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

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 Guu-Codon in the A-Site and Paromomycin., PDB code: 2uub 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)	29.99 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.440, 400.440, 173.360, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.3

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 Guu-Codon in the A-Site and Paromomycin. also contains other interesting chemical elements:

Magnesium	(Mg)	218 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

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 Guu-Codon in the A-Site and Paromomycin. (pdb code 2uub). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 35 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 Guu-Codon in the A-Site and Paromomycin., PDB code: 2uub:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1805 b:68.0 occ:1.00 O4 A:U304 2.7 45.7 1.0 O6 A:G293 2.8 43.9 1.0 O6 A:G305 2.9 46.5 1.0 C4 A:U304 3.7 43.4 1.0 C6 A:G305 3.7 46.0 1.0 N3 A:U304 3.9 42.2 1.0 C6 A:G293 3.9 40.7 1.0 N6 A:A303 4.0 32.9 1.0 N1 A:G305 4.1 45.7 1.0 N7 A:G293 4.4 40.1 1.0 C5 A:G293 4.5 40.7 1.0 K A:K1810 4.6 0.1 1.0 O4 A:U294 4.6 46.4 1.0 OP2 A:G292 4.6 40.3 1.0 C5 A:G305 4.8 47.0 1.0

Potassium binding site 2 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1806 b:72.8 occ:1.00 O4 A:U229 2.8 37.9 1.0 O4 A:U133 3.0 45.7 1.0 O6 A:G230 3.0 39.2 1.0 C4 A:U133 3.9 43.0 1.0 C4 A:U229 3.9 37.0 1.0 N4 A:C132 4.0 42.5 1.0 C6 A:G230 4.0 37.2 1.0 N3 A:U133 4.1 40.9 1.0 C5 A:U229 4.4 38.3 1.0 N7 A:G230 4.7 36.9 1.0 C5 A:G230 4.7 36.5 1.0

Potassium binding site 3 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1807 b:76.9 occ:1.00 O4 A:U863 3.1 46.3 1.0 C4 A:U863 3.8 44.8 1.0 N3 A:U863 4.1 45.7 1.0 OP1 A:U1078 4.2 37.1 1.0 OP2 A:C866 4.3 38.2 1.0 O5' A:A865 4.4 38.6 1.0 OP1 A:A865 4.7 42.0 1.0 C5' A:A865 4.7 37.9 1.0 O3' A:G1077 4.9 38.8 1.0 C5 A:U863 5.0 44.2 1.0

Potassium binding site 4 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1808 b:81.8 occ:1.00 OP1 A:G577 3.5 32.5 1.0 N7 A:G577 3.5 31.2 1.0 OP1 A:U813 3.6 44.3 1.0 OP2 A:U813 3.8 41.6 1.0 P A:U813 4.2 40.5 1.0 C8 A:G577 4.2 31.3 1.0 N6 A:A816 4.6 27.6 1.0 C5 A:G577 4.7 29.7 1.0 O6 A:G577 4.8 31.7 1.0 P A:G577 4.9 31.4 1.0

Potassium binding site 5 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1809 b:92.5 occ:1.00 O6 A:G895 3.5 42.1 1.0 N7 A:G894 3.6 45.9 1.0 O6 A:G894 3.7 48.5 1.0 N7 A:G895 4.2 41.1 1.0 C5 A:G894 4.2 45.3 1.0 C6 A:G894 4.3 46.1 1.0 C6 A:G895 4.4 40.8 1.0 C8 A:G894 4.6 46.9 1.0 C5 A:G895 4.6 40.3 1.0 C5 A:C893 4.6 45.4 1.0 N4 A:C904 4.7 37.2 1.0 N4 A:C893 4.8 42.4 1.0 N4 A:C896 4.8 41.4 1.0 C4 A:C893 4.9 44.0 1.0

Potassium binding site 6 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1810 b:0.1 occ:1.00 OP1 A:C291 2.8 42.3 1.0 O6 A:G305 2.9 46.5 1.0 O4 A:U304 3.5 45.7 1.0 N7 A:G305 3.7 47.5 1.0 C6 A:G305 3.7 46.0 1.0 P A:C291 3.8 39.9 1.0 C4 A:U304 3.9 43.4 1.0 OP2 A:C291 3.9 38.8 1.0 C5 A:G305 4.0 47.0 1.0 C5 A:U304 4.3 44.2 1.0 O3' A:C290 4.5 40.1 1.0 K A:K1805 4.6 68.0 1.0 N3 A:U304 4.6 42.2 1.0 C8 A:G305 4.9 48.1 1.0 N1 A:G305 5.0 45.7 1.0

Potassium binding site 7 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1811 b:86.8 occ:1.00 OP1 A:G576 3.0 36.8 1.0 OP2 A:G577 3.2 31.7 1.0 P A:G576 4.4 34.5 1.0 OP1 A:G575 4.4 36.1 1.0 C5' A:G576 4.5 35.9 1.0 C5' A:G577 4.6 30.9 1.0 O3' A:G575 4.6 36.4 1.0 P A:G577 4.6 31.4 1.0 OP2 A:A815 4.7 34.2 1.0 OP1 A:A815 4.7 33.8 1.0 OP2 A:G575 4.7 39.7 1.0 O5' A:G576 5.0 35.7 1.0

Potassium binding site 8 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1812 b:91.7 occ:1.00 O6 A:G898 3.5 44.5 1.0 N7 A:G898 3.7 40.6 1.0 C6 A:G898 4.2 41.0 1.0 C5 A:G898 4.3 40.9 1.0 N4 A:C897 4.7 35.1 1.0 C5 A:C897 4.8 37.0 1.0 C8 A:G898 4.8 40.4 1.0 C4 A:C897 5.0 36.0 1.0

Potassium binding site 9 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1813 b:88.4 occ:1.00 O6 A:G257 2.7 66.0 1.0 OP2 A:G266 3.3 45.1 1.0 MG A:MG1748 3.6 70.9 1.0 O6 A:G258 3.6 63.2 1.0 C6 A:G257 3.7 63.1 1.0 OP1 A:G266 3.9 47.6 1.0 P A:G266 4.1 46.9 1.0 N7 A:G257 4.2 62.0 1.0 O4 A:U256 4.2 59.0 1.0 C5 A:G257 4.3 62.5 1.0 N7 A:G258 4.4 65.1 1.0 N4 A:C268 4.5 58.9 1.0 C6 A:G258 4.5 64.0 1.0 N4 A:C269 4.6 68.5 1.0 MG Q:MG201 4.7 52.6 1.0 C5 A:G258 4.8 64.5 1.0 C4 A:U256 4.8 61.5 1.0 N1 A:G257 4.8 61.4 1.0 C5 A:U256 5.0 62.4 1.0

Potassium binding site 10 out of 35 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 Guu-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 Guu-Codon in the A-Site and Paromomycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:K1814 b:95.5 occ:1.00 OP1 A:A535 2.6 57.3 1.0 O3' A:U534 3.3 57.8 1.0 O4 A:U512 3.6 60.0 1.0 P A:A535 3.6 56.9 1.0 O2' A:U534 4.0 58.2 1.0 C5' A:A535 4.1 51.8 1.0 O6 A:G538 4.1 55.9 1.0 N4 A:C513 4.2 58.9 1.0 O5' A:A535 4.3 55.0 1.0 OP2 A:C536 4.4 53.5 1.0 O6 A:G537 4.4 56.1 1.0 C3' A:U534 4.5 58.9 1.0 C4 A:U512 4.7 61.8 1.0 N6 A:A539 4.7 58.3 1.0 C2' A:U534 4.8 58.9 1.0 OP2 A:A535 4.8 56.4 1.0 N4 A:C536 4.9 44.6 1.0 C5 A:C536 5.0 48.7 1.0

A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.P.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