Magnesium in PDB 3vqy: Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2):
6.1.1.26;

The structure of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2), PDB code: 3vqy was solved by T.Yanagisawa, T.Sumida, R.Ishii, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.76 / 2.40
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	103.355, 103.355, 70.906, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2) (pdb code 3vqy). 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 Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2), PDB code: 3vqy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2)


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 Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:38.3 occ:1.00 O1B A:ANP501 2.2 35.3 1.0 O A:HOH601 2.3 42.1 1.0 O1G A:ANP501 2.3 37.8 1.0 O A:HOH697 2.4 36.3 1.0 O A:HOH685 2.4 38.2 1.0 O A:HOH656 2.5 34.2 1.0 PB A:ANP501 3.4 36.0 1.0 PG A:ANP501 3.5 39.3 1.0 NH1 A:ARG330 3.7 39.6 1.0 OE1 A:GLU283 3.7 68.5 1.0 N3B A:ANP501 4.0 37.3 1.0 O3G A:ANP501 4.1 38.3 1.0 NE2 A:HIS338 4.2 41.5 1.0 CD A:GLU283 4.2 69.6 1.0 NE2 A:GLN287 4.3 53.9 1.0 OE2 A:GLU283 4.3 69.0 1.0 OE1 A:GLN287 4.4 54.4 1.0 OE1 A:GLU332 4.4 48.9 1.0 O2B A:ANP501 4.4 35.6 1.0 O3A A:ANP501 4.5 38.5 1.0 O A:HOH670 4.6 54.0 1.0 OE2 A:GLU332 4.7 53.8 1.0 CD2 A:HIS338 4.7 40.2 1.0 CD A:GLN287 4.8 53.2 1.0 O2G A:ANP501 4.9 35.8 1.0 CZ A:ARG330 4.9 41.0 1.0 N7 A:ANP501 4.9 32.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2)


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 Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Boclys and Amppnp (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:56.6 occ:1.00 OG A:SER399 2.4 40.4 1.0 O2B A:ANP501 2.4 35.6 1.0 OE2 A:GLU396 2.7 45.5 1.0 O A:HOH640 2.9 49.6 1.0 O2A A:ANP501 2.9 39.4 1.0 OE1 A:GLU396 2.9 50.4 1.0 CD A:GLU396 3.1 47.3 1.0 CB A:SER399 3.5 39.5 1.0 PB A:ANP501 3.7 36.0 1.0 O3A A:ANP501 4.0 38.5 1.0 PA A:ANP501 4.0 38.1 1.0 OD2 A:ASP389 4.1 55.9 1.0 N3B A:ANP501 4.1 37.3 1.0 CG A:GLU396 4.4 44.3 1.0 CA A:SER399 4.7 39.0 1.0 CG A:ASP389 4.8 53.7 1.0 O1A A:ANP501 4.8 37.2 1.0 OD1 A:ASP389 4.8 56.6 1.0 O3' A:ANP501 5.0 35.2 1.0 O3G A:ANP501 5.0 38.3 1.0 O1B A:ANP501 5.0 35.3 1.0

T.Yanagisawa, T.Sumida, R.Ishii, S.Yokoyama. A Novel Crystal Form of Pyrrolysyl-Trna Synthetase Reveals the Pre- and Post-Aminoacyl-Trna Synthesis Conformational States of the Adenylate and Aminoacyl Moieties and An Asparagine Residue in the Catalytic Site Acta Crystallogr.,Sect.D V. 69 5 2013.
ISSN: ISSN 0907-4449
PubMed: 23275158
DOI: 10.1107/S0907444912039881