Magnesium in PDB 3vqv: Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Amppnp (Re-Refined)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Amppnp (Re-Refined):
6.1.1.26;

The structure of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Amppnp (Re-Refined), PDB code: 3vqv 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)	42.07 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.876, 104.876, 70.433, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Amppnp (Re-Refined) (pdb code 3vqv). 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 Amppnp (Re-Refined), PDB code: 3vqv:
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 Amppnp (Re-Refined)


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 Amppnp (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.4 occ:1.00 O A:HOH772 2.0 37.6 1.0 O2B A:ANP501 2.1 37.9 1.0 O A:HOH752 2.1 32.6 1.0 O2G A:ANP501 2.1 36.9 1.0 O A:HOH768 2.2 37.4 1.0 O A:HOH779 2.2 41.1 1.0 PG A:ANP501 3.4 35.8 1.0 PB A:ANP501 3.4 37.5 1.0 N3B A:ANP501 3.9 36.5 1.0 NH1 A:ARG330 4.0 35.6 1.0 NE2 A:HIS338 4.0 37.1 1.0 OE1 A:GLU283 4.0 66.7 1.0 O A:HOH694 4.0 39.9 1.0 O3G A:ANP501 4.0 38.1 1.0 O A:HOH678 4.1 52.7 1.0 OE1 A:GLU332 4.1 36.0 1.0 O A:HOH809 4.2 55.7 1.0 OE2 A:GLU283 4.2 66.9 1.0 OE2 A:GLU332 4.3 38.0 1.0 O1B A:ANP501 4.4 37.0 1.0 NE2 A:GLN287 4.4 38.8 1.0 O3A A:ANP501 4.4 36.4 1.0 CD A:GLU283 4.5 66.6 1.0 CD2 A:HIS338 4.5 35.5 1.0 OE1 A:GLN287 4.5 44.6 1.0 CD A:GLU332 4.7 38.4 1.0 O1G A:ANP501 4.7 35.3 1.0 N7 A:ANP501 4.9 31.3 1.0 CD A:GLN287 4.9 41.6 1.0

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


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 Amppnp (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:45.8 occ:1.00 OG A:SER399 2.2 37.3 1.0 O1B A:ANP501 2.3 37.0 1.0 O1A A:ANP501 2.4 37.5 1.0 OE2 A:GLU396 2.4 34.5 1.0 O A:HOH813 2.5 54.0 1.0 OE1 A:GLU396 2.8 40.8 1.0 CD A:GLU396 2.9 37.3 1.0 PB A:ANP501 3.3 37.5 1.0 CB A:SER399 3.4 34.9 1.0 PA A:ANP501 3.4 31.9 1.0 O3A A:ANP501 3.4 36.4 1.0 N3B A:ANP501 3.6 36.5 1.0 O A:HOH657 3.7 42.5 1.0 O A:HOH822 4.0 60.0 1.0 CG A:GLU396 4.3 34.5 1.0 O A:HOH650 4.4 60.8 1.0 O2A A:ANP501 4.4 33.9 1.0 OD2 A:ASP389 4.4 45.8 1.0 O3' A:ANP501 4.4 33.5 1.0 O A:HOH809 4.4 55.7 1.0 CA A:SER399 4.5 35.3 1.0 O5' A:ANP501 4.5 29.5 1.0 N A:SER399 4.6 33.6 1.0 O2B A:ANP501 4.7 37.9 1.0 C5' A:ANP501 4.7 31.6 1.0 C3' A:ANP501 4.8 30.9 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