Magnesium in PDB 2zce: Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Pyrrolysine and An Atp Analogue

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Pyrrolysine and An Atp Analogue:
6.1.1.26;

The structure of Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Pyrrolysine and An Atp Analogue, PDB code: 2zce was solved by T.Yanagisawa, R.Ishii, 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)	42.05 / 1.80
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.501, 104.501, 70.851, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Pyrrolysine and An Atp Analogue (pdb code 2zce). 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 Pyrrolysine and An Atp Analogue, PDB code: 2zce:
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 Pyrrolysine and An Atp Analogue


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 Pyrrolysine and An Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:62.5 occ:1.00 O A:HOH819 2.2 43.6 1.0 O1G A:ANP501 2.3 47.9 1.0 O A:HOH834 2.3 43.7 1.0 O1B A:ANP501 2.3 65.8 1.0 O A:HOH825 2.3 45.4 1.0 O A:HOH814 2.4 42.1 1.0 PB A:ANP501 3.4 57.5 1.0 PG A:ANP501 3.5 56.3 1.0 OE1 A:GLU283 3.5 84.5 1.0 NH1 A:ARG330 4.0 33.7 1.0 N3B A:ANP501 4.0 53.8 1.0 O A:HOH837 4.1 72.8 1.0 O3G A:ANP501 4.1 62.9 1.0 OE1 A:GLU332 4.2 44.4 1.0 O2B A:ANP501 4.2 61.9 1.0 NE2 A:HIS338 4.2 47.4 1.0 NE2 A:GLN287 4.2 47.6 1.0 CD A:GLU283 4.3 83.7 1.0 OE2 A:GLU283 4.4 82.0 1.0 OE1 A:GLN287 4.5 60.6 1.0 OE2 A:GLU332 4.5 46.4 1.0 CD2 A:HIS338 4.6 43.8 1.0 O3A A:ANP501 4.6 55.5 1.0 O2G A:ANP501 4.8 44.2 1.0 CD A:GLU332 4.8 40.2 1.0 CD A:GLN287 4.8 51.0 1.0 N7 A:ANP501 5.0 36.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Pyrrolysyl-Trna Synthetase in Complex with Pyrrolysine and An Atp Analogue


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 Pyrrolysine and An Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:49.1 occ:1.00 O2B A:ANP501 2.3 61.9 1.0 OG A:SER399 2.3 45.3 1.0 O1A A:ANP501 2.4 47.5 1.0 OE2 A:GLU396 2.5 41.1 1.0 OE1 A:GLU396 3.0 46.8 1.0 CD A:GLU396 3.1 46.5 1.0 PB A:ANP501 3.3 57.5 1.0 O3A A:ANP501 3.3 55.5 1.0 PA A:ANP501 3.3 44.8 1.0 CB A:SER399 3.4 41.1 1.0 N3B A:ANP501 3.5 53.8 1.0 O2A A:ANP501 4.1 39.4 1.0 OXT A:PYL601 4.3 80.3 1.0 O3' A:ANP501 4.4 36.4 1.0 OD2 A:ASP389 4.5 59.9 1.0 CG A:GLU396 4.5 40.1 1.0 CA A:SER399 4.5 39.8 1.0 O5' A:ANP501 4.6 40.7 1.0 O1B A:ANP501 4.7 65.8 1.0 O3G A:ANP501 4.8 62.9 1.0 C3' A:ANP501 4.8 44.7 1.0 PG A:ANP501 4.9 56.3 1.0 N A:SER399 4.9 39.0 1.0 C5' A:ANP501 4.9 39.2 1.0

T.Yanagisawa, R.Ishii, R.Fukunaga, T.Kobayashi, K.Sakamoto, S.Yokoyama. Crystallographic Studies on Multiple Conformational States of Active-Site Loops in Pyrrolysyl-Trna Synthetase J.Mol.Biol. V. 378 634 2008.
ISSN: ISSN 0022-2836
PubMed: 18387634
DOI: 10.1016/J.JMB.2008.02.045