Sodium in PDB 5dvz: Holo Trpb From Pyrococcus Furiosus

All present enzymatic activity of Holo Trpb From Pyrococcus Furiosus:
4.2.1.20;

The structure of Holo Trpb From Pyrococcus Furiosus, PDB code: 5dvz 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)	39.33 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.051, 111.882, 160.832, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.8

The binding sites of Sodium atom in the Holo Trpb From Pyrococcus Furiosus (pdb code 5dvz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Holo Trpb From Pyrococcus Furiosus, PDB code: 5dvz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Holo Trpb From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Holo Trpb From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:29.4 occ:1.00 O A:HOH613 2.4 27.1 1.0 O A:HOH601 2.6 33.6 1.0 O A:TYR301 2.7 33.9 1.0 OG A:SER265 2.7 32.6 1.0 O A:GLY303 2.8 28.8 1.0 O A:SER263 2.9 30.3 1.0 OG A:SER263 3.4 32.6 1.0 C A:GLY303 3.7 29.1 1.0 C A:TYR301 3.8 34.3 1.0 CB A:SER265 3.8 32.2 1.0 O A:GLY227 3.9 25.5 1.0 O A:HOH579 3.9 25.9 1.0 N A:GLY303 4.0 32.2 1.0 C A:SER263 4.0 31.8 1.0 C A:PRO302 4.1 34.0 1.0 N A:SER265 4.2 32.0 1.0 CA A:GLY303 4.3 31.1 1.0 O A:PRO302 4.4 34.6 1.0 CB A:SER263 4.4 32.6 1.0 C A:GLY227 4.4 24.6 1.0 CA A:PRO302 4.5 35.3 1.0 N A:PRO302 4.6 35.0 1.0 CA A:SER265 4.7 32.8 1.0 CA A:SER263 4.7 32.9 1.0 O A:LEU299 4.7 32.7 1.0 N A:VAL304 4.8 28.1 1.0 CA A:GLY227 4.8 24.8 1.0 CA A:TYR301 4.8 34.6 1.0 OE2 A:GLU251 4.8 27.6 1.0 CB A:TYR301 4.9 33.6 1.0 CD2 A:TYR301 4.9 33.5 1.0 CB A:VAL304 5.0 26.1 1.0

Sodium binding site 2 out of 4 in the Holo Trpb From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Holo Trpb From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:20.7 occ:1.00 O B:HOH614 2.2 30.3 1.0 O B:TYR301 2.4 34.4 1.0 O B:HOH536 2.5 33.9 1.0 O B:GLY303 2.7 27.7 1.0 OG B:SER265 2.8 30.1 1.0 O B:SER263 2.9 28.6 1.0 OG B:SER263 3.1 28.4 0.5 C B:TYR301 3.6 35.6 1.0 CB B:SER265 3.7 29.5 1.0 C B:GLY303 3.8 28.9 1.0 O B:GLY227 3.9 24.0 1.0 C B:SER263 3.9 28.8 1.0 C B:PRO302 4.0 34.9 1.0 N B:GLY303 4.0 33.0 1.0 O B:HOH584 4.1 25.8 1.0 CB B:SER263 4.1 28.6 0.5 CB B:SER263 4.2 28.8 0.5 O B:PRO302 4.2 34.6 1.0 N B:SER265 4.2 29.3 1.0 CA B:GLY303 4.4 31.4 1.0 CA B:PRO302 4.4 36.7 1.0 N B:PRO302 4.5 36.7 1.0 C B:GLY227 4.5 23.4 1.0 CA B:SER263 4.5 29.3 0.5 CA B:SER263 4.5 29.4 0.5 CA B:TYR301 4.6 36.6 1.0 CA B:SER265 4.6 29.9 1.0 N B:TYR301 4.7 36.4 1.0 CB B:TYR301 4.7 35.3 1.0 CD2 B:TYR301 4.7 34.9 1.0 O B:LEU299 4.7 32.9 1.0 CA B:GLY227 4.8 23.3 1.0 N B:VAL304 4.9 27.5 1.0 OE2 B:GLU251 5.0 25.3 1.0 N B:ALA264 5.0 29.3 1.0 CD1 B:LEU282 5.0 39.7 1.0

Sodium binding site 3 out of 4 in the Holo Trpb From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Holo Trpb From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:23.4 occ:1.00 O C:TYR301 2.5 39.3 1.0 O C:HOH582 2.5 29.6 1.0 O C:HOH544 2.6 36.4 1.0 O C:SER263 2.7 32.5 1.0 OG C:SER265 2.8 33.5 1.0 O C:GLY303 2.8 32.9 1.0 OG C:SER263 3.0 33.7 1.0 C C:TYR301 3.7 40.2 1.0 CB C:SER265 3.7 33.8 1.0 O C:GLY227 3.8 27.8 1.0 C C:SER263 3.8 33.4 1.0 C C:GLY303 3.9 33.8 1.0 O C:HOH551 4.0 29.0 1.0 C C:PRO302 4.1 39.7 1.0 CB C:SER263 4.1 33.8 1.0 O C:PRO302 4.2 40.1 1.0 N C:SER265 4.2 33.9 1.0 N C:GLY303 4.2 37.8 1.0 C C:GLY227 4.3 26.9 1.0 CA C:SER263 4.4 34.3 1.0 CA C:PRO302 4.5 41.4 1.0 CA C:GLY303 4.5 36.2 1.0 N C:PRO302 4.6 41.4 1.0 CA C:SER265 4.6 34.5 1.0 CA C:TYR301 4.6 40.8 1.0 CB C:TYR301 4.7 40.0 1.0 CA C:GLY227 4.7 26.7 1.0 N C:TYR301 4.8 40.0 1.0 N C:ALA264 4.9 33.7 1.0 OE2 C:GLU251 4.9 29.2 1.0 N C:VAL304 4.9 32.3 1.0

Sodium binding site 4 out of 4 in the Holo Trpb From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Holo Trpb From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:19.8 occ:1.00 O D:HOH577 2.4 26.9 1.0 O D:TYR301 2.4 36.7 1.0 O D:HOH623 2.6 27.1 1.0 O D:GLY303 2.8 23.6 1.0 OG D:SER265 2.8 28.3 1.0 O D:SER263 2.9 27.0 1.0 OG D:SER263 3.2 27.8 1.0 C D:TYR301 3.7 37.6 1.0 CB D:SER265 3.7 27.7 1.0 O D:GLY227 3.8 21.7 1.0 C D:GLY303 3.8 24.2 1.0 C D:SER263 3.9 27.6 1.0 O D:HOH575 4.0 25.6 1.0 N D:GLY303 4.1 26.2 1.0 C D:PRO302 4.1 27.5 1.0 CB D:SER263 4.2 27.8 1.0 N D:SER265 4.2 27.4 1.0 C D:GLY227 4.3 21.3 1.0 CA D:GLY303 4.4 25.6 1.0 CA D:PRO302 4.4 28.1 1.0 N D:PRO302 4.5 27.5 1.0 CA D:SER263 4.5 28.4 1.0 O D:PRO302 4.6 28.3 1.0 CA D:SER265 4.6 28.1 1.0 CA D:TYR301 4.6 37.4 1.0 CA D:GLY227 4.7 21.4 1.0 CB D:TYR301 4.8 36.5 1.0 OE2 D:GLU251 4.9 23.1 1.0 N D:VAL304 4.9 23.5 1.0 N D:TYR301 4.9 37.3 1.0 N D:ALA264 5.0 28.1 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