Sodium in PDB 4nd7: Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form

All present enzymatic activity of Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form:
6.1.1.1;

The structure of Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form, PDB code: 4nd7 was solved by R.B.Cooley, C.M.Driggers, P.A.Karplus, R.A.Mehl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.770, 101.770, 72.280, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27.8

The binding sites of Sodium atom in the Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form (pdb code 4nd7). 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 Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form, PDB code: 4nd7:

Sodium binding site 1 out of 1 in the Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Apo 3-Nitro-Tyrosine Trna Synthetase (5B) in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:37.8 occ:1.00 OD2 A:ASP27 2.4 82.6 1.0 O A:HOH1103 2.7 42.1 1.0 CG A:ASP27 3.6 76.1 1.0 OD1 A:ASP27 4.2 72.7 1.0 CB A:ASP27 4.7 70.3 1.0

R.B.Cooley, J.L.Feldman, C.M.Driggers, T.A.Bundy, A.L.Stokes, P.A.Karplus, R.A.Mehl. Structural Basis of Improved Second-Generation 3-Nitro-Tyrosine Trna Synthetases. Biochemistry V. 53 1916 2014.
ISSN: ISSN 0006-2960
PubMed: 24611875
DOI: 10.1021/BI5001239