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Sodium in PDB 1d7r: Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA

Enzymatic activity of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA

All present enzymatic activity of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA:
4.1.1.64;

Protein crystallography data

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA, PDB code: 1d7r was solved by V.N.Malashkevich, M.D.Toney, P.Strop, J.Keller, J.N.Jansonius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.650, 152.650, 86.220, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1d7r:

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA (pdb code 1d7r). 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 the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA, PDB code: 1d7r:

Sodium binding site 1 out of 1 in 1d7r

Go back to Sodium Binding Sites List in 1d7r
Sodium binding site 1 out of 1 in the Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA


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 the Complex of 2,2-Dialkylglycine Decarboxylase with 5PA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na435

b:18.3
occ:1.00
 O A:ALA95 2.5 37.2 1.0
O A:THR98 2.5 26.2 1.0
O A:PRO99 2.7 27.3 1.0
O A:LEU102 2.7 24.0 1.0
OG1 A:THR98 2.9 19.3 1.0
C A:THR98 3.3 29.6 1.0
C A:PRO99 3.4 30.4 1.0
C A:ALA95 3.6 29.3 1.0
C A:LEU102 3.8 22.8 1.0
CB A:THR98 3.9 15.0 1.0
CA A:THR98 4.0 26.1 1.0
N A:PRO99 4.0 22.8 1.0
N A:PRO100 4.0 32.3 1.0
N A:THR98 4.1 22.3 1.0
N A:LEU102 4.1 20.7 1.0
CA A:PRO100 4.1 23.4 1.0
CA A:ALA95 4.2 24.8 1.0
CA A:PRO99 4.2 19.9 1.0
CB A:LEU102 4.2 19.7 1.0
CA A:LEU102 4.3 25.5 1.0
N A:GLY101 4.5 27.4 1.0
O A:HOH547 4.6 35.0 1.0
C A:PRO100 4.6 23.9 1.0
N A:ASN96 4.7 21.2 1.0
O A:LEU94 4.7 24.0 1.0
CB A:ALA95 4.9 26.4 1.0
N A:ASP103 5.0 18.5 1.0
C A:ASN96 5.0 35.1 1.0
OD1 A:ASP103 5.0 23.9 1.0

Reference:

V.N.Malashkevich, P.Strop, J.W.Keller, J.N.Jansonius, M.D.Toney. Crystal Structures of Dialkylglycine Decarboxylase Inhibitor Complexes. J.Mol.Biol. V. 294 193 1999.
ISSN: ISSN 0022-2836
PubMed: 10556038
DOI: 10.1006/JMBI.1999.3254
Page generated: Tue Dec 15 05:22:57 2020

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