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

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

The structure of Crystal Structure of the Catalytic Domain of Pyrrolysyl- Trna Synthetase in Complex with Boclys and An Atp Analogue, PDB code: 2zin was solved by T.Yanagisawa, 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)	34.28 / 1.79
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.710, 104.710, 70.550, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Pyrrolysyl- Trna Synthetase in Complex with Boclys and An Atp Analogue (pdb code 2zin). 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 An Atp Analogue, PDB code: 2zin:
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 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 Boclys and An Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:43.7 occ:1.00 O1G A:ANP501 2.1 38.6 1.0 O1B A:ANP501 2.2 40.6 1.0 O A:HOH2161 2.2 34.3 1.0 O A:HOH2188 2.3 35.6 1.0 O A:HOH2141 2.3 42.2 1.0 O A:HOH2193 2.3 46.5 1.0 PB A:ANP501 3.3 43.6 1.0 PG A:ANP501 3.3 39.4 1.0 N3B A:ANP501 3.7 38.5 1.0 NH1 A:ARG330 3.8 33.3 1.0 O3G A:ANP501 4.0 47.6 1.0 O A:HOH2076 4.0 59.2 1.0 O A:HOH2225 4.0 49.0 1.0 NE2 A:HIS338 4.1 40.5 1.0 OE1 A:GLU332 4.2 38.2 1.0 OE1 A:GLU283 4.2 89.1 1.0 O2B A:ANP501 4.3 48.1 1.0 O3A A:ANP501 4.4 44.7 1.0 CD2 A:HIS338 4.4 35.7 1.0 NE2 A:GLN287 4.4 39.6 1.0 OE2 A:GLU332 4.4 41.6 1.0 OE1 A:GLN287 4.5 50.1 1.0 OE2 A:GLU283 4.5 82.5 1.0 O2G A:ANP501 4.6 35.9 1.0 CD A:GLU283 4.6 86.9 1.0 N7 A:ANP501 4.7 33.4 1.0 CD A:GLU332 4.7 42.7 1.0 CD A:GLN287 4.9 44.0 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 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 Boclys and An Atp Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:47.5 occ:1.00 O2B A:ANP501 2.2 48.1 1.0 OG A:SER399 2.3 44.5 1.0 O A:HOH2060 2.3 60.5 1.0 O1A A:ANP501 2.4 43.6 1.0 OE2 A:GLU396 2.6 39.7 1.0 OE1 A:GLU396 3.1 52.9 1.0 CD A:GLU396 3.2 51.2 1.0 CB A:SER399 3.2 43.4 1.0 O3A A:ANP501 3.3 44.7 1.0 PB A:ANP501 3.3 43.6 1.0 PA A:ANP501 3.4 39.9 1.0 O A:HOH2057 3.6 56.0 1.0 N3B A:ANP501 3.7 38.5 1.0 O2A A:ANP501 4.4 37.3 1.0 CA A:SER399 4.5 41.0 1.0 N A:LBY601 4.5 61.7 1.0 OD2 A:ASP389 4.5 60.5 1.0 O3' A:ANP501 4.5 38.8 1.0 CG A:GLU396 4.6 38.5 1.0 O5' A:ANP501 4.6 37.6 1.0 O1B A:ANP501 4.7 40.6 1.0 C5' A:ANP501 4.8 35.2 1.0 N A:SER399 4.8 40.9 1.0 C3' A:ANP501 4.9 40.2 1.0

T.Yanagisawa, R.Ishii, R.Fukunaga, T.Kobayashi, K.Sakamoto, S.Yokoyama. Multistep Engineering of Pyrrolysyl-Trna Synthetase to Genetically Encode N(Varepsilon)-(O-Azidobenzyloxycarbonyl) Lysine For Site-Specific Protein Modification Chem.Biol. V. 15 1187 2008.
ISSN: ISSN 1074-5521
PubMed: 19022179
DOI: 10.1016/J.CHEMBIOL.2008.10.004