Magnesium in PDB 3vqw: Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase

All present enzymatic activity of Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase:
6.1.1.26;

The structure of Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase, PDB code: 3vqw 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)	42.16 / 2.40
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.091, 105.091, 70.629, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 27

The binding sites of Magnesium atom in the Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase (pdb code 3vqw). 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 Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase, PDB code: 3vqw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-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 Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.7 occ:1.00 O1B A:ANP501 2.5 59.2 1.0 O A:HOH734 2.6 65.4 1.0 O1G A:ANP501 2.6 73.7 1.0 O3G A:ANP501 3.3 74.2 1.0 PG A:ANP501 3.4 69.2 1.0 OE1 A:GLU283 3.4 0.3 1.0 PB A:ANP501 3.6 59.3 1.0 NE2 A:GLN287 3.8 44.8 1.0 N3B A:ANP501 4.1 66.8 1.0 NH1 A:ARG330 4.1 67.8 1.0 CD A:GLU283 4.3 0.2 1.0 OE1 A:GLU332 4.3 59.4 1.0 OE2 A:GLU332 4.5 63.5 1.0 NE2 A:HIS338 4.5 47.1 1.0 O2B A:ANP501 4.6 69.0 1.0 OE1 A:GLN287 4.6 58.9 1.0 CD A:GLN287 4.6 55.0 1.0 OE2 A:GLU283 4.7 0.1 1.0 O3A A:ANP501 4.8 67.4 1.0 CD2 A:HIS338 4.8 45.8 1.0 O2G A:ANP501 4.8 38.1 1.0 CD A:GLU332 4.9 72.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase


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 Semet Substituted Catalytic Domain of Pyrrolysyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:71.8 occ:1.00 O2B A:ANP501 2.3 69.0 1.0 OG A:SER399 2.4 55.3 1.0 O1A A:ANP501 2.6 65.6 1.0 OE1 A:GLU396 2.8 54.2 1.0 OE2 A:GLU396 2.8 54.9 1.0 CD A:GLU396 3.1 55.3 1.0 O A:HOH645 3.2 49.4 1.0 O A:HOH648 3.3 53.4 1.0 PB A:ANP501 3.4 59.3 1.0 CB A:SER399 3.5 38.5 1.0 O3A A:ANP501 3.6 67.4 1.0 PA A:ANP501 3.7 62.0 1.0 N3B A:ANP501 3.7 66.8 1.0 C5' A:ANP501 4.4 67.9 1.0 CG A:GLU396 4.5 31.6 1.0 O5' A:ANP501 4.5 56.1 1.0 OD2 A:ASP389 4.5 51.6 1.0 CA A:SER399 4.7 39.3 1.0 O1B A:ANP501 4.8 59.2 1.0 O A:HOH691 4.8 58.7 1.0 O2A A:ANP501 4.8 50.2 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