Potassium in PDB 5wnp: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnp was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.000, 400.000, 173.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.4

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium	(Mg)	253 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 5wnp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 22 binding sites of Potassium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1833 b:0.1 occ:1.00 O4 A:U229 3.1 0.5 1.0 O4 A:U133 3.6 0.3 1.0 C4 A:U229 4.0 0.1 1.0 C5 A:U229 4.3 0.1 1.0 O6 A:G230 4.4 0.8 1.0 N7 A:A228 4.5 0.1 1.0 C4 A:U133 4.7 0.9 1.0 OP2 A:A228 4.8 0.2 1.0 N3 A:U133 4.9 0.2 1.0 N4 A:C132 5.0 0.7 1.0

Potassium binding site 2 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1834 b:0.3 occ:1.00 O4 A:U863 3.4 0.1 1.0 OP2 A:C866 4.0 0.1 1.0 C4 A:U863 4.4 0.1 1.0 OP1 A:U1078 4.5 0.4 1.0 N3 A:U863 4.6 0.7 1.0 O3' A:G1077 4.6 0.9 1.0 O6 A:G867 4.9 0.3 1.0 O5' A:A865 4.9 0.1 1.0 OP1 A:A865 5.0 0.2 1.0

Potassium binding site 3 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1835 b:0.9 occ:1.00 OP1 A:G576 2.8 0.5 1.0 P A:G576 3.8 0.6 1.0 OP2 A:G576 4.0 0.6 1.0 OP1 A:G575 4.0 0.4 1.0 OP2 A:G577 4.3 0.2 1.0 O5' A:G576 4.4 97.3 1.0 OP1 A:A815 4.5 0.1 1.0 OP2 A:G575 4.5 0.3 1.0 P A:G575 4.7 0.0 1.0 OP2 A:A815 4.7 0.1 1.0 C5' A:G576 4.9 0.0 1.0 O5' A:G575 4.9 0.4 1.0

Potassium binding site 4 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1836 b:0.0 occ:1.00 N7 A:G1088 3.7 0.3 1.0 O6 A:G1088 3.9 0.2 1.0 N7 A:G1087 4.1 0.5 1.0 OP2 A:G1087 4.2 1.0 1.0 O6 A:G1089 4.2 0.9 1.0 C5 A:G1088 4.4 0.1 1.0 C8 A:G1087 4.5 0.5 1.0 O4 A:U1090 4.5 0.6 1.0 C6 A:G1088 4.5 0.3 1.0 N7 A:G1089 4.6 0.2 1.0 C5 A:G1087 4.7 0.8 1.0 C8 A:G1088 4.7 0.6 1.0 OP2 A:G1088 4.8 0.3 1.0

Potassium binding site 5 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1837 b:0.0 occ:1.00 O2 A:C840 3.7 0.8 1.0 O6 A:G838 3.8 0.7 1.0 N3 A:C840 4.0 0.1 1.0 C2 A:C840 4.1 0.2 1.0 O6 A:G837 4.2 0.4 1.0 N7 A:G837 4.3 0.8 1.0 N7 A:G838 4.5 0.5 1.0 C6 A:G838 4.7 0.8 1.0 C6 A:G837 4.8 0.9 1.0 C5 A:G837 4.9 0.5 1.0 C4 A:C840 4.9 0.6 1.0

Potassium binding site 6 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1838 b:0.3 occ:1.00 O4 A:U14 3.3 0.6 1.0 OP2 A:U17 4.0 0.1 1.0 OP1 A:U17 4.2 1.0 1.0 C4 A:U14 4.4 0.4 1.0 OP2 A:U12 4.5 0.4 1.0 P A:U17 4.7 1.0 1.0 OP1 A:U12 4.7 0.1 1.0 N3 A:U14 4.9 0.3 1.0 OP2 A:U13 5.0 0.5 1.0

Potassium binding site 7 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1839 b:0.6 occ:1.00 OP2 A:C536 2.9 0.8 1.0 MG A:MG1727 3.1 0.5 1.0 N7 A:G537 3.9 0.2 1.0 P A:C536 4.2 0.2 1.0 OP2 A:G537 4.4 0.4 1.0 O5' A:C536 4.4 0.9 1.0 OP1 A:A535 4.5 0.5 1.0 C8 A:G537 4.6 0.8 1.0 O6 A:G538 4.7 0.8 1.0 C5 A:G537 4.8 0.3 1.0 O6 A:G537 4.8 1.0 1.0 N7 A:G538 4.8 0.4 1.0 C5 A:C536 4.9 0.1 1.0 C5' A:A535 4.9 0.1 1.0

Potassium binding site 8 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1840 b:1.0 occ:1.00 OP2 A:G492 3.2 0.4 1.0 OP1 A:G438 3.7 0.9 1.0 OP2 A:G438 4.0 0.7 1.0 N7 A:G494 4.1 0.7 1.0 O6 A:G494 4.2 0.8 1.0 P A:G438 4.2 0.6 1.0 P A:G492 4.3 0.5 1.0 O5' A:G438 4.6 0.8 1.0 O5' A:G492 4.7 0.8 1.0 OP1 A:G492 4.8 0.1 1.0 OP2 A:G494 4.8 0.3 1.0 C5 A:G494 4.9 0.5 1.0 C6 A:G494 4.9 0.7 1.0

Potassium binding site 9 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1841 b:0.6 occ:1.00 O4 A:U192 3.6 0.1 1.0 O A:HOH2039 4.2 0.2 1.0 O6 A:G191 4.5 0.9 1.0 N7 A:G191 4.5 0.7 1.0 C4 A:U192 4.6 0.5 1.0 OP2 A:U190L 4.6 0.0 1.0 N6 A:A185 4.9 0.6 1.0

Potassium binding site 10 out of 22 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:K1842 b:0.7 occ:1.00 O A:HOH2107 3.1 0.4 1.0 O A:HOH2081 3.4 0.8 1.0 O6 A:G474 3.4 0.1 1.0 O6 A:G475 3.7 0.8 1.0 N7 A:G474 3.9 0.1 1.0 C6 A:G474 4.0 0.3 1.0 MG A:MG1675 4.1 0.9 1.0 OP2 A:A463 4.1 0.5 1.0 C5 A:G474 4.2 0.8 1.0 N7 A:G475 4.4 0.3 1.0 C6 A:G475 4.6 0.4 1.0 OP2 A:G462 4.6 0.9 1.0 C5 A:G475 4.9 0.7 1.0 C8 A:G474 5.0 0.8 1.0

J.Choi, G.Indrisiunaite, H.Demirci, K.W.Ieong, J.Wang, A.Petrov, A.Prabhakar, G.Rechavi, D.Dominissini, C.He, M.Ehrenberg, J.D.Puglisi. 2'-O-Methylation in Mrna Disrupts Trna Decoding During Translation Elongation. Nat. Struct. Mol. Biol. V. 25 208 2018.
ISSN: ESSN 1545-9985
PubMed: 29459784
DOI: 10.1038/S41594-018-0030-Z