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Magnesium in PDB 4gkk: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin, PDB code: 4gkk was solved by W.A.Cantara, F.V.Murphy Iv, J.L.Spears, H.Demirci, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.47 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.370, 402.370, 175.620, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.6

Other elements in 4gkk:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin (pdb code 4gkk). 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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin, PDB code: 4gkk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 186 in 4gkk

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Magnesium binding site 1 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:59.9
occ:1.00
O2 A:C684 3.0 68.5 1.0
O6 A:G686 3.3 77.2 1.0
OP2 A:A685 3.7 86.9 1.0
O2' A:C684 3.9 67.4 1.0
C6 A:G686 4.2 77.2 1.0
C2 A:C684 4.2 68.4 1.0
C1' A:C684 4.2 68.1 1.0
OP1 A:A685 4.4 86.1 1.0
P A:A685 4.5 86.3 1.0
C2' A:C684 4.6 67.5 1.0
N1 A:C684 4.7 68.1 1.0
C5 A:G686 4.9 77.2 1.0
N1 A:G686 5.0 77.3 1.0

Magnesium binding site 2 out of 186 in 4gkk

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Magnesium binding site 2 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:90.9
occ:1.00
O6 A:G152 3.1 0.9 1.0
O6 A:G153 3.9 0.4 1.0
O6 A:G151 3.9 0.9 1.0
O4 A:U158 4.0 0.5 1.0
N4 A:C157 4.1 0.1 1.0
C6 A:G152 4.3 0.6 1.0
C6 A:G153 4.8 0.1 1.0
C4 A:U158 4.9 0.1 1.0
C6 A:G151 4.9 0.8 1.0
N3 A:U158 4.9 1.0 1.0

Magnesium binding site 3 out of 186 in 4gkk

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Magnesium binding site 3 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:61.2
occ:1.00
O6 A:G252 2.3 78.0 1.0
O6 A:G253 3.2 77.7 1.0
C6 A:G252 3.4 78.5 1.0
MG A:MG1625 3.5 64.6 1.0
OP1 A:G261 3.6 67.9 1.0
OP2 A:G261 3.7 66.9 1.0
O4 A:U251 3.9 64.1 1.0
C6 A:G253 4.1 78.0 1.0
P A:G261 4.1 67.0 1.0
C5 A:G252 4.1 79.1 1.0
N7 A:G252 4.1 79.4 1.0
N7 A:G253 4.2 79.3 1.0
N4 A:C264 4.4 82.0 1.0
C4 A:U251 4.5 64.7 1.0
N1 A:G252 4.5 78.3 1.0
C5 A:G253 4.5 78.7 1.0
N4 A:C263 4.5 76.8 1.0
C5 A:U251 4.6 64.8 1.0
O5' A:G261 4.7 66.6 1.0

Magnesium binding site 4 out of 186 in 4gkk

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Magnesium binding site 4 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:

Magnesium binding site 5 out of 186 in 4gkk

Go back to Magnesium Binding Sites List in 4gkk
Magnesium binding site 5 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:77.9
occ:1.00
O6 A:G279 3.6 56.9 1.0
OP1 A:A277 3.7 45.5 1.0
N7 A:G279 3.9 58.2 1.0
OP2 A:C278 4.0 58.5 1.0
C6 A:G279 4.4 56.8 1.0
C5 A:G279 4.5 57.4 1.0
N4 A:C278 4.6 55.7 1.0
O6 A:G280 4.6 55.0 1.0
C5 A:C278 4.8 57.5 1.0
C4 A:C278 4.9 56.5 1.0
C8 A:G279 4.9 58.5 1.0
P A:A277 5.0 46.0 1.0

Magnesium binding site 6 out of 186 in 4gkk

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Magnesium binding site 6 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:51.0
occ:1.00
OP1 A:G713 3.8 46.5 1.0
OP2 A:G714 4.1 45.6 1.0
OP1 A:C1504 4.1 42.2 1.0
N7 A:G714 4.5 48.0 1.0
C8 A:G714 4.9 48.3 1.0
P A:G713 5.0 47.3 1.0
OP2 A:G801 5.0 52.4 1.0

Magnesium binding site 7 out of 186 in 4gkk

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Magnesium binding site 7 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:76.2
occ:1.00
O2 A:C1317 2.7 67.7 1.0
O2' A:C1317 3.3 66.2 1.0
OP2 A:G1318 3.6 64.1 1.0
C1' A:C1317 3.7 66.9 1.0
C2 A:C1317 3.8 67.9 1.0
O6 A:G1318 4.0 66.8 1.0
C2' A:C1317 4.2 66.3 1.0
OP2 A:G919 4.3 66.6 1.0
N1 A:C1317 4.3 67.3 1.0
C6 A:G1318 4.6 66.4 1.0
N7 A:G1318 4.8 64.6 1.0
O4' A:C1317 4.8 67.0 1.0
C5 A:G1318 4.9 65.5 1.0
N3 A:C1317 4.9 68.8 1.0
P A:G1318 5.0 63.6 1.0

Magnesium binding site 8 out of 186 in 4gkk

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Magnesium binding site 8 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:97.0
occ:1.00
O4 A:U1132 4.3 0.6 1.0
N4 A:C1131 4.5 0.0 1.0
C5 A:C1131 4.6 0.1 1.0
C4 A:C1131 5.0 0.4 1.0

Magnesium binding site 9 out of 186 in 4gkk

Go back to Magnesium Binding Sites List in 4gkk
Magnesium binding site 9 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:66.6
occ:1.00
OP1 A:G560 3.5 39.6 1.0
N7 A:G560 3.8 40.3 1.0
OP1 A:U796 4.0 41.8 1.0
OP2 A:U796 4.1 43.7 1.0
C8 A:G560 4.3 40.2 1.0
P A:U796 4.6 42.7 1.0
N6 A:A799 4.6 40.0 1.0
P A:G560 4.8 39.6 1.0
C5 A:G560 5.0 40.6 1.0

Magnesium binding site 10 out of 186 in 4gkk

Go back to Magnesium Binding Sites List in 4gkk
Magnesium binding site 10 out of 186 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-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 Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aua-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:89.8
occ:1.00
O2 A:C502 2.7 66.3 1.0
O2' A:C502 3.3 67.7 1.0
O4' A:A503 3.5 82.6 1.0
C2 A:C502 3.9 65.0 1.0
C4' A:A503 4.2 83.7 1.0
C2' A:C502 4.2 66.2 1.0
C1' A:A503 4.3 81.9 1.0
C5' A:A503 4.6 84.0 1.0
C1' A:C502 4.6 65.3 1.0
OP1 A:G500 4.7 94.1 1.0
N3 A:C502 4.7 64.2 1.0
N1 A:C502 4.8 64.4 1.0
O3' A:U499 4.9 99.1 1.0

Reference:

W.A.Cantara, F.V.Murphy, H.Demirci, P.F.Agris. Expanded Use of Sense Codons Is Regulated By Modified Cytidines in Trna. Proc.Natl.Acad.Sci.Usa V. 110 10964 2013.
ISSN: ISSN 0027-8424
PubMed: 23781103
DOI: 10.1073/PNAS.1222641110
Page generated: Mon Dec 14 16:26:22 2020

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