Sodium in PDB 5kwe: Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N

The structure of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N, PDB code: 5kwe was solved by M.Dal Lago, A.C.Terwisschavvan Scheltinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.744, 70.126, 118.342, 90.00, 100.72, 90.00
R / Rfree (%)	13.8 / 16.6

The structure of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N (pdb code 5kwe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N, PDB code: 5kwe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:18.4 occ:1.00 O A:HOH623 2.4 29.9 1.0 O A:HOH666 2.4 32.4 1.0 OG A:SER55 2.4 13.4 1.0 O A:HOH615 2.4 23.4 1.0 O A:HOH474 2.5 13.6 1.0 O A:HOH485 2.5 19.2 1.0 CB A:SER55 3.5 9.9 1.0 OE1 A:GLU56 4.1 16.1 1.0 N A:SER55 4.1 11.5 1.0 O A:HOH509 4.2 22.7 1.0 O A:HOH657 4.2 26.6 1.0 O A:HOH626 4.3 23.6 1.0 OE2 A:GLU56 4.4 13.2 1.0 O A:HOH681 4.4 30.5 1.0 CA A:SER55 4.4 11.6 1.0 O A:HOH491 4.5 17.1 1.0 O A:HOH675 4.5 18.8 1.0 CD A:GLU56 4.5 15.5 1.0 O A:HOH500 4.6 19.4 1.0

Sodium binding site 2 out of 4 in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:24.1 occ:1.00 O B:HOH609 2.3 20.4 1.0 O B:HOH639 2.4 25.0 1.0 OG B:SER55 2.5 15.2 1.0 O B:HOH561 2.5 14.6 1.0 O B:HOH469 2.5 22.0 1.0 CB B:SER55 3.4 10.8 1.0 N B:SER55 4.1 11.6 1.0 O B:HOH679 4.1 31.1 1.0 O B:HOH690 4.3 17.9 1.0 OE1 B:GLU56 4.3 15.9 1.0 CA B:SER55 4.4 10.2 1.0 O B:HOH481 4.4 22.7 1.0 OE2 B:GLU56 4.5 12.9 1.0 O B:HOH424 4.5 25.4 1.0 O B:HOH528 4.6 24.2 1.0 CD B:GLU56 4.7 13.2 1.0

Sodium binding site 3 out of 4 in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:19.3 occ:1.00 O C:HOH641 2.3 29.1 1.0 O C:HOH499 2.4 19.2 1.0 OG C:SER55 2.4 13.5 1.0 O C:HOH631 2.4 22.2 1.0 O C:HOH684 2.5 24.9 1.0 O C:HOH463 2.6 13.4 1.0 CB C:SER55 3.5 11.8 1.0 OE1 C:GLU56 4.1 15.8 1.0 N C:SER55 4.1 9.5 1.0 O C:HOH444 4.2 21.0 1.0 O C:HOH676 4.3 29.1 1.0 O C:HOH647 4.3 27.6 1.0 O C:HOH679 4.3 28.0 1.0 OE2 C:GLU56 4.4 11.5 1.0 CA C:SER55 4.4 9.8 1.0 O C:HOH698 4.4 19.4 1.0 O C:HOH476 4.5 15.7 1.0 CD C:GLU56 4.6 13.5 1.0 O C:HOH538 4.6 19.0 1.0

Sodium binding site 4 out of 4 in the Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Thermostable Mutant of Halohydrin Dehalogenase Hhec - C153N within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:23.5 occ:1.00 O D:HOH632 2.3 25.2 1.0 O D:HOH417 2.4 25.6 1.0 OG D:SER55 2.4 16.6 1.0 O D:HOH538 2.5 16.0 1.0 CB D:SER55 3.4 12.6 1.0 N D:SER55 4.1 11.2 1.0 OE1 D:GLU56 4.2 15.9 1.0 O D:HOH695 4.2 31.8 1.0 CA D:SER55 4.3 11.4 1.0 O D:HOH491 4.3 20.7 1.0 O D:HOH421 4.4 24.9 1.0 OE2 D:GLU56 4.5 12.6 1.0 O D:HOH467 4.5 22.8 1.0 CD D:GLU56 4.6 16.2 1.0

H.Arabnejad, M.Dal Lago, P.A.Jekel, R.J.Floor, A.W.H.Thunnissen, A.C.Terwisscha Van Scheltinga, H.J.Wijma, D.B.Janssen. A Robust Cosolvent-Compatible Halohydrin Dehalogenase By Computational Library Design. Protein Eng. Des. Sel. V. 30 173 2017.
ISSN: ESSN 1741-0134
PubMed: 27999093
DOI: 10.1093/PROTEIN/GZW068