Magnesium in PDB 3t1y: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin, PDB code: 3t1y was solved by F.V.Murphy, F.A.P.Vendeix, W.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.A.P.Malkiewicz, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.972, 400.972, 174.647, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 26.8

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and 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 - 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 - 186;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin (pdb code 3t1y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 186 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin, PDB code: 3t1y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:51.8 occ:0.90 O6 A:G686 2.7 57.3 1.0 O2 A:C684 3.0 52.4 1.0 O2' A:C684 3.2 54.5 1.0 C6 A:G686 3.6 57.3 1.0 OP2 A:A685 4.1 59.0 1.0 N1 A:G686 4.2 57.3 1.0 C2 A:C684 4.2 52.4 1.0 C2' A:C684 4.2 54.5 1.0 C1' A:C684 4.2 54.5 1.0 C5 A:G686 4.5 57.3 1.0 N1 A:C684 4.7 52.4 1.0 N7 A:G686 5.0 57.3 1.0

Magnesium binding site 2 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:86.0 occ:0.91 O6 A:G151 2.2 94.3 1.0 O6 A:G150 3.0 89.6 1.0 C6 A:G151 3.2 94.3 1.0 O4 A:U158 3.5 92.6 1.0 N7 A:G151 3.8 94.3 1.0 C6 A:G150 3.8 89.6 1.0 C5 A:G151 3.8 94.3 1.0 N4 A:C159 4.1 86.0 1.0 O6 A:G152 4.3 0.7 1.0 N1 A:G151 4.4 94.3 1.0 N1 A:G150 4.5 89.6 1.0 C4 A:U158 4.6 92.6 1.0 C5 A:G150 4.8 89.6 1.0 N3 A:U158 4.8 92.6 1.0 N4 A:C157 5.0 96.8 1.0 C4 A:C159 5.0 86.0 1.0

Magnesium binding site 3 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:64.0 occ:0.94 O6 A:G252 2.6 58.5 1.0 O6 A:G253 3.3 65.2 1.0 C6 A:G252 3.5 58.5 1.0 N7 A:G252 3.6 58.5 1.0 OP2 A:G261 3.7 54.5 1.0 C5 A:G252 3.9 58.5 1.0 O4 A:U251 4.0 55.9 1.0 C6 A:G253 4.1 65.2 1.0 OP1 A:G261 4.2 54.5 1.0 N7 A:G253 4.2 65.2 1.0 C4 A:U251 4.4 55.9 1.0 P A:G261 4.4 52.9 1.0 C5 A:G253 4.5 65.2 1.0 C5 A:U251 4.5 55.9 1.0 N4 A:C263 4.7 57.9 1.0 N1 A:G252 4.7 58.5 1.0 C8 A:G252 4.8 58.5 1.0 N4 A:C264 4.9 62.5 1.0

Magnesium binding site 4 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:0.7 occ:0.91 N7 A:G76 2.9 42.0 1.0 O6 A:G76 3.4 42.0 1.0 O6 A:G75 3.5 51.5 1.0 N7 A:G75 3.7 51.5 1.0 C6 A:G75 3.7 51.5 1.0 C5 A:G76 3.8 42.0 1.0 C5 A:G75 3.8 51.5 1.0 C6 A:G76 3.9 42.0 1.0 C8 A:G76 4.0 42.0 1.0 C8 A:G75 4.5 51.5 1.0 N1 A:G75 4.6 51.5 1.0 C4 A:G75 4.7 51.5 1.0

Magnesium binding site 5 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:33.5 occ:0.58 O6 A:G279 2.7 41.8 1.0 C6 A:G279 3.4 41.8 1.0 O6 A:G280 3.5 44.2 1.0 N7 A:G279 3.5 41.8 1.0 C5 A:G279 3.7 41.8 1.0 N7 A:G280 4.1 44.2 1.0 C6 A:G280 4.3 44.2 1.0 MG A:MG1732 4.4 13.6 0.4 C5 A:G280 4.6 44.2 1.0 N1 A:G279 4.6 41.8 1.0 N4 A:C237 4.6 41.7 1.0 C8 A:G279 4.7 41.8 1.0 N4 A:C278 4.8 42.0 1.0 N4 A:C236 4.9 41.5 1.0 OP1 A:A277 5.0 43.9 1.0

Magnesium binding site 6 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:47.8 occ:0.75 OP2 A:G714 3.8 36.3 1.0 N7 A:G714 3.8 36.3 1.0 OP1 A:G713 4.0 34.6 1.0 C8 A:G714 4.3 36.3 1.0 OP1 A:C1504 4.4 36.3 1.0 P A:G713 4.9 35.8 1.0

Magnesium binding site 7 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.9 occ:0.85 O2 A:C1317 2.7 58.9 1.0 O2' A:C1317 3.2 56.5 1.0 OP2 A:G919 3.6 53.4 1.0 C2 A:C1317 3.8 58.9 1.0 C2' A:C1317 4.1 56.5 1.0 C1' A:C1317 4.4 56.5 1.0 OP1 A:G919 4.5 53.4 1.0 P A:G919 4.5 49.8 1.0 N1 A:C1317 4.6 58.9 1.0 N3 A:C1317 4.6 58.9 1.0 OP2 A:G1318 4.9 49.6 1.0 O6 A:G1318 4.9 49.6 1.0

Magnesium binding site 8 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:62.3 occ:0.67 OP2 A:G1102 2.5 98.3 1.0 N7 A:G1102 3.8 98.3 1.0 P A:G1102 3.9 99.7 1.0 C8 A:G1102 4.1 98.3 1.0 O5' A:G1102 4.2 99.7 1.0 OP1 A:G1102 4.7 98.3 1.0 OP2 A:U1130 4.7 90.4 1.0 O3' A:C1101 5.0 90.0 1.0

Magnesium binding site 9 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:39.7 occ:0.70 OP1 A:G560 3.1 29.9 1.0 N7 A:G560 3.3 29.9 1.0 OP2 A:U796 3.7 34.2 1.0 C8 A:G560 3.7 29.9 1.0 OP1 A:U796 4.2 34.2 1.0 N6 A:A799 4.3 33.8 1.0 P A:G560 4.4 31.1 1.0 P A:U796 4.5 34.2 1.0 C5 A:G560 4.6 29.9 1.0 O3' A:G559 4.7 33.1 1.0 O5' A:G560 4.7 31.1 1.0

Magnesium binding site 10 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-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 A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aag-Codon in the A-Site and Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:66.9 occ:0.90 O2 A:C502 2.7 56.1 1.0 O4' A:A503 3.5 52.3 1.0 O2' A:C502 3.8 54.8 1.0 O2' A:U499 3.9 67.2 1.0 C2 A:C502 3.9 56.1 1.0 C1' A:A503 4.1 52.3 1.0 O3' A:U499 4.1 67.2 1.0 C4' A:A503 4.3 52.3 1.0 C2' A:C502 4.5 54.8 1.0 OP1 A:G500 4.5 68.3 1.0 N3 A:C502 4.6 56.1 1.0 N9 A:A503 4.9 54.6 1.0 C1' A:C502 4.9 54.8 1.0 N1 A:C502 4.9 56.1 1.0 C5' A:A503 5.0 52.3 1.0

F.A.Vendeix, F.V.Murphy, W.A.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.Malkiewicz, P.F.Agris. Human Trna(LYS3)(Uuu) Is Pre-Structured By Natural Modifications For Cognate and Wobble Codon Binding Through Keto-Enol Tautomerism. J.Mol.Biol. V. 416 467 2012.
ISSN: ISSN 0022-2836
PubMed: 22227389
DOI: 10.1016/J.JMB.2011.12.048