Magnesium in PDB 4rrf: Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA

All present enzymatic activity of Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA:
6.1.1.3;

The structure of Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA, PDB code: 4rrf was solved by S.Ahmad, A.S.K.Yerabham, V.Kamarthapu, R.Sankaranarayanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.595, 52.813, 98.315, 90.00, 104.04, 90.00
R / Rfree (%)	19.4 / 23.9

The structure of Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA (pdb code 4rrf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA, PDB code: 4rrf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:34.3 occ:1.00 O C:HOH322 1.8 31.4 1.0 O B:HOH363 2.0 36.2 1.0 O B:HOH333 2.0 33.5 1.0 O C:HOH329 2.1 25.2 1.0 O C:HOH355 2.3 28.2 1.0 OD2 C:ASP13 4.3 25.6 1.0 OD1 C:ASP13 4.3 24.2 1.0 NZ B:LYS20 4.3 49.1 1.0 O C:LYS129 4.4 24.1 1.0 O B:HOH353 4.4 35.9 1.0 O C:HOH312 4.5 24.5 1.0 CG C:ASP13 4.7 22.4 1.0 CB B:ALA123 4.8 18.0 1.0 CA C:LYS129 4.9 21.8 1.0

Magnesium binding site 2 out of 2 in the Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Editing Domain of Threonyl-Trna Synthetase From Methanococcus Jannaschii with L-SER3AA within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:30.3 occ:1.00 O D:HOH316 1.9 24.2 1.0 O D:HOH350 2.0 30.1 1.0 O D:HOH305 2.1 31.5 1.0 O D:HOH366 2.1 31.4 1.0 O D:HOH333 2.2 29.1 1.0 O A:HOH627 2.5 32.9 1.0 OD1 D:ASP13 4.1 23.6 1.0 OD2 D:ASP13 4.1 20.5 1.0 CG D:ASP13 4.5 22.4 1.0 O D:HOH303 4.5 24.4 1.0 O D:LYS129 4.6 23.2 1.0 CA D:LYS129 4.8 21.1 1.0 O A:HOH646 4.8 32.7 1.0 NZ A:LYS20 4.9 42.8 1.0

S.Ahmad, S.Muthukumar, S.K.Kuncha, S.B.Routh, A.S.Yerabham, T.Hussain, V.Kamarthapu, S.P.Kruparani, R.Sankaranarayanan. Specificity and Catalysis Hardwired at the Rna-Protein Interface in A Translational Proofreading Enzyme. Nat Commun V. 6 7552 2015.
ISSN: ESSN 2041-1723
PubMed: 26113036
DOI: 10.1038/NCOMMS8552