Sodium in PDB 4jd5: Crystal Structure of Benzoylformate Decarboxylase Mutant L403E

All present enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E:
4.1.1.7;

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E, PDB code: 4jd5 was solved by W.R.P.Novak, F.H.Andrews, A.R.Tom, P.R.Gunderman, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.36 / 1.33
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.550, 95.790, 137.150, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 15.2

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E (pdb code 4jd5). 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 Crystal Structure of Benzoylformate Decarboxylase Mutant L403E, PDB code: 4jd5:

Sodium binding site 1 out of 1 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Benzoylformate Decarboxylase Mutant L403E within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:6.9 occ:0.50 O A:LEU118 2.4 6.7 1.0 O A:ARG120 2.5 4.7 0.7 O A:ARG120 2.7 8.9 0.3 O A:ASN117 2.8 7.0 1.0 C A:LEU118 3.3 6.3 1.0 O A:HOH737 3.3 10.7 0.5 C A:ARG120 3.6 6.0 0.7 C A:ARG120 3.7 8.2 0.3 CA A:LEU118 3.7 7.5 1.0 C A:ASN117 3.8 6.6 1.0 N A:ARG120 3.9 7.7 0.3 N A:ARG120 3.9 6.6 0.7 CA A:ARG120 4.2 8.4 0.3 CE A:MET79 4.2 10.0 0.5 N A:PRO119 4.2 7.0 1.0 N A:LEU118 4.3 6.3 1.0 CA A:ARG120 4.3 6.6 0.7 C A:PRO119 4.3 7.3 1.0 CB A:ARG120 4.5 9.4 0.3 CA A:PRO119 4.6 7.6 1.0 CB A:ARG120 4.7 7.3 0.7 N A:PRO121 4.7 7.5 1.0 CD A:PRO121 4.9 8.2 1.0 O A:PRO119 4.9 9.0 1.0

F.H.Andrews, A.R.Tom, P.R.Gunderman, W.R.Novak, M.J.Mcleish. A Bulky Hydrophobic Residue Is Not Required to Maintain the V-Conformation of Enzyme-Bound Thiamin Diphosphate. Biochemistry V. 52 3028 2013.
ISSN: ISSN 0006-2960
PubMed: 23607689
DOI: 10.1021/BI400368J