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Sodium in PDB 1d7s: Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Dcs

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

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

Protein crystallography data

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Dcs, PDB code: 1d7s 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 / 2.05
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.880, 152.880, 86.360, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1d7s:

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Dcs 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 Dcs (pdb code 1d7s). 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 Dcs, PDB code: 1d7s:

Sodium binding site 1 out of 1 in 1d7s

Go back to Sodium Binding Sites List in 1d7s
Sodium binding site 1 out of 1 in the Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Dcs


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 Dcs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na435

b:16.5
occ:1.00
 O A:ALA95 2.4 45.9 1.0
O A:PRO99 2.5 31.3 1.0
O A:LEU102 2.6 34.2 1.0
O A:THR98 2.6 29.9 1.0
OG1 A:THR98 3.0 21.9 1.0
C A:PRO99 3.3 32.6 1.0
C A:THR98 3.4 33.4 1.0
C A:ALA95 3.6 40.4 1.0
C A:LEU102 3.7 29.4 1.0
N A:PRO100 4.0 30.9 1.0
CB A:THR98 4.1 26.4 1.0
N A:LEU102 4.1 21.1 1.0
CA A:PRO100 4.1 22.7 1.0
N A:PRO99 4.1 28.0 1.0
CB A:LEU102 4.2 18.5 1.0
CA A:THR98 4.2 25.7 1.0
CA A:ALA95 4.2 25.7 1.0
CA A:PRO99 4.2 23.2 1.0
N A:THR98 4.2 23.4 1.0
O A:HOH547 4.2 51.6 1.0
CA A:LEU102 4.2 25.3 1.0
N A:GLY101 4.6 25.6 1.0
C A:PRO100 4.7 25.4 1.0
N A:ASN96 4.7 26.2 1.0
N A:ASP103 4.8 20.9 1.0
CB A:ALA95 4.9 21.1 1.0
O A:LEU94 4.9 24.6 1.0
OD1 A:ASP103 5.0 28.1 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: Sun Oct 6 18:02:58 2024

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