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Sodium in PDB 1dgd: An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase

Enzymatic activity of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase

All present enzymatic activity of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase:
4.1.1.64;

Protein crystallography data

The structure of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase, PDB code: 1dgd was solved by E.Hohenester, J.N.Jansonius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.700, 152.700, 86.600, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase (pdb code 1dgd). 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 An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase, PDB code: 1dgd:

Sodium binding site 1 out of 1 in 1dgd

Go back to Sodium Binding Sites List in 1dgd
Sodium binding site 1 out of 1 in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na435

b:18.9
occ:1.00
 O A:PRO99 2.2 24.4 1.0
O A:HOH540 2.3 29.1 1.0
O A:THR98 2.4 26.9 1.0
O A:LEU102 2.4 24.8 1.0
O A:ALA95 2.4 21.3 1.0
OG1 A:THR98 2.9 18.2 1.0
C A:THR98 3.1 25.8 1.0
C A:PRO99 3.1 24.8 1.0
C A:LEU102 3.5 23.9 1.0
C A:ALA95 3.6 20.8 1.0
CB A:THR98 3.7 19.0 1.0
N A:PRO99 3.7 26.0 1.0
CA A:THR98 3.8 22.5 1.0
CB A:LEU102 3.8 21.7 1.0
N A:LEU102 3.9 24.5 1.0
N A:PRO100 3.9 25.1 1.0
N A:THR98 3.9 23.1 1.0
CA A:PRO99 3.9 25.1 1.0
CA A:LEU102 4.0 23.3 1.0
CA A:PRO100 4.1 23.6 1.0
CA A:ALA95 4.2 20.2 1.0
C A:PRO100 4.5 23.3 1.0
N A:GLY101 4.6 22.5 1.0
O A:LEU94 4.6 23.0 1.0
N A:ASN96 4.7 21.5 1.0
N A:ASP103 4.7 22.9 1.0
C A:ASN96 4.8 24.9 1.0
CA A:ASN96 4.9 22.4 1.0
CB A:ALA95 5.0 19.8 1.0
CD A:PRO100 5.0 23.6 1.0

Reference:

E.Hohenester, J.W.Keller, J.N.Jansonius. An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase. Biochemistry V. 33 13561 1994.
ISSN: ISSN 0006-2960
PubMed: 7947767
DOI: 10.1021/BI00250A008
Page generated: Tue Dec 15 05:23:05 2020

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