Zinc in PDB 2vqf: 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: 2vqf 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)	49.92 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.481, 402.481, 175.969, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.8

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)	214 atoms
Potassium	(K)	73 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 2vqf). 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: 2vqf:
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:0.7 occ:1.00 SG D:CYS9 3.2 85.2 1.0 SG D:CYS26 3.2 94.2 1.0 SG D:CYS31 3.5 93.2 1.0 O D:LEU19 3.6 0.0 1.0 SG D:CYS12 3.7 84.0 1.0 CB D:CYS26 4.4 0.2 1.0 CB D:CYS9 4.5 89.1 1.0 CA D:CYS26 4.6 0.1 1.0 CB D:CYS12 4.7 83.6 1.0 CA D:CYS9 4.7 89.4 1.0 C D:LEU19 4.8 0.4 1.0 CB D:CYS31 4.9 0.2 1.0 N D:ALA32 5.0 0.3 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:0.7 occ:1.00 SG N:CYS27 2.1 97.6 1.0 SG N:CYS43 2.3 73.7 1.0 SG N:CYS40 2.6 88.4 1.0 SG N:CYS24 2.7 97.0 1.0 CB N:CYS27 2.9 97.8 1.0 CB N:CYS24 3.3 97.2 1.0 N N:CYS27 3.5 97.6 1.0 CB N:CYS40 3.6 89.9 1.0 CA N:CYS27 3.8 98.2 1.0 CB N:CYS43 4.0 76.5 1.0 CB N:ARG29 4.1 0.5 1.0 N2 A:G1202 4.2 95.6 1.0 C N:ARG26 4.3 96.1 1.0 N N:CYS40 4.3 93.1 1.0 C N:CYS27 4.5 98.3 1.0 CB N:ARG26 4.5 94.8 1.0 N3 A:G1202 4.5 94.8 1.0 CA N:CYS40 4.6 91.2 1.0 N N:GLY28 4.6 99.2 1.0 N N:CYS43 4.6 81.5 1.0 N N:ARG29 4.7 0.7 1.0 CA N:ARG26 4.8 96.1 1.0 CA N:CYS24 4.8 98.3 1.0 O2' A:G1202 4.9 96.3 1.0 C2 A:G1202 4.9 94.9 1.0 CA N:CYS43 4.9 78.7 1.0 N N:ARG26 4.9 97.5 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