Sodium in PDB 6htk: X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate, PDB code: 6htk was solved by P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.11 / 2.00
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.650, 47.010, 114.080, 90.00, 108.91, 90.00
R / Rfree (%)	16.9 / 19.7

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate also contains other interesting chemical elements:

Potassium	(K)	1 atom
Bromine	(Br)	6 atoms
Iron	(Fe)	8 atoms

The binding sites of Sodium atom in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate (pdb code 6htk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate, PDB code: 6htk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:37.4 occ:1.00 OE2 A:GLU380 2.5 24.8 1.0 O A:VAL386 2.6 23.3 1.0 O A:PHE389 2.6 24.1 1.0 O A:HOH760 3.0 44.1 1.0 O A:HOH874 3.1 42.0 1.0 CD A:GLU380 3.5 24.6 1.0 C A:VAL386 3.6 20.3 1.0 C A:PHE389 3.7 22.0 1.0 OE1 A:GLU380 3.8 25.6 1.0 N A:VAL386 4.0 24.4 1.0 CB A:PHE389 4.3 22.6 1.0 CA A:VAL386 4.3 20.8 1.0 CA A:PHE389 4.3 21.0 1.0 N A:PHE389 4.3 23.2 1.0 CD2 A:PHE389 4.4 23.7 1.0 N A:ASP387 4.5 21.2 1.0 CA A:ASP387 4.7 24.0 1.0 CG A:PHE389 4.7 24.3 1.0 CB A:VAL386 4.8 21.6 1.0 N A:VAL390 4.8 24.0 1.0 CG A:GLU380 4.8 22.1 1.0 C A:PRO385 5.0 24.8 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with (R)-(+)- Indoline-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na511 b:38.9 occ:1.00 OE2 B:GLU380 2.4 26.2 1.0 O B:PHE389 2.6 20.0 1.0 O B:VAL386 2.7 20.1 1.0 O B:HOH949 2.9 35.1 1.0 O B:HOH761 3.1 43.2 1.0 CD B:GLU380 3.4 26.4 1.0 O B:HOH926 3.5 41.4 1.0 C B:VAL386 3.6 20.2 1.0 C B:PHE389 3.7 19.5 1.0 OE1 B:GLU380 3.8 27.1 1.0 N B:VAL386 4.0 22.6 1.0 CB B:PHE389 4.3 18.2 1.0 N B:PHE389 4.4 21.6 1.0 CA B:PHE389 4.4 20.5 1.0 CA B:VAL386 4.4 19.6 1.0 CD2 B:PHE389 4.4 23.5 1.0 N B:ASP387 4.6 20.5 1.0 O B:HOH676 4.7 39.5 1.0 CG B:GLU380 4.7 22.0 1.0 CA B:ASP387 4.8 20.6 1.0 CB B:VAL386 4.8 19.7 1.0 CG B:PHE389 4.8 22.0 1.0 N B:VAL390 4.8 20.1 1.0 O B:HOH881 4.8 42.1 1.0

P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet. Radical S-Adenosyl-L-Methionine Tryptophan Lyase (Nosl): How the Protein Controls the Carboxyl Radical •CO2-Migration. J.Am.Chem.Soc. V. 140 16661 2018.
ISSN: ESSN 1520-5126
PubMed: 30418774
DOI: 10.1021/JACS.8B09142