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Magnesium in PDB 2uu9: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin.

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin., PDB code: 2uu9 was solved by A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.P.Vendeix, P.F.Agris, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.943, 400.943, 174.219, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.8

Other elements in 2uu9:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. also contains other interesting chemical elements:

Potassium (K) 36 atoms
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 - 161;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. (pdb code 2uu9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 161 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin., PDB code: 2uu9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 1 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:20.5
occ:1.00
O2' A:C701 2.8 45.2 1.0
O6 A:G703 3.0 49.1 1.0
O2 A:C701 3.2 47.2 1.0
OP2 A:A702 3.7 44.4 1.0
C6 A:G703 3.9 48.4 1.0
C2' A:C701 3.9 43.3 1.0
C1' A:C701 4.0 43.7 1.0
C2 A:C701 4.2 46.2 1.0
N1 A:G703 4.6 48.1 1.0
N1 A:C701 4.6 44.7 1.0
C5 A:G703 4.8 48.7 1.0
P A:A702 4.9 43.9 1.0

Magnesium binding site 2 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 2 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:83.0
occ:1.00
O6 A:G157 2.5 83.5 1.0
O6 A:G156 3.2 74.7 1.0
C6 A:G157 3.7 84.8 1.0
O4 A:U164 3.7 86.4 1.0
N4 A:C165 3.9 79.0 1.0
C6 A:G156 4.1 74.4 1.0
O6 A:G158 4.2 90.3 1.0
N7 A:G157 4.2 86.7 1.0
N3 A:U164 4.3 88.1 1.0
C5 A:G157 4.3 85.9 1.0
C4 A:U164 4.5 87.6 1.0
N1 A:G157 4.8 84.1 1.0
C4 A:C165 4.9 79.4 1.0
C5 A:G156 4.9 75.0 1.0
N7 A:G156 5.0 75.7 1.0

Magnesium binding site 3 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 3 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:33.3
occ:1.00
K A:K1763 2.6 80.1 1.0
O6 A:G260 3.7 48.2 1.0
O6 A:G259 4.1 53.1 1.0
N7 A:G258 4.2 54.7 1.0
OP2 A:G265 4.5 39.8 1.0
MG A:MG1616 4.5 28.9 1.0
N7 A:G259 4.5 51.6 1.0
C6 A:G260 4.7 46.7 1.0
O6 A:G258 4.8 55.9 1.0
C5 A:G258 4.9 54.7 1.0
C8 A:G258 5.0 54.9 1.0

Magnesium binding site 4 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 4 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:12.5
occ:1.00
OP1 A:A1500 2.7 23.9 1.0
OP1 A:G1508 2.8 30.9 1.0
O3' A:A1499 2.9 27.8 1.0
OP1 A:G1521 2.9 29.6 1.0
P A:A1500 3.4 27.2 1.0
P A:G1521 3.8 29.6 1.0
C5' A:A1500 3.8 30.5 1.0
P A:G1508 3.9 30.1 1.0
OP2 A:G1521 4.0 31.1 1.0
O2' A:A1499 4.0 31.1 1.0
MG A:MG1728 4.0 6.2 1.0
C3' A:A1499 4.1 28.3 1.0
O5' A:A1500 4.1 29.3 1.0
O5' A:G1508 4.3 29.3 1.0
OP2 A:G1508 4.4 28.4 1.0
C4' A:A1499 4.5 28.0 1.0
O3' A:G1520 4.5 28.0 1.0
C2' A:A1499 4.7 28.4 1.0
C5' A:G1508 4.7 29.2 1.0
OP2 A:A1500 4.7 29.4 1.0
OP1 A:G1505 4.8 34.8 1.0
OP2 A:C1509 4.9 30.1 1.0

Magnesium binding site 5 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 5 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:50.6
occ:1.00
OP1 A:C1527 3.8 24.0 1.0
OP2 A:G731 4.0 30.1 1.0
OP1 A:G730 4.2 29.5 1.0
N7 A:G731 4.4 32.0 1.0
C8 A:G731 4.9 31.3 1.0

Magnesium binding site 6 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 6 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:61.8
occ:1.00
O2 A:C519 2.7 45.1 1.0
O2' A:C519 2.8 41.5 1.0
O4' A:A520 3.2 42.9 1.0
C2' A:C519 3.6 41.2 1.0
C2 A:C519 3.9 44.7 1.0
C4' A:A520 4.0 42.4 1.0
C1' A:C519 4.0 42.2 1.0
C1' A:A520 4.1 44.1 1.0
OP1 A:G517 4.3 53.8 1.0
C5' A:A520 4.4 42.2 1.0
N1 A:C519 4.5 43.9 1.0
O3' A:U516 4.7 54.3 1.0
O2' A:U516 4.8 54.5 1.0
N3 A:C519 4.9 46.0 1.0
N9 A:A520 4.9 48.0 1.0

Magnesium binding site 7 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 7 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:9.2
occ:1.00
N7 A:G799 4.0 32.9 1.0
O6 A:G799 4.2 35.1 1.0
O6 A:G798 4.2 31.8 1.0
O6 A:G800 4.3 18.6 1.0
N7 A:G798 4.4 32.7 1.0
OP2 A:A781 4.8 25.9 1.0
C6 A:G800 4.8 17.9 1.0
C5 A:G799 4.8 33.2 1.0
C6 A:G799 4.9 33.4 1.0
C6 A:G798 4.9 33.1 1.0
C5 A:G798 5.0 32.9 1.0

Magnesium binding site 8 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 8 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:20.5
occ:1.00
OP2 A:G21 4.0 31.2 1.0
N7 A:G21 4.2 37.5 1.0
OP2 A:U20 4.4 30.1 1.0
OP1 A:U561 4.4 29.3 1.0
O E:GLY124 4.7 25.0 1.0
C8 A:G21 4.7 36.2 1.0

Magnesium binding site 9 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 9 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:58.2
occ:1.00
O2' A:G854 2.9 32.4 1.0
O3' A:G854 3.0 30.3 1.0
OP1 A:G724 3.0 77.9 1.0
OP1 A:G855 3.4 32.4 1.0
OP2 A:G725 3.5 49.5 1.0
P A:G855 3.8 30.8 1.0
C3' A:G854 3.8 31.6 1.0
C2' A:G854 3.9 32.4 1.0
C4' A:G854 4.0 31.8 1.0
P A:G724 4.2 76.9 1.0
O5' A:G855 4.4 32.0 1.0
OP2 A:G724 4.6 76.6 1.0
P A:G725 4.8 49.9 1.0
O3' A:U723 4.8 77.6 1.0
C1' A:G854 4.9 33.4 1.0
O4' A:G854 4.9 31.9 1.0

Magnesium binding site 10 out of 161 in 2uu9

Go back to Magnesium Binding Sites List in 2uu9
Magnesium binding site 10 out of 161 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1611

b:1.0
occ:1.00
N7 A:G758 2.0 39.0 1.0
N7 A:G581 2.0 24.7 1.0
C8 A:G758 2.9 39.9 1.0
C8 A:G581 3.1 27.5 1.0
C5 A:G581 3.1 27.1 1.0
C5 A:G758 3.1 39.9 1.0
O6 A:G581 3.4 27.2 1.0
C6 A:G581 3.6 26.7 1.0
O6 A:G758 3.7 42.7 1.0
C6 A:G758 3.8 40.1 1.0
OP2 A:G758 3.9 29.3 1.0
N9 A:G758 4.1 37.0 1.0
N9 A:G581 4.2 28.0 1.0
C4 A:G581 4.2 26.6 1.0
OP2 A:G581 4.3 35.5 1.0
C4 A:G758 4.3 37.9 1.0
OP2 A:U580 4.6 29.3 1.0
N1 A:G581 4.9 26.2 1.0
C5 A:U757 4.9 35.7 1.0

Reference:

A.Weixlbaumer, F.V.Murphy 4Th., A.Dziergowska, A.Malkiewicz, F.A.Vendeix, P.F.Agris, V.Ramakrishnan. Mechanism For Expanding the Decoding Capacity of Transfer Rnas By Modification of Uridines. Nat. Struct. Mol. Biol. V. 14 498 2007.
ISSN: ISSN 1545-9993
PubMed: 17496902
DOI: 10.1038/NSMB1242
Page generated: Mon Dec 14 07:38:57 2020

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