Sodium in PDB 5kvc: Thermostable Mutant of Halohydrin Dehalogenase (Hhec)

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

Resolution Low / High (Å)	41.86 / 1.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.839, 81.839, 155.609, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 19.6

The structure of Thermostable Mutant of Halohydrin Dehalogenase (Hhec) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

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

Sodium binding site 1 out of 2 in the Thermostable Mutant of Halohydrin Dehalogenase (Hhec)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:35.3 occ:1.00 O A:HOH435 2.4 39.4 1.0 OG A:SER55 2.4 28.9 1.0 O A:HOH579 2.4 46.3 1.0 O A:HOH587 2.5 41.5 1.0 O A:HOH410 2.5 29.4 1.0 CB A:SER55 3.4 24.6 1.0 N A:SER55 4.1 28.0 1.0 O A:HOH617 4.2 35.3 1.0 OE1 A:GLU56 4.3 30.8 1.0 OE2 A:GLU56 4.3 25.4 1.0 O A:HOH618 4.3 40.5 1.0 CA A:SER55 4.3 25.7 1.0 O A:HOH433 4.4 38.9 1.0 O A:HOH509 4.4 38.2 1.0 CD A:GLU56 4.5 25.5 1.0 O A:HOH515 4.6 36.0 1.0

Sodium binding site 2 out of 2 in the Thermostable Mutant of Halohydrin Dehalogenase (Hhec)


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:31.2 occ:1.00 O B:HOH563 2.3 35.6 1.0 OG B:SER55 2.4 26.3 1.0 O B:HOH597 2.4 40.4 1.0 O B:HOH454 2.4 31.5 1.0 O B:HOH566 2.5 35.1 1.0 O B:HOH438 2.5 26.3 1.0 CB B:SER55 3.5 25.2 1.0 OE1 B:GLU56 4.1 28.4 1.0 O B:HOH413 4.1 31.2 1.0 N B:SER55 4.1 21.4 1.0 O B:HOH602 4.1 38.1 1.0 OE2 B:GLU56 4.3 25.0 1.0 CA B:SER55 4.4 22.1 1.0 O B:HOH458 4.4 37.3 1.0 O B:HOH595 4.4 31.2 1.0 O B:HOH487 4.5 30.9 1.0 CD B:GLU56 4.5 28.9 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