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Sodium in PDB 5lth: Crystal Structure of the Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate

Protein crystallography data

The structure of Crystal Structure of the Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate, PDB code: 5lth was solved by M.Ortmayer, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.01 / 1.76
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.380, 80.380, 144.790, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Other elements in 5lth:

The structure of Crystal Structure of the Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate (pdb code 5lth). 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 Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate, PDB code: 5lth:

Sodium binding site 1 out of 1 in 5lth

Go back to Sodium Binding Sites List in 5lth
Sodium binding site 1 out of 1 in the Crystal Structure of the Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate


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 Alpha Subunit of Heme Dependent Oxidative N- Demethylase (Hodm) in Complex with the Dimethylamine Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.6
occ:0.50
O4 A:PEG403 2.8 35.5 1.0
O2 A:PEG403 2.8 30.3 1.0
O A:HOH649 3.1 38.4 1.0
C4 A:PEG403 3.4 34.4 1.0
C3 A:PEG403 3.5 32.4 1.0
C2 A:PEG403 3.6 26.6 1.0
OE1 A:GLU33 4.4 34.1 1.0
OE2 A:GLU33 4.9 49.9 1.0
CD A:GLU33 4.9 34.3 1.0

Reference:

M.Ortmayer, P.Lafite, B.R.Menon, T.Tralau, K.Fisher, L.Denkhaus, N.S.Scrutton, S.E.Rigby, A.W.Munro, S.Hay, D.Leys. An Oxidative N-Demethylase Reveals Pas Transition From Ubiquitous Sensor to Enzyme. Nature V. 539 593 2016.
ISSN: ESSN 1476-4687
PubMed: 27851736
DOI: 10.1038/NATURE20159
Page generated: Tue Dec 15 11:14:13 2020

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