:C386 3.2 0.0 1.0 N3 A:A60 3.6 0.6 1.0 N3 A:G378 3.7 0.5 1.0 O2' A:C386 3.8 0.4 1.0 C4 A:A60 3.8 0.5 1.0 O4' A:A60 3.8 0.7 1.0 C1' A:G61 3.9 0.9 1.0 N2 A:G377 3.9 0.7 1.0 C2 A:A60 3.9 0.3 1.0 C2' A:G61 4.0 0.8 1.0 N2 A:G378 4.1 0.9 1.0 C2 A:G378 4.2 1.0 1.0 N9 A:A60 4.2 0.2 1.0 O4' A:G61 4.3 0.4 1.0 C2' A:C386 4.3 0.8 1.0 C2 A:C386 4.3 0.1 1.0 C1' A:C386 4.3 0.8 1.0 C5 A:A60 4.4 0.4 1.0 C1' A:A60 4.4 0.1 1.0 N1 A:A60 4.5 0.5 1.0 C4 A:G378 4.5 0.3 1.0 C4' A:G61 4.7 0.8 1.0 C6 A:A60 4.7 0.7 1.0 C1' A:G378 4.7 0.3 1.0 N1 A:C386 4.8 0.7 1.0 C8 A:A60 4.9 0.8 1.0 N9 A:G378 4.9 0.1 1.0 C3' A:G61 4.9 0.3 1.0 C4' A:A60 5.0 0.3 1.0

Magnesium binding site 2 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:0.5 occ:1.00 O A:HOH2004 2.1 78.8 1.0 O A:HOH2007 2.1 95.5 1.0 O A:HOH2006 2.1 57.0 1.0 O A:HOH2005 2.1 93.2 1.0 O A:HOH2003 2.1 65.0 1.0 O A:HOH2720 3.2 50.1 1.0 N7 A:G377 3.5 0.8 1.0 O6 A:G377 3.8 0.8 1.0 N7 A:G376 3.9 0.4 1.0 C5 A:G377 4.3 0.2 1.0 C8 A:G376 4.4 0.2 1.0 C6 A:G377 4.4 0.7 1.0 C5 A:G376 4.5 1.0 1.0 C8 A:G377 4.5 0.2 1.0 O6 A:G376 4.8 0.1 1.0 C6 A:G376 4.9 0.5 1.0

Magnesium binding site 3 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:91.7 occ:1.00 O A:HOH2010 2.1 0.1 1.0 O A:HOH2009 2.1 0.4 1.0 O A:HOH2008 2.1 91.6 1.0 O6 A:G650 3.6 99.7 1.0 OP2 A:A753 3.9 0.7 1.0 O6 A:G649 3.9 0.7 1.0 N7 A:G649 4.0 0.1 1.0 N7 A:G650 4.1 0.4 1.0 C6 A:G650 4.5 0.3 1.0 C6 A:G649 4.6 0.2 1.0 C5 A:G649 4.6 0.1 1.0 C5 A:G650 4.7 0.5 1.0 P A:A753 4.9 0.2 1.0

Magnesium binding site 4 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:1.0 occ:1.00 O A:HOH2014 2.1 66.7 1.0 O A:HOH2013 2.1 0.2 1.0 O A:HOH2012 2.1 0.9 1.0 O A:HOH2011 2.1 0.4 1.0 OP2 A:G750 2.5 0.5 1.0 OP2 A:C749 3.1 0.8 1.0 P A:G750 3.7 0.6 1.0 O6 A:G752 4.1 0.6 1.0 OP1 A:G750 4.2 0.8 1.0 N7 A:G750 4.2 0.0 1.0 O5' A:G750 4.4 0.9 1.0 P A:C749 4.5 0.8 1.0 C8 A:G750 4.7 0.0 1.0 O3' A:C748 4.8 0.1 1.0 O3' A:C749 5.0 0.6 1.0

Magnesium binding site 5 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:87.4 occ:1.00 OP2 A:G654 2.5 0.7 1.0 P A:G654 3.9 0.1 1.0 O5' A:A653 4.3 0.1 1.0 C5' A:A653 4.3 0.0 1.0 C3' A:A653 4.4 0.6 1.0 O3' A:A653 4.5 1.0 1.0 C4' A:A653 4.5 0.7 1.0 N6 A:A655 4.5 0.8 1.0 N7 A:A655 4.7 0.3 1.0 O5' A:G654 4.7 0.8 1.0 OP1 A:G654 5.0 96.5 1.0 N4 A:C656 5.0 85.5 1.0

Magnesium binding site 6 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.9 occ:1.00 O A:HOH2016 2.1 87.4 1.0 O A:HOH2018 2.1 35.0 1.0 O A:HOH2015 2.1 54.2 1.0 O A:HOH2017 2.1 77.8 1.0 OP2 A:G117 2.4 0.4 1.0 OP2 A:G289 2.4 0.2 1.0 O4 A:U118 3.6 95.9 1.0 OP1 A:A116 3.7 74.1 1.0 OP2 A:A116 3.7 0.2 1.0 P A:G289 3.7 0.3 1.0 P A:G117 3.7 0.4 1.0 N7 A:G117 3.9 0.2 1.0 P A:A116 4.1 1.0 1.0 C3' A:A288 4.2 86.7 1.0 O5' A:G117 4.3 98.5 1.0 OP1 A:G289 4.3 91.6 1.0 C4 A:U118 4.3 95.9 1.0 C5 A:U118 4.3 0.3 1.0 O3' A:A116 4.4 80.8 1.0 C3' A:A116 4.5 86.3 1.0 O3' A:A288 4.5 83.3 1.0 C8 A:A288 4.5 0.3 1.0 C8 A:G117 4.6 0.3 1.0 O5' A:A288 4.7 92.5 1.0 O6 A:G117 4.7 94.0 1.0 C2' A:A288 4.8 87.8 1.0 OP1 A:G117 4.8 0.6 1.0 O5' A:G289 4.8 0.8 1.0 C5 A:G117 4.9 0.7 1.0 OP2 A:A288 4.9 0.5 1.0 C5' A:G289 4.9 0.3 1.0 C5' A:A116 4.9 0.1 1.0 O5' A:A116 4.9 75.6 1.0 N7 A:A288 5.0 99.5 1.0 O2' A:G115 5.0 86.0 1.0

Magnesium binding site 7 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:73.5 occ:1.00 OP2 A:C48 2.4 0.9 1.0 OP1 A:G115 3.0 0.0 1.0 P A:C48 3.4 0.5 1.0 O3' A:C47 3.5 0.9 1.0 O5' A:C48 3.6 96.8 1.0 OP2 A:U49 3.9 0.0 1.0 O3' A:U114 3.9 0.5 1.0 OP1 A:A51 4.0 0.2 1.0 P A:G115 4.0 0.6 1.0 O2' A:C47 4.3 0.2 1.0 C3' A:C47 4.6 0.1 1.0 OP1 A:C48 4.8 0.5 1.0 C5' A:C48 4.8 94.0 1.0

Magnesium binding site 8 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:0.8 occ:1.00 O A:HOH2021 2.1 68.9 1.0 O A:HOH2022 2.1 0.2 1.0 O A:HOH2020 2.1 0.8 1.0 O A:HOH2019 2.1 70.7 1.0 OP2 A:U652 4.0 0.3 1.0 N7 A:G752 4.2 0.6 1.0 OP1 A:C651 4.5 0.6 1.0 OP2 A:C651 4.5 0.3 1.0 OP2 A:U751 4.6 0.6 1.0 C8 A:G752 4.8 0.7 1.0 OP2 A:G752 4.8 0.4 1.0 P A:C651 5.0 0.3 1.0

Magnesium binding site 9 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:81.5 occ:1.00 O A:HOH2024 2.1 70.8 1.0 O A:HOH2023 2.1 86.6 1.0 O A:HOH2025 2.1 83.0 1.0 O6 A:G800 3.7 0.8 1.0 O6 A:G799 3.7 0.1 1.0 O A:HOH2187 4.0 97.6 1.0 OP2 A:A781 4.2 0.0 1.0 C6 A:G800 4.3 0.1 1.0 N7 A:G799 4.4 0.3 1.0 N1 A:G800 4.6 0.9 1.0 C6 A:G799 4.7 0.8 1.0 N7 A:G798 4.9 0.6 1.0 C5 A:G799 5.0 0.8 1.0

Magnesium binding site 10 out of 344 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound


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 Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Codon, Crystallographically Disordered Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position, and Streptomycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:0.9 occ:1.00 O A:HOH2026 2.1 70.3 1.0 O A:HOH2027 2.1 51.1 1.0 OP1 A:G1508 2.5 0.8 1.0 OP1 A:A1500 2.5 0.9 1.0 O3' A:A1507 2.8 96.4 1.0 OP1 A:G1505 3.0 0.6 1.0 P A:G1508 3.2 0.5 1.0 C5' A:G1508 3.5 0.1 1.0 O5' A:G1505 3.7 0.6 1.0 P A:A1500 3.7 0.3 1.0 OP2 A:C1501 3.8 0.6 1.0 O5' A:G1508 3.8 0.9 1.0 OP1 A:G1504 3.9 0.4 1.0 P A:G1505 3.9 0.5 1.0 C3' A:G1504 4.0 0.6 1.0 C3' A:A1507 4.0 0.5 1.0 O2' A:A1507 4.1 0.3 1.0 O5' A:A1500 4.2 0.3 1.0 O5' A:G1504 4.4 0.7 1.0 P A:G1504 4.4 0.2 1.0 OP2 A:A1500 4.4 1.0 1.0 OP2 A:G1504 4.4 1.0 1.0 O3' A:G1504 4.5 0.8 1.0 OP2 A:G1508 4.5 0.2 1.0 O2' A:U1506 4.5 0.4 1.0 C4' A:A1507 4.5 0.5 1.0 MG A:MG1731 4.6 68.5 1.0 C2' A:A1507 4.6 0.3 1.0 C2' A:G1504 4.7 0.2 1.0 C5' A:A1500 4.8 0.5 1.0 C4' A:G1508 4.8 0.1 1.0 O2' A:G1504 4.9 0.9 1.0 P A:C1501 4.9 0.2 1.0 C5' A:G1505 4.9 0.0 1.0 O3' A:A1499 4.9 0.6 1.0

H.Demirci, F.Murphy, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl. A Structural Basis For Streptomycin-Induced Misreading of the Genetic Code. Nat Commun V. 4 1355 2013.
ISSN: ESSN 2041-1723
PubMed: 23322043
DOI: 10.1038/NCOMMS2346