Sodium in PDB 5dw0: Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine

All present enzymatic activity of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine:
4.2.1.20;

The structure of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine, PDB code: 5dw0 was solved by A.R.Buller, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.241, 109.131, 160.797, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.1

The binding sites of Sodium atom in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine (pdb code 5dw0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine, PDB code: 5dw0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:42.0 occ:1.00 O A:HOH516 2.3 43.9 1.0 O A:TYR301 2.6 32.5 1.0 O A:HOH514 2.6 42.7 1.0 O A:GLY303 2.8 35.9 1.0 O A:SER263 2.9 35.8 1.0 OG A:SER265 2.9 43.3 1.0 OG A:SER263 3.5 36.8 1.0 N A:GLY303 3.7 34.6 1.0 C A:GLY303 3.7 33.4 1.0 C A:TYR301 3.8 34.3 1.0 CB A:SER265 3.8 39.3 1.0 O A:GLY227 3.9 33.9 1.0 C A:SER263 4.0 33.4 1.0 O A:HOH549 4.1 24.9 1.0 N A:SER265 4.1 35.4 1.0 C A:PRO302 4.2 35.1 1.0 CA A:GLY303 4.2 34.8 1.0 CA A:PRO302 4.4 36.3 1.0 CB A:SER263 4.4 35.0 1.0 N A:PRO302 4.6 34.9 1.0 CA A:SER265 4.6 37.7 1.0 C A:GLY227 4.6 31.0 1.0 CA A:SER263 4.6 33.7 1.0 N A:VAL304 4.8 33.7 1.0 OE2 A:GLU251 4.8 36.5 1.0 CA A:TYR301 4.9 34.7 1.0 CD1 A:LEU282 4.9 37.4 1.0 O A:PRO302 4.9 37.9 1.0 N A:ALA264 4.9 33.1 1.0

Sodium binding site 2 out of 4 in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:43.6 occ:1.00 O B:HOH513 2.6 46.2 1.0 O B:HOH528 2.6 57.4 1.0 O B:TYR301 2.6 42.9 1.0 O B:GLY303 2.7 41.1 1.0 OG B:SER265 2.8 50.6 1.0 O B:SER263 3.0 43.2 1.0 OG B:SER263 3.6 48.1 1.0 C B:GLY303 3.6 40.7 1.0 CB B:SER265 3.7 47.8 1.0 N B:GLY303 3.7 44.4 1.0 C B:TYR301 3.8 43.2 1.0 O B:GLY227 3.8 34.9 1.0 C B:SER263 4.0 42.8 1.0 N B:SER265 4.1 45.0 1.0 CA B:GLY303 4.2 43.2 1.0 O B:HOH516 4.2 35.8 1.0 C B:PRO302 4.2 44.6 1.0 CA B:PRO302 4.5 43.8 1.0 CB B:SER263 4.5 43.9 1.0 CA B:SER265 4.5 46.4 1.0 C B:GLY227 4.5 33.1 1.0 N B:PRO302 4.6 43.2 1.0 N B:VAL304 4.7 40.8 1.0 CA B:SER263 4.7 43.1 1.0 OE2 B:GLU251 4.8 40.4 1.0 CA B:TYR301 4.8 41.8 1.0 CA B:GLY227 4.9 33.0 1.0 N B:TYR301 5.0 40.8 1.0 N B:ALA264 5.0 43.4 1.0 CB B:VAL304 5.0 39.4 1.0

Sodium binding site 3 out of 4 in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:36.4 occ:1.00 O C:HOH512 2.2 37.6 1.0 O C:HOH528 2.6 41.3 1.0 O C:TYR301 2.7 33.9 1.0 O C:GLY303 2.7 33.5 1.0 OG C:SER265 2.8 41.4 1.0 O C:SER263 3.0 34.7 1.0 OG C:SER263 3.3 35.9 1.0 C C:GLY303 3.7 33.0 1.0 CB C:SER265 3.8 38.4 1.0 C C:TYR301 3.9 35.1 1.0 C C:SER263 3.9 32.3 1.0 N C:GLY303 3.9 36.3 1.0 O C:GLY227 4.0 31.6 1.0 O C:HOH531 4.0 29.2 1.0 N C:SER265 4.1 36.2 1.0 CA C:GLY303 4.2 34.4 1.0 C C:PRO302 4.3 37.1 1.0 CB C:SER263 4.4 33.6 1.0 CA C:PRO302 4.5 37.2 1.0 C C:GLY227 4.6 29.9 1.0 CA C:SER263 4.6 32.3 1.0 CA C:SER265 4.6 36.8 1.0 N C:PRO302 4.7 35.7 1.0 OE2 C:GLU251 4.8 34.8 1.0 N C:VAL304 4.8 31.6 1.0 O C:PRO302 4.8 40.5 1.0 N C:ALA264 4.9 33.1 1.0 CA C:GLY227 4.9 29.6 1.0 CA C:TYR301 4.9 35.3 1.0

Sodium binding site 4 out of 4 in the Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Trpb From Pyrococcus Furiosus with L-Serine Bound As the External Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:38.9 occ:1.00 O D:HOH529 2.2 43.7 1.0 O D:HOH531 2.3 67.7 1.0 O D:TYR301 2.6 37.7 1.0 O D:GLY303 2.7 41.2 1.0 OG D:SER265 2.9 45.3 1.0 O D:SER263 3.0 43.5 1.0 OG D:SER263 3.2 46.3 1.0 CB D:SER265 3.7 43.9 1.0 C D:GLY303 3.7 40.5 1.0 C D:TYR301 3.8 41.2 1.0 O D:GLY227 3.9 36.3 1.0 C D:SER263 4.0 42.7 1.0 N D:GLY303 4.0 43.2 1.0 O D:HOH515 4.1 34.1 1.0 N D:SER265 4.2 42.5 1.0 C D:PRO302 4.2 44.5 1.0 CB D:SER263 4.3 44.9 1.0 CA D:GLY303 4.3 41.9 1.0 C D:GLY227 4.5 33.2 1.0 CA D:PRO302 4.6 44.2 1.0 CA D:SER265 4.6 43.0 1.0 CA D:SER263 4.6 43.0 1.0 O D:PRO302 4.7 48.9 1.0 N D:PRO302 4.7 43.0 1.0 CA D:TYR301 4.8 41.9 1.0 N D:VAL304 4.8 40.5 1.0 CA D:GLY227 4.8 34.1 1.0 OE2 D:GLU251 4.9 37.7 1.0 N D:TYR301 4.9 40.2 1.0 O D:VAL226 4.9 33.4 1.0 N D:ALA264 5.0 42.8 1.0 CB D:TYR301 5.0 42.8 1.0

A.R.Buller, S.Brinkmann-Chen, D.K.Romney, M.Herger, J.Murciano-Calles, F.H.Arnold. Directed Evolution of the Tryptophan Synthase Beta-Subunit For Stand-Alone Function Recapitulates Allosteric Activation. Proc.Natl.Acad.Sci.Usa V. 112 14599 2015.
ISSN: ESSN 1091-6490
PubMed: 26553994
DOI: 10.1073/PNAS.1516401112