Sodium in PDB 4k0d: Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942

The structure of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942, PDB code: 4k0d was solved by P.R.Pokkuluri, J.C.Mack, J.Bearden, E.Rakowski, M.Schiffer, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.693, 75.184, 51.031, 90.00, 105.18, 90.00
R / Rfree (%)	19.8 / 25.2

The structure of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	5 atoms

The binding sites of Sodium atom in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 (pdb code 4k0d). 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 Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942, PDB code: 4k0d:

Sodium binding site 1 out of 1 in the Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Periplasmic Sensor Domain of Sensor Histidine Kinase, ADEH_2942 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:38.9 occ:1.00 OE1 B:GLU153 2.4 39.2 1.0 NE2 A:HIS175 2.9 42.4 0.4 OE2 B:GLU153 3.0 52.1 1.0 CD2 A:HIS175 3.0 41.5 0.4 CD B:GLU153 3.1 47.9 1.0 O B:HOH303 3.1 50.1 1.0 NH1 B:ARG160 4.0 37.3 0.6 CE1 A:HIS175 4.1 42.6 0.4 CG A:HIS175 4.3 41.3 0.4 CG B:GLU153 4.5 41.8 1.0 O A:ALA171 4.6 34.3 1.0 CB A:ALA171 4.6 33.0 1.0 ND1 A:HIS175 4.8 44.5 0.4

P.R.Pokkuluri, J.Dwulit-Smith, N.E.Duke, R.Wilton, J.C.Mack, J.Bearden, E.Rakowski, G.Babnigg, H.Szurmant, A.Joachimiak, M.Schiffer. Analysis of Periplasmic Sensor Domains From Anaeromyxobacter Dehalogenans 2CP-C: Structure of One Sensor Domain From A Histidine Kinase and Another From A Chemotaxis Protein. Microbiologyopen V. 2 766 2013.
PubMed: 23897711
DOI: 10.1002/MBO3.112