Sodium in PDB 3rc2: Crystal Structure of KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation

The structure of Crystal Structure of KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation, PDB code: 3rc2 was solved by H.M.Holden, R.L.Kubiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.087, 104.822, 144.469, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.3

The structure of Crystal Structure of KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation (pdb code 3rc2). 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 KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation, PDB code: 3rc2:

Sodium binding site 1 out of 1 in the Crystal Structure of KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation


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 KIJD10, A 3-Ketoreductase From Actinomadura Kijaniata in Complex with Tdp-Benzene and Nadp; Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na339 b:16.8 occ:1.00 OD2 A:ASP328 2.6 21.6 1.0 O A:ALA326 2.7 20.6 1.0 O A:THR324 2.7 30.5 1.0 O A:ARG323 2.9 28.8 1.0 O A:HOH540 2.9 40.6 1.0 C A:THR324 3.4 27.9 1.0 O A:HOH404 3.6 30.0 1.0 CG A:ASP328 3.7 20.7 1.0 N A:ALA326 3.8 23.0 1.0 C A:ALA326 3.8 23.6 1.0 CA A:THR324 3.9 29.6 1.0 C A:ARG323 4.0 27.4 1.0 CA A:ALA326 4.3 22.3 1.0 OD1 A:ASP328 4.3 22.6 1.0 N A:THR324 4.3 28.6 1.0 C A:GLY325 4.3 22.1 1.0 N A:GLY325 4.3 25.1 1.0 CB A:ALA326 4.4 22.9 1.0 CA A:GLY325 4.7 25.3 1.0 O A:HOH457 4.8 24.0 1.0 CB A:ASP328 4.9 23.6 1.0 N A:ARG327 5.0 22.0 1.0 N A:ASP328 5.0 20.9 1.0

R.L.Kubiak, H.M.Holden. Combined Structural and Functional Investigation of A C-3''-Ketoreductase Involved in the Biosynthesis of Dtdp-L-Digitoxose. Biochemistry V. 50 5905 2011.
ISSN: ISSN 0006-2960
PubMed: 21598943
DOI: 10.1021/BI200514B