Sodium in PDB 6xex: Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A/V139Q

The structure of Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A/V139Q, PDB code: 6xex 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)	42.03 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.800, 108.800, 83.108, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 21

The binding sites of Sodium atom in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A/V139Q (pdb code 6xex). 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/V139Q, PDB code: 6xex:
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/V139Q


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/V139Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:37.9 occ:1.00 O A:ASN187 2.3 20.2 1.0 O A:HOH621 2.4 21.9 0.7 OD1 A:ASN190 2.5 30.6 1.0 O A:HOH631 2.7 36.3 1.0 O A:HOH485 2.7 25.2 1.0 C A:ASN187 3.5 18.6 1.0 CG A:ASN190 3.6 29.5 1.0 O A:HOH421 3.8 25.0 0.7 O A:HOH621 3.9 17.4 0.3 N A:GLY191 3.9 20.7 1.0 O A:HOH639 4.0 29.7 1.0 CA A:ASN187 4.2 17.7 1.0 N A:ASN190 4.2 22.4 1.0 ND2 A:ASN190 4.2 31.7 1.0 C A:MET188 4.3 16.7 1.0 O A:MET188 4.3 16.9 1.0 N A:MET188 4.4 17.7 1.0 CA A:GLY191 4.6 21.1 1.0 C A:ASN190 4.6 21.6 1.0 CA A:MET188 4.6 17.8 1.0 N A:THR189 4.6 18.3 1.0 CB A:ASN187 4.6 18.2 1.0 CA A:ASN190 4.7 23.8 1.0 CB A:ASN190 4.7 24.8 1.0 O A:HOH484 4.7 24.6 1.0 O A:HOH638 4.7 27.0 1.0

Sodium binding site 2 out of 2 in the Structure of Serratia Marcescens 2,3-Butanediol Dehydrogenase Mutant Q247A/V139Q


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/V139Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:46.0 occ:1.00 O B:LEU183 2.0 30.4 1.0 OG B:SER182 2.6 21.3 1.0 N B:ALA210 3.0 25.0 1.0 C B:LEU183 3.1 25.2 1.0 N B:LEU183 3.2 25.2 1.0 CA B:ALA209 3.3 27.3 1.0 CB B:SER182 3.4 23.3 1.0 C B:SER182 3.5 23.4 1.0 CB B:ALA209 3.6 31.0 1.0 C B:ALA209 3.6 27.1 1.0 CA B:LEU183 3.6 30.9 1.0 CB B:ALA210 3.9 26.8 1.0 CD1 B:ILE204 4.0 26.6 1.0 CA B:SER182 4.0 21.9 1.0 CA B:ALA210 4.1 27.5 1.0 O B:SER182 4.1 20.4 1.0 N B:VAL184 4.2 27.8 1.0 CB B:LEU183 4.3 37.6 1.0 CE2 A:PHE229 4.5 22.2 1.0 CA B:VAL184 4.5 27.5 1.0 N B:ALA209 4.5 26.6 1.0 CZ A:PHE229 4.6 22.0 1.0 O B:ARG208 4.7 26.6 1.0 O B:HOH494 4.8 43.3 1.0 O B:ALA210 4.9 26.9 1.0 O B:ALA209 4.9 24.7 1.0 N B:SER182 4.9 19.9 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