Magnesium in PDB 6dti: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin, PDB code: 6dti was solved by W.A.Cantara, H.Demirci, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.34 / 3.54
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	404.540, 404.540, 176.620, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

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 - 94;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin (pdb code 6dti). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 94 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin, PDB code: 6dti:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:0.7 occ:1.00 OP2 A:A838 2.7 0.7 1.0 P A:A838 3.9 0.9 1.0 N7 A:G839 4.2 93.5 1.0 OP1 A:A838 4.3 0.5 1.0 O6 A:G839 4.3 94.0 1.0 O5' A:A838 4.5 0.6 1.0 OP2 A:A837 4.5 0.3 1.0 OP1 A:A837 4.6 0.4 1.0 N2 A:G847 4.9 87.3 1.0 N4 A:C840 4.9 94.8 1.0 C5 A:G839 5.0 93.5 1.0 P A:A837 5.0 1.0 1.0

Magnesium binding site 2 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:96.5 occ:1.00 OP2 A:G572 3.0 0.5 1.0 OP1 A:G572 3.2 0.9 1.0 P A:G572 3.6 0.6 1.0 OP1 A:G628 3.7 0.9 1.0 OP2 A:C629 3.7 0.4 1.0 O2' A:G571 3.8 0.7 1.0 C2' A:G571 4.2 0.1 1.0 C3' A:G571 4.2 0.2 1.0 OP1 A:C629 4.3 0.8 1.0 O3' A:G571 4.4 0.2 1.0 P A:C629 4.4 1.0 1.0 P A:G628 4.7 0.1 1.0 O5' A:G628 4.9 0.2 1.0 O3' A:G628 4.9 0.4 1.0 O5' A:G572 4.9 0.5 1.0 C5' A:G628 4.9 0.9 1.0

Magnesium binding site 3 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:86.8 occ:1.00 OP1 A:C635 4.1 0.9 1.0 OP2 A:U636 4.3 0.7 1.0 N7 A:G736 4.3 0.4 1.0 OP2 A:G736 4.5 1.0 1.0 OP2 A:U735 4.5 0.9 1.0 OP2 A:C635 4.5 0.3 1.0 C8 A:G736 4.6 0.4 1.0 P A:C635 4.7 0.8 1.0 OP1 A:U735 4.8 1.0 1.0

Magnesium binding site 4 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:0.5 occ:1.00 O6 A:G588 2.7 0.1 1.0 O4 A:U589 3.1 0.2 1.0 N4 A:C618 3.5 97.7 1.0 C6 A:G588 3.9 0.9 1.0 O4 A:U587 3.9 0.0 1.0 O6 A:G617 3.9 0.9 1.0 C4 A:U589 4.1 0.9 1.0 N3 A:U589 4.5 0.1 1.0 C4 A:U587 4.8 0.5 1.0 C4 A:C618 4.8 98.0 1.0 N1 A:G588 4.8 0.3 1.0 C5 A:G588 4.9 0.4 1.0 C6 A:G617 5.0 1.0 1.0

Magnesium binding site 5 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:81.6 occ:1.00 OP2 A:A567 3.7 98.4 1.0 O4 A:U741 3.7 87.5 1.0 N2 A:G742 3.7 89.1 1.0 O6 A:G568 3.8 92.9 1.0 N4 A:C740 3.8 87.1 1.0 O6 A:G569 4.0 90.7 1.0 C2 A:G742 4.3 88.6 1.0 N1 A:G742 4.3 89.2 1.0 NH2 O:ARG68 4.6 0.6 1.0 OP2 A:U566 4.6 99.9 1.0 N7 A:G568 4.6 93.7 1.0 C6 A:G568 4.7 92.3 1.0 C4 A:U741 4.8 86.5 1.0

Magnesium binding site 6 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:95.2 occ:1.00 OP1 A:G532 2.4 0.0 1.0 N4 A:C399 3.4 0.1 1.0 OP1 A:A531 3.5 0.3 1.0 O6 A:G398 3.7 0.8 1.0 P A:G532 3.8 0.1 1.0 O5' A:G532 4.0 0.9 1.0 N7 A:G398 4.3 0.3 1.0 N4 A:C397 4.3 0.4 1.0 C5 A:C397 4.4 0.1 1.0 C4 A:C399 4.5 0.2 1.0 C6 A:G398 4.6 0.6 1.0 C5' A:A531 4.7 0.5 1.0 C4 A:C397 4.7 0.4 1.0 C3' A:A531 4.7 0.9 1.0 OP2 A:G532 4.7 0.6 1.0 C5 A:C399 4.8 0.2 1.0 O3' A:A531 4.8 0.6 1.0 C5 A:G398 4.8 0.4 1.0 C4' A:A531 4.9 0.9 1.0 P A:A531 4.9 0.2 1.0

Magnesium binding site 7 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:89.9 occ:1.00 OP2 A:G100 2.6 0.3 1.0 O6 A:G322 2.9 0.3 1.0 N7 A:A321 2.9 94.5 1.0 O2' A:G320 3.0 98.7 1.0 OP1 A:G100 3.2 1.0 1.0 P A:G100 3.4 1.0 1.0 C8 A:A321 3.6 94.3 1.0 C6 A:G322 3.8 0.1 1.0 C5 A:A321 4.1 94.3 1.0 O3' A:G320 4.2 99.0 1.0 N7 A:G322 4.3 0.6 1.0 C5 A:G322 4.3 0.7 1.0 C2' A:G320 4.4 98.5 1.0 N6 A:A321 4.5 94.8 1.0 O5' A:G100 4.5 0.2 1.0 O3' A:C99 4.6 0.1 1.0 C6 A:A321 4.7 94.4 1.0 C3' A:G320 4.8 98.9 1.0 N1 A:G322 4.8 0.2 1.0 N9 A:A321 4.9 94.1 1.0

Magnesium binding site 8 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:93.7 occ:1.00 N7 A:G387 4.0 0.4 1.0 C5 A:C386 4.1 0.7 1.0 OP2 A:G387 4.2 0.5 1.0 N7 A:G388 4.5 0.9 1.0 C6 A:C386 4.5 0.0 1.0 O6 A:G388 4.6 0.2 1.0 OP2 A:C386 4.7 0.3 1.0 C8 A:G387 4.8 0.8 1.0 O6 A:G387 4.8 0.2 1.0 C4 A:C386 4.9 0.3 1.0 C5 A:G387 5.0 0.1 1.0

Magnesium binding site 9 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:99.3 occ:1.00 OP2 A:A913 2.7 0.3 1.0 OP2 A:G1320 3.0 95.7 1.0 OP1 A:C914 3.4 0.8 1.0 O2' A:C912 3.6 0.5 1.0 O3' A:A913 3.8 0.2 1.0 P A:C914 3.9 0.6 1.0 P A:G1320 3.9 96.7 1.0 OP1 A:G1320 3.9 96.2 1.0 P A:A913 4.0 0.9 1.0 OP2 A:C914 4.0 0.6 1.0 O3' A:C912 4.2 0.5 1.0 O5' A:A913 4.6 0.7 1.0 C5' A:A913 4.6 0.0 1.0 C3' A:A913 4.6 0.7 1.0 O5' A:G1320 4.7 97.8 1.0 C2' A:C912 4.8 0.3 1.0 OP2 A:C1321 5.0 0.1 1.0

Magnesium binding site 10 out of 94 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and 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 Complexed with An Unmodifed Anticodon Stem Loop (Asl) of Escherichia Coli Transfer Rna Arginine 2 (TRNAARG2) Bound to An Mrna with An Cgu-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:94.6 occ:1.00 OP1 A:G922 2.3 0.3 1.0 OP2 A:G923 2.4 0.0 1.0 P A:G922 3.4 0.3 1.0 P A:G923 3.7 0.8 1.0 OP2 A:G922 3.8 0.1 1.0 O5' A:G922 4.0 0.3 1.0 N7 A:A924 4.0 0.2 1.0 O5' A:G923 4.1 0.2 1.0 OP2 A:A924 4.2 99.4 1.0 OP1 A:G923 4.4 0.7 1.0 O6 A:G1210 4.5 0.0 1.0 C5' A:G922 4.5 0.2 1.0 O6 A:G925 4.6 0.2 1.0 C8 A:A924 4.6 0.1 1.0 O3' A:U921 4.7 0.9 1.0 C5 A:A924 4.8 0.0 1.0 N6 A:A924 4.9 0.2 1.0 O3' A:G922 5.0 0.4 1.0 N4 A:C926 5.0 0.7 1.0

W.A.Cantara, S.Vangaveti, K.L.Sarachan, J.L.Spears, H.Demirci, F.V.Murphy Iv, S.V.Ranganathan, P.F.Agris. A Structural Basis For Restricted Codon Recognition Mediated By 2-Thiocytidine in Trna Containing A Wobble Position Inosine To Be Published.