Zinc 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
Potassium	(K)	62 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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 D:Zn301 b:0.2 occ:1.00 SG D:CYS26 2.9 68.6 1.0 SG D:CYS9 3.1 54.0 1.0 SG D:CYS31 3.4 76.9 1.0 SG D:CYS12 3.5 56.8 1.0 O D:CYS31 3.7 83.4 1.0 O D:LEU19 3.8 80.9 1.0 CB D:CYS26 4.3 72.8 1.0 CB D:CYS9 4.4 58.2 1.0 CB D:CYS12 4.6 56.4 1.0 CA D:CYS9 4.6 59.0 1.0 CA D:CYS26 4.6 73.9 1.0 C D:CYS31 4.7 81.8 1.0 CD D:LYS22 4.7 72.1 1.0 CB D:CYS31 4.7 79.2 1.0 CA D:CYS31 4.8 81.1 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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 N:Zn101 b:73.0 occ:1.00 SG N:CYS27 2.3 79.4 1.0 CB N:CYS27 2.3 73.3 1.0 SG N:CYS43 2.4 37.5 1.0 SG N:CYS24 2.7 66.2 1.0 SG N:CYS40 2.8 57.5 1.0 CB N:CYS24 3.2 66.0 1.0 CA N:CYS27 3.4 71.8 1.0 N N:CYS27 3.4 70.3 1.0 CB N:ARG29 3.4 70.8 1.0 CB N:CYS40 3.5 56.3 1.0 C N:CYS27 4.1 71.4 1.0 N N:ARG29 4.1 72.3 1.0 CB N:CYS43 4.2 45.6 1.0 N N:GLY28 4.3 72.2 1.0 O2' A:G1202 4.3 65.4 1.0 N N:CYS40 4.4 58.6 1.0 CA N:ARG29 4.4 71.1 1.0 CG N:ARG29 4.5 69.8 1.0 C N:ARG26 4.5 68.4 1.0 CA N:CYS40 4.6 57.3 1.0 CA N:CYS24 4.7 66.7 1.0 N3 A:G1202 4.7 62.8 1.0 N2 A:G1202 4.8 62.9 1.0 N N:CYS43 4.8 51.0 1.0 O N:CYS27 4.9 70.7 1.0 CB N:ARG26 5.0 67.2 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