Sodium in PDB 6amc: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11:
4.2.1.20;

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11, PDB code: 6amc was solved by A.R.Buller, M.Herger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.438, 110.729, 160.427, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.5

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 (pdb code 6amc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11, PDB code: 6amc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:54.3 occ:1.00 O A:HOH530 2.4 30.9 1.0 O A:HOH574 2.6 41.2 1.0 O A:GLY303 3.0 38.4 1.0 O A:SER263 3.0 39.2 1.0 OG A:SER263 3.3 39.7 1.0 O A:TYR301 3.3 40.4 1.0 OG A:SER265 3.4 38.4 1.0 O A:GLY227 3.6 35.0 1.0 CB A:SER265 3.9 38.4 1.0 C A:GLY303 3.9 38.8 1.0 O A:HOH552 4.0 28.1 1.0 C A:SER263 4.0 39.9 1.0 N A:GLY303 4.2 40.5 1.0 N A:SER265 4.3 39.4 1.0 C A:GLY227 4.3 34.6 1.0 CB A:SER263 4.3 40.1 1.0 CA A:GLY303 4.5 40.0 1.0 C A:TYR301 4.5 41.3 1.0 CA A:GLY227 4.6 34.4 1.0 OE2 A:GLU251 4.6 36.7 1.0 CA A:SER263 4.7 40.4 1.0 CA A:SER265 4.7 39.2 1.0 N A:VAL304 4.9 38.5 1.0 O A:VAL226 4.9 34.7 1.0 O A:HOH525 4.9 34.5 1.0 CB A:VAL304 4.9 37.3 1.0 O A:LEU299 5.0 39.6 1.0

Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:60.4 occ:1.00 O B:HOH510 2.3 55.5 1.0 O B:GLY303 2.6 77.4 1.0 O B:TYR301 2.6 86.4 1.0 OG B:SER265 2.7 62.6 1.0 O B:SER263 3.1 58.3 1.0 O B:GLY227 3.4 48.4 1.0 C B:GLY303 3.6 78.2 1.0 O B:PRO302 3.7 88.3 1.0 CB B:SER265 3.7 63.4 1.0 C B:TYR301 3.7 88.8 1.0 OG B:SER263 3.8 58.9 1.0 C B:PRO302 3.8 88.9 1.0 C B:GLY227 4.1 46.6 1.0 N B:SER265 4.3 62.5 1.0 CA B:PRO302 4.3 92.6 1.0 C B:SER263 4.3 59.7 1.0 N B:GLY303 4.3 86.8 1.0 CB B:VAL304 4.4 69.6 1.0 O B:HOH503 4.5 45.8 1.0 N B:VAL304 4.5 74.9 1.0 N B:PRO302 4.5 92.4 1.0 CA B:GLY303 4.5 83.2 1.0 CA B:VAL304 4.6 70.7 1.0 CA B:GLY227 4.6 45.6 1.0 CA B:SER265 4.6 64.0 1.0 CB B:TYR301 4.6 86.2 1.0 OE2 B:GLU251 4.7 56.1 1.0 CA B:TYR301 4.7 88.5 1.0 CB B:SER263 4.7 58.1 1.0 CG2 B:VAL304 4.8 67.1 1.0 CA B:SER263 5.0 59.6 1.0

Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:48.8 occ:1.00 O C:HOH531 2.7 31.1 1.0 O C:HOH540 2.8 38.0 1.0 O C:SER263 2.8 35.1 1.0 OG C:SER265 2.9 36.2 1.0 O C:GLY303 2.9 36.2 1.0 OG C:SER263 3.2 36.9 1.0 O C:TYR301 3.3 36.1 1.0 CB C:SER265 3.7 36.6 1.0 C C:SER263 3.8 35.8 1.0 C C:GLY303 3.9 37.0 1.0 N C:SER265 4.0 36.5 1.0 N C:GLY303 4.1 37.7 1.0 O C:HOH542 4.1 25.1 1.0 O C:GLY227 4.2 30.1 1.0 CB C:SER263 4.2 35.9 1.0 CA C:GLY303 4.4 38.0 1.0 CA C:SER263 4.4 36.1 1.0 CA C:SER265 4.5 37.2 1.0 C C:TYR301 4.6 36.4 1.0 O C:HOH551 4.7 40.6 1.0 N C:ALA264 4.8 36.3 1.0 C C:GLY227 4.8 29.3 1.0 OE2 C:GLU251 4.8 33.5 1.0 N C:VAL304 4.9 37.3 1.0

Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:49.6 occ:1.00 O D:HOH519 2.4 45.7 1.0 O D:SER263 2.5 57.9 1.0 O D:TYR301 2.7 73.8 1.0 O D:GLY303 2.8 64.8 1.0 OG D:SER265 3.0 63.1 1.0 OG D:SER263 3.0 62.1 1.0 C D:SER263 3.6 59.5 1.0 C D:TYR301 3.8 74.3 1.0 C D:GLY303 3.8 65.7 1.0 O D:GLY227 3.8 53.1 1.0 CB D:SER263 4.0 60.7 1.0 CB D:SER265 4.1 62.6 1.0 N D:GLY303 4.1 69.3 1.0 C D:PRO302 4.1 72.0 1.0 N D:SER265 4.1 60.9 1.0 CA D:SER263 4.3 60.1 1.0 CA D:GLY303 4.4 67.6 1.0 O D:PRO302 4.5 71.5 1.0 C D:GLY227 4.5 52.1 1.0 CA D:PRO302 4.5 73.8 1.0 OE2 D:GLU251 4.6 54.2 1.0 CB D:TYR301 4.6 74.4 1.0 N D:PRO302 4.6 74.1 1.0 N D:ALA264 4.7 59.5 1.0 CA D:TYR301 4.7 74.3 1.0 CA D:GLY227 4.8 51.3 1.0 CA D:SER265 4.8 62.5 1.0 N D:VAL304 4.8 64.2 1.0 O D:LEU299 4.9 68.2 1.0 CB D:VAL304 4.9 62.9 1.0 CA D:ALA264 4.9 59.4 1.0

A.R.Buller, P.Van Roye, J.K.B.Cahn, R.A.Scheele, M.Herger, F.H.Arnold. Directed Evolution Mimics Allosteric Activation By Stepwise Tuning of the Conformational Ensemble. J. Am. Chem. Soc. V. 140 7256 2018.
ISSN: ESSN 1520-5126
PubMed: 29712420
DOI: 10.1021/JACS.8B03490