Magnesium in PDB 4l87: Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution:
6.1.1.11;

The structure of Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution, PDB code: 4l87 was solved by X.Xu, X.-L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	144.69 / 2.90
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.074, 167.074, 65.156, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 26.8

The binding sites of Magnesium atom in the Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution (pdb code 4l87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution, PDB code: 4l87:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution


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 Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:57.1 occ:1.00 NZ A:LYS376 3.0 63.9 1.0 OE2 A:GLU391 3.2 70.5 1.0 OD2 A:ASP378 3.3 67.5 1.0 CD A:GLU391 3.7 70.2 1.0 CE A:LYS376 3.8 63.9 1.0 OE1 A:GLU391 3.9 70.4 1.0 CG A:ASP378 4.3 67.3 1.0 OG A:SER394 4.4 63.0 1.0 OD1 A:ASP378 4.7 67.3 1.0 O2S A:SSA501 4.9 57.3 1.0 CG A:GLU391 4.9 69.8 1.0 CD A:LYS376 5.0 63.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Human Seryl-Trna Synthetase in Complex with Ser-Sa at 2.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:50.0 occ:1.00 O9 A:SSA501 3.5 57.5 1.0 OE1 A:GLU246 3.5 62.0 1.0 NH2 A:ARG302 3.8 58.5 1.0 NH1 A:ARG302 3.8 58.7 1.0 O1S A:SSA501 3.9 56.4 1.0 OG1 A:THR271 3.9 57.2 1.0 C9 A:SSA501 4.0 57.6 1.0 N8 A:SSA501 4.1 57.4 1.0 CZ A:ARG302 4.1 58.5 1.0 NE2 A:GLN242 4.2 60.2 1.0 OE2 A:GLU246 4.2 62.5 1.0 CD A:GLU246 4.3 62.0 1.0 S1 A:SSA501 4.7 56.7 1.0 CD A:GLN242 4.9 60.3 1.0 OE2 A:GLU273 5.0 59.2 1.0

X.Xu, Y.Shi, X.L.Yang. Crystal Structure of Human Seryl-Trna Synthetase and Ser-Sa Complex Reveals A Molecular Lever Specific to Higher Eukaryotes. Structure V. 21 2078 2013.
ISSN: ISSN 0969-2126
PubMed: 24095058
DOI: 10.1016/J.STR.2013.08.021