Potassium in PDB 2vqe: Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding

The structure of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding, PDB code: 2vqe was solved by S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino, K.Takai, K.Watanabe, V.Ramakrishnan, T.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.998, 401.998, 175.648, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 28.3

The structure of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding also contains other interesting chemical elements:

Magnesium	(Mg)	206 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 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 62;

Binding sites:

The binding sites of Potassium atom in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding (pdb code 2vqe). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 62 binding sites of Potassium where determined in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding, PDB code: 2vqe:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1800 b:65.0 occ:1.00 O6 A:G293 2.8 31.8 1.0 O6 A:G305 2.8 36.3 1.0 O4 A:U304 3.0 32.6 1.0 C6 A:G305 3.6 33.4 1.0 N3 A:U304 3.8 30.9 1.0 C4 A:U304 3.8 30.6 1.0 C6 A:G293 3.8 30.7 1.0 N6 A:A303 3.9 24.2 1.0 N1 A:G305 4.0 32.4 1.0 N7 A:G293 4.3 31.2 1.0 C5 A:G293 4.5 31.5 1.0 OP2 A:G292 4.5 32.4 1.0 O4 A:U294 4.5 26.5 1.0 C5 A:G305 4.8 34.9 1.0 N1 A:G293 5.0 29.8 1.0 C6 A:A303 5.0 23.6 1.0 K A:K1844 5.0 0.3 1.0

Potassium binding site 2 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1801 b:76.5 occ:1.00 O4 A:U229 2.9 31.1 1.0 O4 A:U133 3.3 31.2 1.0 O6 A:G230 3.3 30.9 1.0 C4 A:U229 3.8 27.1 1.0 C5 A:U229 4.1 27.4 1.0 C4 A:U133 4.2 27.6 1.0 N4 A:C132 4.3 24.5 1.0 N3 A:U133 4.3 26.0 1.0 C6 A:G230 4.3 29.6 1.0 N7 A:G230 4.6 29.3 1.0 C5 A:G230 4.8 28.8 1.0

Potassium binding site 3 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1802 b:73.5 occ:1.00 O4 A:U863 3.2 48.2 1.0 C4 A:U863 3.8 45.8 1.0 OP2 A:C866 4.1 32.7 1.0 N3 A:U863 4.1 45.3 1.0 OP1 A:U1078 4.4 25.3 1.0 O5' A:A865 4.5 34.5 1.0 OP1 A:A865 4.6 37.4 1.0 C5 A:U863 4.8 44.2 1.0 O6 A:G867 4.9 40.2 1.0 C5' A:A865 4.9 34.8 1.0

Potassium binding site 4 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1803 b:97.3 occ:1.00 OP1 A:G577 3.4 26.4 1.0 N7 A:G577 3.5 16.7 1.0 OP2 A:U813 3.8 27.0 1.0 OP1 A:U813 3.9 29.0 1.0 C8 A:G577 4.1 16.5 1.0 N6 A:A816 4.4 21.9 1.0 P A:U813 4.4 25.9 1.0 C5 A:G577 4.7 13.2 1.0 P A:G577 4.8 25.5 1.0

Potassium binding site 5 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1804 b:0.9 occ:1.00 O6 A:G895 3.1 28.6 1.0 N7 A:G894 3.7 27.2 1.0 O6 A:G894 3.9 26.0 1.0 C6 A:G895 4.0 26.1 1.0 N7 A:G895 4.1 26.8 1.0 C5 A:G894 4.3 26.1 1.0 C6 A:G894 4.4 24.6 1.0 C5 A:G895 4.4 24.9 1.0 N4 A:C896 4.6 29.4 1.0 C8 A:G894 4.6 27.0 1.0 N4 A:C904 4.7 27.8 1.0 C5 A:C893 4.8 38.2 1.0 O6 A:G903 4.9 27.3 1.0 N4 A:C893 5.0 36.4 1.0

Potassium binding site 6 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1805 b:0.9 occ:1.00 O6 A:G305 3.3 36.3 1.0 N7 A:G305 3.4 36.6 1.0 OP1 A:C291 3.5 29.4 1.0 OP2 A:C291 3.7 27.9 1.0 O4 A:U304 3.7 32.6 1.0 C6 A:G305 4.0 33.4 1.0 C5 A:G305 4.0 34.9 1.0 P A:C291 4.0 28.4 1.0 C4 A:U304 4.1 30.6 1.0 C5 A:U304 4.3 31.0 1.0 C8 A:G305 4.5 36.2 1.0 N3 A:U304 4.7 30.9 1.0 O3' A:C290 4.8 28.2 1.0

Potassium binding site 7 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1806 b:0.8 occ:1.00 OP1 A:G576 2.7 29.1 1.0 O3' A:G575 3.6 26.4 1.0 P A:G576 3.9 26.3 1.0 OP2 A:G577 3.9 25.3 1.0 OP1 A:G575 4.1 27.9 1.0 OP2 A:G575 4.5 26.6 1.0 C5' A:G576 4.6 24.6 1.0 P A:G575 4.7 25.4 1.0 O5' A:G576 4.7 27.1 1.0 OP1 A:A815 4.9 22.1 1.0 C3' A:G575 5.0 23.2 1.0 OP2 A:G576 5.0 29.1 1.0 OP2 A:A815 5.0 19.2 1.0

Potassium binding site 8 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1807 b:93.6 occ:1.00 O4 A:U296 3.2 21.1 1.0 O6 A:G297 3.5 31.0 1.0 MG A:MG1625 3.6 93.6 1.0 C4 A:U296 4.1 21.7 1.0 C5 A:U296 4.3 21.4 1.0 C6 A:G297 4.5 26.5 1.0

Potassium binding site 9 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1808 b:90.8 occ:1.00 O6 A:G898 3.2 28.7 1.0 OP2 A:A900 3.3 29.9 1.0 N7 A:G898 3.5 24.4 1.0 C6 A:G898 3.5 25.9 1.0 C5 A:G898 3.6 24.6 1.0 OP1 A:A900 3.6 30.2 1.0 P A:A900 3.9 31.1 1.0 MG A:MG1773 4.1 96.5 1.0 C8 A:G898 4.3 23.5 1.0 N1 A:G898 4.5 25.9 1.0 C4 A:G898 4.5 24.7 1.0 O3' A:C899 4.7 29.5 1.0 N9 A:G898 4.9 23.8 1.0

Potassium binding site 10 out of 62 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:K1809 b:0.6 occ:1.00 O6 A:G257 2.9 53.0 1.0 O6 A:G258 3.1 51.2 1.0 OP2 A:G266 3.6 38.7 1.0 C6 A:G257 3.8 51.2 1.0 N7 A:G258 3.9 54.7 1.0 C6 A:G258 3.9 52.7 1.0 MG A:MG1603 4.0 0.7 1.0 N7 A:G257 4.1 51.8 1.0 OP1 A:G266 4.1 37.9 1.0 C5 A:G258 4.2 53.5 1.0 C5 A:G257 4.3 51.4 1.0 P A:G266 4.4 38.6 1.0 N4 A:C268 4.6 48.8 1.0 O4 A:U256 4.7 50.0 1.0 N4 A:C269 4.8 53.1 1.0 N1 A:G257 5.0 49.4 1.0

S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino, K.Takai, K.Watanabe, V.Ramakrishnan, T.Suzuki. Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U.G Wobble Pairing During Decoding. J.Biol.Chem. V. 283 18801 2008.
ISSN: ISSN 0021-9258
PubMed: 18456657
DOI: 10.1074/JBC.M800233200