Sodium in PDB 6ze4: Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide

The structure of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide, PDB code: 6ze4 was solved by L.Svecova, T.Skalova, P.Kolenko, T.Koval, L.H.Oestergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.38 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.562, 109.875, 116.113, 90, 90, 90
R / Rfree (%)	17 / 20.2

The structure of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide (pdb code 6ze4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide, PDB code: 6ze4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na709 b:34.5 occ:1.00 O A:HOH1370 2.6 41.4 1.0 O A:VAL589 2.7 24.4 1.0 O A:HOH1072 2.7 30.4 1.0 O A:VAL586 2.7 19.2 1.0 O A:HOH1208 2.8 22.3 1.0 C A:VAL586 3.8 19.1 1.0 C A:VAL589 3.8 24.7 1.0 N A:GLY588 3.9 19.9 1.0 O A:HOH989 3.9 26.9 1.0 N A:VAL589 4.0 25.1 1.0 CA A:TYR587 4.1 20.5 1.0 CB A:LYS585 4.1 19.5 1.0 NE2 A:GLN590 4.2 32.7 1.0 C A:TYR587 4.3 18.5 1.0 N A:TYR587 4.4 19.8 1.0 O A:HOH914 4.4 39.9 1.0 O A:HOH1540 4.5 34.9 1.0 C A:LYS585 4.5 17.7 1.0 CA A:VAL589 4.6 26.0 1.0 O A:LYS585 4.6 16.6 1.0 N A:VAL586 4.6 18.2 1.0 N A:GLN590 4.8 22.4 1.0 O A:HOH1158 4.8 35.7 1.0 C A:GLY588 4.8 23.5 1.0 CD A:LYS585 4.9 23.4 1.0 CA A:GLY588 4.9 22.7 1.0 CA A:VAL586 4.9 19.3 1.0 CA A:LYS585 4.9 18.9 1.0

Sodium binding site 2 out of 2 in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Oxo-N-[(1S)-1-(Pyridin-3-Yl)Ethyl]-4-(Thiophen-2-Yl) Butanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na709 b:34.6 occ:1.00 O B:HOH1234 2.7 24.0 1.0 O B:VAL589 2.8 26.2 1.0 O B:HOH1064 2.8 31.1 1.0 O B:HOH1372 2.9 30.6 1.0 O B:VAL586 2.9 21.0 1.0 C B:VAL586 3.8 19.6 1.0 O B:HOH1039 3.9 24.0 1.0 N B:GLY588 3.9 20.2 1.0 C B:VAL589 4.0 24.3 1.0 NE2 B:GLN590 4.1 30.0 1.0 CB B:LYS585 4.1 22.6 1.0 N B:VAL589 4.1 22.7 1.0 CA B:TYR587 4.2 21.1 1.0 N B:TYR587 4.4 21.1 1.0 O B:HOH1148 4.4 38.1 1.0 O B:HOH1546 4.4 29.1 1.0 C B:TYR587 4.4 19.9 1.0 C B:LYS585 4.6 18.3 1.0 O B:LYS585 4.6 17.6 1.0 N B:VAL586 4.7 18.0 1.0 CA B:VAL589 4.7 24.5 1.0 CD B:LYS585 4.9 25.8 1.0 N B:GLN590 4.9 23.4 1.0 C B:GLY588 4.9 23.6 1.0 CA B:GLY588 4.9 21.8 1.0 O B:HOH1326 4.9 47.3 1.0 CA B:VAL586 4.9 19.3 1.0 CA B:LYS585 5.0 19.6 1.0

L.Svecova, L.H.Ostergaard, T.Skalova, K.M.Schnorr, T.Koval', P.Kolenko, J.Stransky, D.Sedlak, J.Duskova, M.Trundova, J.Hasek, J.Dohnalek. Crystallographic Fragment Screening-Based Study of A Novel Fad-Dependent Oxidoreductase From Chaetomium Thermophilum Acta Crystallogr.,Sect.D 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321003533