Sodium in PDB 3dsq: Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase

The structure of Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase, PDB code: 3dsq was solved by M.M.Lee, M.K.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.32 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.183, 68.467, 96.288, 90.00, 136.36, 90.00
R / Rfree (%)	23.5 / 28.3

The structure of Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase (pdb code 3dsq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase, PDB code: 3dsq:

Sodium binding site 1 out of 1 in the Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na289 b:53.5 occ:1.00 O B:GLN167 2.7 40.4 1.0 O B:GLN164 3.0 53.5 1.0 OG B:SER163 3.0 42.8 1.0 C B:GLN167 3.8 38.3 1.0 C B:GLN164 3.9 52.9 1.0 CB B:SER163 4.0 47.6 1.0 O B:HOH304 4.3 29.1 1.0 CA B:HIS168 4.4 31.0 1.0 CA B:GLY165 4.4 50.9 1.0 N B:HIS168 4.5 35.4 1.0 N B:GLN164 4.5 52.1 1.0 N B:GLY165 4.6 52.5 1.0 N B:GLN167 4.7 43.8 1.0 CA B:GLN167 4.8 41.4 1.0 C B:GLY165 4.8 50.2 1.0 C B:SER163 4.8 51.3 1.0 CA B:GLN164 4.9 53.9 1.0 O B:GLY165 5.0 51.1 1.0

M.M.Lee, R.Jiang, R.Jain, R.C.Larue, J.Krzycki, M.K.Chan. Structure of Desulfitobacterium Hafniense Pylsc, A Pyrrolysyl-Trna Synthetase. Biochem.Biophys.Res.Commun. V. 374 470 2008.
ISSN: ISSN 0006-291X
PubMed: 18656445
DOI: 10.1016/J.BBRC.2008.07.074