Sodium in PDB 6vsp: Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A

The structure of Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A, PDB code: 6vsp was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.675, 108.675, 82.948, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 22.2

The binding sites of Sodium atom in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A (pdb code 6vsp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A, PDB code: 6vsp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:38.0 occ:1.00 O A:ASN187 2.2 19.7 1.0 OD1 A:ASN190 2.4 31.5 1.0 O A:HOH401 2.4 12.9 0.5 O A:HOH506 2.7 21.6 1.0 O A:HOH646 2.8 33.5 1.0 O3B A:NAD302 3.3 46.9 0.5 C A:ASN187 3.3 18.2 1.0 O A:HOH451 3.5 25.4 0.7 CG A:ASN190 3.5 27.9 1.0 O A:HOH630 3.6 46.4 1.0 N A:GLY191 3.8 22.3 1.0 CA A:ASN187 4.0 17.9 1.0 O A:HOH652 4.1 31.4 1.0 N A:ASN190 4.1 21.4 1.0 ND2 A:ASN190 4.2 31.1 1.0 O2B A:NAD302 4.3 47.1 0.5 C3B A:NAD302 4.3 46.5 0.5 C A:MET188 4.4 16.7 0.5 O A:MET188 4.4 16.5 0.5 C A:MET188 4.4 16.9 0.5 O A:MET188 4.4 16.6 0.5 N A:MET188 4.4 17.0 0.5 N A:MET188 4.4 16.8 0.5 C A:ASN190 4.5 21.3 1.0 CB A:ASN187 4.5 17.1 1.0 CA A:ASN190 4.6 22.4 1.0 CA A:GLY191 4.6 23.0 1.0 CB A:ASN190 4.6 25.0 1.0 O A:HOH403 4.6 20.1 0.5 CA A:MET188 4.7 16.8 0.5 CA A:MET188 4.7 16.4 0.5 N A:THR189 4.7 16.8 1.0 C2B A:NAD302 4.9 46.7 0.5 O A:HOH527 4.9 23.9 1.0 C A:THR189 5.0 18.4 1.0

Sodium binding site 2 out of 2 in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:34.0 occ:0.50 O B:VAL237 2.8 17.1 1.0 N B:SER182 2.8 23.8 1.0 OG B:SER182 2.8 36.0 1.0 O B:LEU183 3.1 43.9 1.0 CB B:ALA210 3.2 33.3 1.0 O B:SER182 3.3 37.9 1.0 C B:SER182 3.4 35.8 1.0 CA B:SER182 3.4 30.5 1.0 CB B:PRO181 3.5 20.0 1.0 CA B:PRO181 3.6 18.8 1.0 C B:PRO181 3.6 21.3 1.0 CE2 A:PHE229 3.7 23.5 1.0 CB B:SER182 3.7 33.4 1.0 C B:LEU183 3.8 41.7 1.0 C B:VAL237 3.9 17.4 1.0 CG2 B:VAL184 3.9 39.8 1.0 CD2 A:PHE229 4.0 20.4 1.0 N B:LEU183 4.0 42.9 1.0 CA B:ASP238 4.3 19.8 1.0 N B:ALA210 4.4 30.5 1.0 CA B:ALA210 4.4 33.1 1.0 N B:VAL184 4.5 38.6 1.0 N B:ASP238 4.5 19.5 1.0 CA B:LEU183 4.6 49.4 1.0 CZ A:PHE229 4.7 23.3 1.0 CG2 B:VAL215 4.7 21.6 1.0 O B:PRO181 4.8 20.6 1.0 CA B:VAL184 4.8 37.7 1.0 CB B:VAL184 5.0 37.5 1.0

V.Subramanian, V.V.Lunin, S.J.Farmer, M.Alahuhta, K.T.Moore, A.Ho, Y.B.Chaudhari, M.Zhang, M.E.Himmel, S.R.Decker. Phylogenetics-Based Identification and Characterization of A Superior 2,3-Butanediol Dehydrogenase For Zymomonas Mobilis Expression. Biotechnol Biofuels V. 13 186 2020.
ISSN: ESSN 1754-6834
PubMed: 33292448
DOI: 10.1186/S13068-020-01820-X