Magnesium in PDB 1x55: Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue

All present enzymatic activity of Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue:
6.1.1.22;

The structure of Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue, PDB code: 1x55 was solved by W.Iwasaki, S.Sekine, 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)	30.33 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.212, 68.024, 75.604, 90.00, 117.35, 90.00
R / Rfree (%)	17.3 / 19.9

The binding sites of Magnesium atom in the Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue (pdb code 1x55). 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 Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue, PDB code: 1x55:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate 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 Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:16.1 occ:1.00 O A:HOH1028 2.3 10.9 1.0 OE1 A:GLU357 2.4 15.3 1.0 OAY A:NSS3002 2.4 12.0 1.0 O A:HOH1052 2.4 13.1 1.0 O A:HOH1033 2.5 11.7 1.0 O2 A:PO43001 2.6 19.4 1.0 CD A:GLU357 3.2 17.1 1.0 OE2 A:GLU357 3.4 20.4 1.0 SBE A:NSS3002 3.6 12.5 1.0 P A:PO43001 3.9 12.6 1.0 O A:HOH1087 3.9 17.7 1.0 OAX A:NSS3002 4.0 12.9 1.0 O3 A:PO43001 4.0 27.4 1.0 O A:HOH1004 4.2 12.7 1.0 OD2 A:ASP348 4.2 14.0 1.0 OD1 A:ASP348 4.2 14.7 1.0 O A:HOH1006 4.3 12.9 1.0 O4 A:PO43001 4.5 26.2 1.0 O3' A:NSS3002 4.5 12.2 1.0 MG A:MG2002 4.5 20.7 1.0 CA A:GLY360 4.5 13.2 1.0 CG A:GLU357 4.5 15.6 1.0 NAT A:NSS3002 4.6 11.0 1.0 CG A:ASP348 4.6 14.6 1.0 C3' A:NSS3002 4.6 12.3 1.0 O5' A:NSS3002 4.7 12.2 1.0 O A:HOH1062 4.8 18.3 1.0 NZ A:LYS330 4.8 11.8 1.0 O A:HOH1155 4.9 20.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate 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 Asparaginyl-Trna Synthetase From Pyrococcus Horikoshii Complexed with Asparaginyl-Adenylate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:20.7 occ:1.00 O A:HOH1122 2.3 23.8 1.0 O A:HOH1087 2.4 17.7 1.0 O A:HOH1048 2.4 20.1 1.0 O A:HOH1029 2.5 15.6 1.0 O A:HOH1155 2.5 20.3 1.0 O A:HOH1033 2.5 11.7 1.0 OD2 A:ASP303 3.7 25.0 1.0 O A:HOH1192 3.8 21.1 1.0 OD2 A:ASP348 4.0 14.0 1.0 NZ A:LYS330 4.1 11.8 1.0 O A:HOH1066 4.2 20.8 1.0 O A:HOH1062 4.3 18.3 1.0 O A:HOH1060 4.4 18.4 1.0 O A:HOH1110 4.5 24.9 1.0 MG A:MG2001 4.5 16.1 1.0 O A:HOH1052 4.5 13.1 1.0 O A:HOH1028 4.6 10.9 1.0 CD A:LYS330 4.6 12.1 1.0 O3 A:PO43001 4.7 27.4 1.0 O A:LEU304 4.7 20.1 1.0 CG A:ASP303 4.8 25.9 1.0 CE2 A:TYR325 4.9 15.5 1.0 O A:ILE329 4.9 15.5 1.0 CE A:LYS330 5.0 11.2 1.0

W.Iwasaki, S.Sekine, C.Kuroishi, S.Kuramitsu, M.Shirouzu, S.Yokoyama. Structural Basis of the Water-Assisted Asparagine Recognition By Asparaginyl-Trna Synthetase. J.Mol.Biol. V. 360 329 2006.
ISSN: ISSN 0022-2836
PubMed: 16753178
DOI: 10.1016/J.JMB.2006.04.068