Sodium in PDB 4xj5: Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form

The structure of Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj5 was solved by K.Kato, R.Ishii, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.950, 50.060, 72.270, 90.00, 93.40, 90.00
R / Rfree (%)	17.5 / 19.3

The structure of Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form (pdb code 4xj5). 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 Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form, PDB code: 4xj5:

Sodium binding site 1 out of 1 in the Crystal Structure of Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound 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 Vibrio Cholerae Dncv 3'-Deoxy Gtp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:25.2 occ:1.00 O A:LYS369 2.8 17.7 1.0 O A:HOH1181 2.8 23.8 1.0 NE1 A:TRP289 2.9 16.7 1.0 N A:LEU373 3.6 16.1 1.0 C A:LYS369 3.7 19.2 1.0 CD1 A:ILE376 3.7 17.7 1.0 CE2 A:TRP289 3.7 16.1 1.0 CA A:LEU373 3.7 15.5 1.0 CB A:LEU373 3.8 15.4 1.0 CZ2 A:TRP289 3.8 17.3 1.0 CD A:GLN293 3.9 18.7 1.0 CD1 A:TRP289 4.0 17.1 1.0 CA A:LYS369 4.0 17.8 1.0 OE1 A:GLN293 4.1 21.4 1.0 CB A:ARG372 4.1 18.9 1.0 CB A:LYS369 4.1 19.8 1.0 NE2 A:GLN293 4.2 18.6 1.0 C A:ARG372 4.2 16.4 1.0 CG A:GLN293 4.3 18.0 1.0 CD1 A:LEU373 4.4 18.1 1.0 CG A:LYS369 4.5 33.2 1.0 CA A:ARG372 4.6 16.6 1.0 CG A:LEU373 4.7 14.8 1.0 N A:LEU370 4.8 16.7 1.0 O A:HOH1172 4.8 40.6 1.0 O A:ARG372 4.9 18.7 1.0 CG1 A:ILE376 5.0 15.5 1.0 CD2 A:TRP289 5.0 16.9 1.0

K.Kato, R.Ishii, S.Hirano, R.Ishitani, O.Nureki. Structural Basis For the Catalytic Mechanism of Dncv, Bacterial Homolog of Cyclic Gmp-Amp Synthase Structure V. 23 843 2015.
ISSN: ISSN 0969-2126
PubMed: 25865248
DOI: 10.1016/J.STR.2015.01.023