Magnesium in PDB 1n33: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin, PDB code: 1n33 was solved by J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.54 / 3.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.599, 401.599, 176.025, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28.4

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 - 106;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin (pdb code 1n33). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 106 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin, PDB code: 1n33:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:34.6 occ:1.23 OP1 A:G944 2.0 0.5 1.0 OP2 A:G945 2.4 95.4 1.0 P A:G944 3.0 0.7 1.0 OP2 A:G944 3.4 0.5 1.0 O5' A:G944 3.4 42.7 1.0 P A:G945 3.8 85.6 1.0 C5' A:G944 4.1 42.7 1.0 O6 A:G947 4.2 93.4 1.0 OP1 A:G945 4.3 95.4 1.0 N7 A:A946 4.4 76.5 1.0 O3' A:U943 4.4 45.3 1.0 O6 A:G1233 4.5 90.8 1.0 O5' A:G945 4.6 63.7 1.0 OP2 A:A946 4.7 57.2 1.0 O3' A:G944 4.8 42.7 1.0 N4 A:C948 4.9 0.5 1.0

Magnesium binding site 2 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1547 b:34.6 occ:1.07 OP1 A:G1224 1.9 94.1 1.0 P A:G1224 2.9 52.7 1.0 OP2 A:G1224 3.1 94.1 1.0 O2' A:C1223 3.7 82.3 1.0 O3' A:C1223 3.9 82.3 1.0 C2' A:C1223 4.1 82.3 1.0 O5' A:G1224 4.2 89.9 1.0 OP1 A:G951 4.2 0.9 1.0 N6 A:A977 4.3 84.8 1.0 N7 A:A977 4.3 84.8 1.0 OP2 A:U952 4.4 99.7 1.0 C3' A:C1223 4.5 82.3 1.0

Magnesium binding site 3 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:34.6 occ:0.65 OP2 A:U17 3.3 66.6 1.0 OP1 A:U17 3.5 66.6 1.0 O4 A:U14 3.8 0.5 1.0 P A:U17 3.8 53.0 1.0 C4 A:U14 4.5 0.5 1.0 N3 A:U14 4.5 0.5 1.0 OP2 A:C18 4.6 53.4 1.0 O5' A:U17 4.7 61.7 1.0

Magnesium binding site 4 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1549 b:34.6 occ:1.06 O6 A:G377 3.3 63.8 1.0 O6 A:G376 3.8 46.5 1.0 N7 A:G376 4.1 46.5 1.0 N7 A:G377 4.1 63.8 1.0 C6 A:G377 4.2 63.8 1.0 C6 A:G376 4.4 46.5 1.0 C5 A:G376 4.5 46.5 1.0 C5 A:G377 4.6 63.8 1.0 O4 A:U387 5.0 0.6 1.0

Magnesium binding site 5 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1550 b:34.6 occ:0.77 OP2 A:G750 2.0 63.6 1.0 OP2 A:C749 2.1 92.7 1.0 P A:C749 3.0 83.7 1.0 OP1 A:C749 3.3 92.7 1.0 P A:G750 3.4 71.4 1.0 O5' A:C749 3.6 55.3 1.0 N7 A:G750 4.0 92.8 1.0 C3' A:C749 4.0 55.3 1.0 O2' A:C748 4.1 0.4 1.0 O5' A:G750 4.1 71.8 1.0 O3' A:C749 4.2 55.3 1.0 C8 A:G750 4.3 92.8 1.0 OP1 A:G750 4.5 63.6 1.0 O3' A:C748 4.5 0.4 1.0 C5' A:C749 4.7 55.3 1.0 C6 A:C749 4.9 0.1 1.0 C4' A:C749 4.9 55.3 1.0 C2' A:C748 5.0 0.4 1.0 C2' A:C749 5.0 55.3 1.0

Magnesium binding site 6 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1551 b:34.6 occ:1.56 OP2 A:A766 2.2 20.7 1.0 O2 A:C812 3.6 33.5 1.0 P A:A766 3.6 43.8 1.0 N4 A:C811 3.7 73.0 1.0 N3 A:C811 3.8 73.0 1.0 O3' A:G765 4.2 37.2 1.0 C4 A:C811 4.2 73.0 1.0 C2 A:C812 4.3 33.5 1.0 O5' A:A766 4.3 85.3 1.0 C3' A:G765 4.5 37.2 1.0 N3 A:C812 4.5 33.5 1.0 N6 A:A768 4.6 52.1 1.0 O4 A:U813 4.7 44.0 1.0 N7 A:A767 4.7 20.7 1.0 OP1 A:A766 4.7 20.7 1.0 C2 A:C811 4.9 73.0 1.0

Magnesium binding site 7 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1552 b:34.6 occ:1.20 OP2 A:A768 2.1 87.6 1.0 P A:A768 3.6 67.5 1.0 O5' A:A768 4.1 51.5 1.0 O5' A:A767 4.2 55.7 1.0 OP2 A:A767 4.2 74.4 1.0 OP1 A:A767 4.4 74.4 1.0 OP1 A:U804 4.5 74.1 1.0 P A:A767 4.5 84.1 1.0 OP1 A:A768 4.5 87.6 1.0 O3' A:A767 4.5 55.7 1.0 C3' A:A767 4.6 55.7 1.0 N7 A:A768 4.6 52.1 1.0 C8 A:A768 4.8 52.1 1.0 C5' A:U804 4.9 76.3 1.0 OP2 A:C805 4.9 55.3 1.0

Magnesium binding site 8 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1553 b:34.6 occ:1.14 O4 A:U772 4.2 91.4 1.0 N7 A:G771 4.3 76.2 1.0 OP2 A:U804 4.4 74.1 1.0 OP1 A:G803 4.6 100.0 1.0 O6 A:G771 4.6 76.2 1.0 N4 A:C770 4.6 39.4 1.0 C5 A:C770 4.8 39.4 1.0 C4 A:C770 4.9 39.4 1.0

Magnesium binding site 9 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1554 b:34.6 occ:1.01 N7 A:G800 3.6 77.9 1.0 O6 A:G800 4.0 77.9 1.0 OP2 A:C779 4.0 98.3 1.0 OP2 A:A780 4.1 0.6 1.0 C5 A:G800 4.4 77.9 1.0 OP2 A:G799 4.5 0.0 1.0 OP2 A:G800 4.5 0.8 1.0 C8 A:G800 4.6 77.9 1.0 C6 A:G800 4.6 77.9 1.0 N7 A:A780 4.7 36.9 1.0 P A:C779 4.8 95.5 1.0 O5' A:C779 4.9 41.7 1.0 C8 A:G799 4.9 92.8 1.0 C5' A:G799 4.9 74.4 1.0 OP1 A:C779 4.9 98.3 1.0 N7 A:G799 5.0 92.8 1.0

Magnesium binding site 10 out of 106 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the Second Codon Position at the A Site with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1555 b:34.6 occ:1.40 OP1 A:C578 2.3 45.7 1.0 OP2 A:G576 3.2 68.5 1.0 P A:C578 3.7 51.0 1.0 O3' A:G577 4.0 96.0 1.0 O2' A:G575 4.1 80.0 1.0 OP1 A:U820 4.1 50.1 1.0 OP2 A:C817 4.2 24.0 1.0 OP2 A:C578 4.6 45.7 1.0 C5' A:G821 4.6 35.3 1.0 P A:G576 4.7 80.9 1.0 O5' A:C578 4.7 75.4 1.0 C5' A:C578 4.8 75.4 1.0 C4' A:G821 4.8 35.3 1.0

J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan. Selection of Trna By the Ribosome Requires A Transition From An Open to A Closed Form Cell(Cambridge,Mass.) V. 111 721 2002.
ISSN: ISSN 0092-8674
PubMed: 12464183
DOI: 10.1016/S0092-8674(02)01086-3