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Potassium 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:

Magnesium (Mg) 161 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Potassium 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 Potassium atom.
In total 36 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 1 out of 36 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 Potassium with other atoms in the K 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:K1756

b:60.8
occ:1.00
O6 A:G305 2.8 42.3 1.0
O4 A:U304 3.0 36.2 1.0
O6 A:G293 3.1 34.0 1.0
C6 A:G305 3.6 39.8 1.0
K A:K1782 3.8 92.6 1.0
N6 A:A303 3.8 28.3 1.0
N3 A:U304 3.8 32.5 1.0
C4 A:U304 3.8 33.8 1.0
N1 A:G305 3.9 38.3 1.0
C6 A:G293 4.1 33.2 1.0
N7 A:G293 4.4 30.4 1.0
OP2 A:G292 4.4 29.4 1.0
C5 A:G293 4.6 32.0 1.0
C5 A:G305 4.8 39.5 1.0
OP1 A:C291 4.9 28.8 1.0
C6 A:A303 4.9 30.0 1.0

Potassium binding site 2 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 2 out of 36 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 Potassium with other atoms in the K 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:K1757

b:68.9
occ:1.00
O4 A:U229 2.8 27.3 1.0
O6 A:G230 3.1 35.3 1.0
O4 A:U133 3.4 34.5 1.0
C4 A:U229 3.8 26.9 1.0
C5 A:U229 4.1 29.2 1.0
C6 A:G230 4.1 32.6 1.0
C4 A:U133 4.2 34.5 1.0
N3 A:U133 4.2 33.5 1.0
N4 A:C132 4.3 31.9 1.0
N7 A:G230 4.7 34.4 1.0
C5 A:G230 4.8 32.8 1.0
N7 A:A228 4.9 37.6 1.0

Potassium binding site 3 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 3 out of 36 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 Potassium with other atoms in the K 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:K1758

b:98.3
occ:1.00
OP2 A:C866 3.2 33.0 1.0
OP1 A:C866 3.5 30.7 1.0
N7 A:G867 3.7 30.6 1.0
P A:C866 3.7 32.5 1.0
O5' A:C866 4.3 32.7 1.0
C8 A:G867 4.3 30.0 1.0
OP2 A:G867 4.6 31.9 1.0
C5 A:G867 4.8 30.2 1.0
O6 A:G867 5.0 31.2 1.0

Potassium binding site 4 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 4 out of 36 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 Potassium with other atoms in the K 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:K1759

b:74.2
occ:1.00
OP1 A:G577 3.3 26.2 1.0
OP1 A:U813 3.4 28.7 1.0
N7 A:G577 3.5 16.2 1.0
C8 A:G577 4.1 15.7 1.0
P A:U813 4.6 27.4 1.0
C5 A:G577 4.7 16.9 1.0
N6 A:A816 4.7 27.4 1.0
P A:G577 4.8 25.8 1.0
O6 A:G577 4.9 17.8 1.0
OP2 A:U813 5.0 26.2 1.0

Potassium binding site 5 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 5 out of 36 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 Potassium with other atoms in the K 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:K1760

b:67.2
occ:1.00
O6 A:G895 3.5 33.7 1.0
N7 A:G895 3.9 33.8 1.0
O6 A:G894 4.0 38.5 1.0
N7 A:G894 4.0 37.9 1.0
N4 A:C896 4.2 30.5 1.0
C6 A:G895 4.3 32.8 1.0
C6 A:G894 4.5 38.4 1.0
C5 A:G894 4.5 38.1 1.0
C5 A:G895 4.5 32.7 1.0
N4 A:C904 4.8 31.0 1.0
C8 A:G894 4.9 37.7 1.0
O6 A:G903 4.9 26.1 1.0

Potassium binding site 6 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 6 out of 36 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 Potassium with other atoms in the K 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:K1761

b:68.9
occ:1.00
O6 A:G305 3.3 42.3 1.0
N7 A:G305 3.3 39.6 1.0
OP2 A:C291 3.4 29.8 1.0
OP1 A:C291 3.5 28.8 1.0
O4 A:U304 3.7 36.2 1.0
C6 A:G305 3.9 39.8 1.0
C5 A:G305 3.9 39.5 1.0
P A:C291 3.9 28.5 1.0
C4 A:U304 4.0 33.8 1.0
C8 A:G305 4.4 40.4 1.0
K A:K1782 4.4 92.6 1.0
C5 A:U304 4.4 33.4 1.0
N3 A:U304 4.6 32.5 1.0
O3' A:C290 4.6 28.2 1.0

Potassium binding site 7 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 7 out of 36 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 Potassium with other atoms in the K 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:K1762

b:75.3
occ:1.00
OP2 A:G577 3.2 25.6 1.0
OP1 A:G576 3.4 28.2 1.0
OP1 A:G575 4.5 26.9 1.0
OP1 A:A815 4.5 26.3 1.0
P A:G576 4.5 28.0 1.0
C5' A:G576 4.7 28.8 1.0
P A:G577 4.7 25.8 1.0
C5' A:G577 4.8 20.6 1.0
OP2 A:A815 4.8 27.8 1.0
OP2 A:G576 4.8 26.7 1.0

Potassium binding site 8 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 8 out of 36 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 Potassium with other atoms in the K 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:K1763

b:80.1
occ:1.00
MG A:MG1604 2.6 33.3 1.0
O6 A:G258 3.8 55.9 1.0
O6 A:G257 3.8 57.4 1.0
N7 A:G258 3.9 54.7 1.0
OP2 A:G266 3.9 38.9 1.0
C6 A:G257 4.5 56.5 1.0
C6 A:G258 4.5 54.7 1.0
C5 A:G258 4.6 54.7 1.0
O6 A:G259 4.6 53.1 1.0
N7 A:G257 4.8 56.4 1.0
C5 A:G257 4.8 56.3 1.0
N4 A:C267 4.9 40.6 1.0
C8 A:G258 5.0 54.9 1.0

Potassium binding site 9 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 9 out of 36 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 Potassium with other atoms in the K 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:K1764

b:69.8
occ:1.00
OP2 A:C936 3.1 39.7 1.0
OP2 A:G1343 3.3 39.1 1.0
O2' A:C934 3.4 39.2 1.0
O3' A:C934 3.6 41.8 1.0
OP2 A:A935 3.8 39.4 1.0
P A:C936 3.8 39.6 1.0
OP1 A:C936 3.9 37.2 1.0
O3' A:A935 4.1 39.8 1.0
P A:A935 4.1 40.9 1.0
O5' A:A935 4.2 39.5 1.0
C5' A:A935 4.3 38.9 1.0
C2' A:C934 4.5 40.1 1.0
P A:G1343 4.5 39.9 1.0
C3' A:A935 4.6 38.8 1.0
C3' A:C934 4.6 40.9 1.0
C1' A:C934 4.7 40.1 1.0
OP2 A:C1344 4.8 40.0 1.0
OP1 A:G1343 4.9 39.8 1.0
O5' A:G1343 4.9 41.0 1.0

Potassium binding site 10 out of 36 in 2uu9

Go back to Potassium Binding Sites List in 2uu9
Potassium binding site 10 out of 36 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 Potassium with other atoms in the K 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:K1765

b:0.9
occ:1.00
O4 A:U14 3.4 30.6 1.0
OP2 A:U17 3.6 32.2 1.0
OP1 A:U17 4.3 34.0 1.0
C4 A:U14 4.4 29.9 1.0
P A:U17 4.5 31.6 1.0
N3 A:U14 4.7 28.9 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: Sun Dec 13 23:11:47 2020

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