Magnesium in PDB 2dlc: Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase

All present enzymatic activity of Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase:
6.1.1.1;

The structure of Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase, PDB code: 2dlc was solved by M.Tsunoda, Y.Kusakabe, N.Tanaka, K.T.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.854, 63.854, 330.334, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 28.9

The binding sites of Magnesium atom in the Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase (pdb code 2dlc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase, PDB code: 2dlc:

Magnesium binding site 1 out of 1 in the Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Ternary Complex of Yeast Tyrosyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg801 b:42.5 occ:1.00 O2P X:YMP601 2.6 46.8 1.0 O X:ALA47 2.7 33.2 1.0 OH X:TYR56 2.8 34.0 1.0 OH X:TYR101 2.9 27.9 1.0 CG2 X:THR49 3.4 34.7 1.0 CB X:THR49 3.5 34.7 1.0 O1P X:YMP601 3.6 46.7 1.0 P X:YMP601 3.6 45.8 1.0 CZ X:TYR101 3.8 28.9 1.0 CE2 X:TYR101 3.9 29.8 1.0 C X:ALA47 3.9 32.9 1.0 N X:THR49 4.1 33.9 1.0 CZ X:TYR56 4.2 34.3 1.0 OG1 X:THR46 4.2 31.9 1.0 N X:ALA47 4.3 32.5 1.0 CA X:THR49 4.4 34.6 1.0 CA X:ALA47 4.5 32.8 1.0 O5' X:YMP601 4.5 48.0 1.0 CB X:ALA47 4.6 32.8 1.0 OG1 X:THR49 4.6 35.5 1.0 N X:GLY50 4.7 35.0 1.0 O X:GLY50 4.8 35.8 1.0 N3P X:YMP601 4.9 48.0 1.0 N X:PRO48 5.0 32.9 1.0 CE1 X:TYR56 5.0 34.5 1.0 C X:THR49 5.0 34.9 1.0 CE2 X:TYR56 5.0 33.6 1.0

M.Tsunoda, Y.Kusakabe, N.Tanaka, S.Ohno, M.Nakamura, T.Senda, T.Moriguchi, N.Asai, M.Sekine, T.Yokogawa, K.Nishikawa, K.T.Nakamura. Structural Basis For Recognition of Cognate Trna By Tyrosyl-Trna Synthetase From Three Kingdoms. Nucleic Acids Res. V. 35 4289 2007.
ISSN: ESSN 1362-4962
PubMed: 17576676
DOI: 10.1093/NAR/GKM417