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Sodium in PDB 4gm1: Crystal Structure of Benzoylformate Decarboxylase Mutant L403S

Enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403S

All present enzymatic activity of Crystal Structure of Benzoylformate Decarboxylase Mutant L403S:
4.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403S, PDB code: 4gm1 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) 23.01 / 1.26
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.519, 95.795, 137.162, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16

Other elements in 4gm1:

The structure of Crystal Structure of Benzoylformate Decarboxylase Mutant L403S also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403S (pdb code 4gm1). 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 L403S, PDB code: 4gm1:

Sodium binding site 1 out of 1 in 4gm1

Go back to Sodium Binding Sites List in 4gm1
Sodium binding site 1 out of 1 in the Crystal Structure of Benzoylformate Decarboxylase Mutant L403S


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 L403S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:6.5
occ:0.50
O A:LEU118 2.5 5.9 1.0
O A:ARG120 2.5 6.6 1.0
O A:ASN117 2.7 6.5 1.0
C A:LEU118 3.2 6.2 1.0
O A:HOH733 3.3 9.4 0.5
C A:ARG120 3.6 6.3 1.0
CA A:LEU118 3.7 6.3 1.0
C A:ASN117 3.8 5.8 1.0
N A:ARG120 3.9 6.2 1.0
N A:LEU118 4.2 5.6 1.0
CA A:ARG120 4.2 6.4 1.0
N A:PRO119 4.2 6.3 1.0
C A:PRO119 4.3 6.9 1.0
CE A:MET79 4.3 7.8 0.5
CA A:PRO119 4.6 7.0 1.0
CB A:ARG120 4.6 7.6 1.0
N A:PRO121 4.7 6.3 1.0
CD A:PRO121 4.9 7.4 1.0
O A:PRO119 4.9 8.0 1.0

Reference:

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
Page generated: Tue Dec 15 06:41:50 2020

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