Magnesium in PDB 2dxi: 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol

All present enzymatic activity of 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol:
6.1.1.17;

The structure of 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol, PDB code: 2dxi was solved by S.Sekine, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.615, 219.119, 135.816, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.7

The binding sites of Magnesium atom in the 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol (pdb code 2dxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol, PDB code: 2dxi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:50.0 occ:1.00 N7 C:A545 4.0 41.9 1.0 OP2 C:G522 4.1 39.8 1.0 N7 C:A546 4.4 38.8 1.0 C8 C:A545 4.5 45.3 1.0 OP2 C:A546 4.7 41.6 1.0 O2 C:C509 4.7 53.6 1.0 N6 C:A546 4.8 37.2 1.0 C5 C:A545 4.8 42.5 1.0 N3 C:C509 4.9 41.7 1.0 N6 C:A545 5.0 40.0 1.0

Magnesium binding site 2 out of 2 in the 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.2 A Crystal Structure of Glutamyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna(Glu), Atp, and L- Glutamol within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:46.2 occ:1.00 O D:HOH1139 2.3 35.3 1.0 O D:HOH1302 2.4 33.2 1.0 N7 D:A546 3.8 41.8 1.0 N7 D:A545 3.9 47.2 1.0 O D:HOH1191 3.9 47.3 1.0 OP2 D:G522 4.2 51.0 1.0 O2 D:C509 4.3 46.6 1.0 C8 D:A545 4.4 48.3 1.0 OP2 D:A546 4.5 40.1 1.0 C8 D:A546 4.6 40.5 1.0 N3 D:C509 4.6 38.1 1.0 C5 D:A545 4.7 44.6 1.0 N6 D:A546 4.7 33.6 1.0 C5 D:A546 4.8 38.3 1.0 C2 D:C509 4.9 39.0 1.0

S.Sekine, M.Shichiri, S.Bernier, R.Chenevert, J.Lapointe, S.Yokoyama. Structural Bases of Transfer Rna-Dependent Amino Acid Recognition and Activation By Glutamyl-Trna Synthetase Structure V. 14 1791 2006.
ISSN: ISSN 0969-2126
PubMed: 17161369
DOI: 10.1016/J.STR.2006.10.005