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Sodium in PDB 6ami: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound:
4.2.1.20;

Protein crystallography data

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

Resolution Low / High (Å) 40.00 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.682, 109.921, 160.267, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound (pdb code 6ami). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound, PDB code: 6ami:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 1 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


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 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:46.0
occ:1.00
 O A:HOH543 2.3 35.9 1.0
O A:GLY303 2.5 48.5 1.0
O A:TYR301 2.6 48.2 1.0
OG A:SER265 2.6 47.3 1.0
O A:SER263 2.7 49.7 1.0
O A:GLY227 3.6 48.0 1.0
C A:GLY303 3.6 49.5 1.0
C A:TYR301 3.7 48.8 1.0
CB A:SER265 3.7 47.6 1.0
C A:SER263 3.8 49.8 1.0
O A:HOH525 3.9 40.3 1.0
N A:GLY303 4.1 51.6 1.0
C A:PRO302 4.1 52.7 1.0
CB A:SER263 4.1 51.6 1.0
N A:SER265 4.2 48.9 1.0
O A:PRO302 4.4 53.3 1.0
CA A:GLY303 4.4 51.2 1.0
C A:GLY227 4.4 46.6 1.0
CA A:SER263 4.5 50.1 1.0
CB A:VAL304 4.5 47.6 1.0
N A:VAL304 4.6 49.0 1.0
CA A:PRO302 4.6 53.2 1.0
CA A:SER265 4.6 48.2 1.0
N A:PRO302 4.6 52.4 1.0
CA A:TYR301 4.6 48.8 1.0
CB A:TYR301 4.6 49.2 1.0
O A:LEU299 4.7 46.3 1.0
CD2 A:TYR301 4.7 51.4 1.0
CA A:VAL304 4.7 47.6 1.0
N A:TYR301 4.8 47.9 1.0
OE2 A:GLU251 4.8 51.6 1.0
CA A:GLY227 4.8 45.1 1.0
N A:ALA264 4.9 50.0 1.0

Sodium binding site 2 out of 5 in 6ami

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Sodium binding site 2 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


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 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:36.8
occ:1.00
 O B:HOH529 2.2 34.9 1.0
O B:GLY303 2.5 35.4 1.0
O B:TYR301 2.5 35.9 1.0
O B:SER263 2.6 36.2 1.0
OG B:SER265 2.9 35.0 1.0
O B:GLY227 3.4 32.2 1.0
C B:GLY303 3.6 36.0 1.0
C B:TYR301 3.7 36.4 1.0
C B:SER263 3.7 36.5 1.0
O B:HOH540 3.8 33.8 1.0
CB B:SER265 3.9 35.3 1.0
CB B:SER263 4.0 37.4 1.0
N B:GLY303 4.1 37.1 1.0
C B:PRO302 4.1 37.6 1.0
N B:SER265 4.2 36.2 1.0
C B:GLY227 4.3 31.6 1.0
CA B:SER263 4.4 37.1 1.0
CA B:GLY303 4.4 37.0 1.0
O B:PRO302 4.4 38.1 1.0
O B:LEU299 4.5 34.3 1.0
CD2 B:TYR301 4.5 35.7 1.0
OE2 B:GLU251 4.6 35.7 1.0
CA B:PRO302 4.6 38.0 1.0
N B:PRO302 4.6 37.4 1.0
CA B:TYR301 4.6 36.0 1.0
N B:VAL304 4.6 36.1 1.0
CB B:TYR301 4.6 35.4 1.0
CA B:SER265 4.7 36.0 1.0
CB B:VAL304 4.7 35.5 1.0
N B:TYR301 4.7 35.6 1.0
N B:ALA264 4.8 36.9 1.0
CA B:GLY227 4.8 31.3 1.0
CA B:VAL304 4.8 35.5 1.0

Sodium binding site 3 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 3 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


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 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:34.0
occ:1.00
 O C:HOH531 2.3 29.6 1.0
O C:GLY303 2.5 36.5 1.0
O C:TYR301 2.5 37.0 1.0
O C:SER263 2.5 39.6 1.0
OG C:SER265 2.7 44.0 1.0
O C:GLY227 3.6 37.9 1.0
C C:GLY303 3.6 37.3 1.0
C C:TYR301 3.7 37.7 1.0
C C:SER263 3.7 39.5 1.0
CB C:SER265 3.8 45.0 1.0
O C:HOH530 3.9 35.2 1.0
CB C:SER263 4.0 38.9 1.0
C C:PRO302 4.1 39.4 1.0
N C:SER265 4.1 42.5 1.0
N C:GLY303 4.1 38.8 1.0
O C:PRO302 4.3 39.9 1.0
CA C:SER263 4.3 39.4 1.0
CA C:GLY303 4.4 38.6 1.0
O C:LEU299 4.5 34.7 1.0
CA C:TYR301 4.5 37.2 1.0
CB C:TYR301 4.5 36.4 1.0
C C:GLY227 4.5 37.1 1.0
CA C:PRO302 4.6 39.9 1.0
N C:PRO302 4.6 39.1 1.0
CA C:SER265 4.6 44.7 1.0
N C:TYR301 4.6 36.6 1.0
N C:VAL304 4.6 37.5 1.0
OE2 C:GLU251 4.7 39.9 1.0
CD2 C:TYR301 4.7 37.0 1.0
CB C:VAL304 4.7 36.7 1.0
N C:ALA264 4.8 39.7 1.0
CA C:VAL304 4.9 36.7 1.0

Sodium binding site 4 out of 5 in 6ami

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Sodium binding site 4 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


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 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:34.9
occ:1.00
 OE1 C:GLN283 2.7 50.1 1.0
O C:GLY287 2.7 55.2 1.0
CD C:GLN283 3.5 48.5 1.0
C C:GLY287 3.7 56.5 1.0
CA C:GLY287 3.9 57.6 1.0
NE2 C:GLN283 4.2 47.4 1.0
CG C:GLN283 4.4 48.0 1.0
O C:VAL271 4.8 48.4 1.0
N C:GLN288 4.9 57.5 1.0

Sodium binding site 5 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 5 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:48.8
occ:1.00
 O D:GLY303 2.5 49.4 1.0
O D:SER263 2.6 51.1 1.0
O D:TYR301 2.7 51.3 1.0
OG D:SER265 2.9 50.1 1.0
O D:GLY227 3.3 44.7 1.0
C D:GLY303 3.6 49.9 1.0
C D:SER263 3.8 51.1 1.0
C D:TYR301 3.8 52.0 1.0
CB D:SER265 3.9 50.1 1.0
N D:SER265 4.1 50.8 1.0
CB D:SER263 4.1 53.3 1.0
N D:GLY303 4.2 52.4 1.0
C D:GLY227 4.3 43.8 1.0
C D:PRO302 4.3 53.5 1.0
CA D:GLY303 4.4 51.7 1.0
OE2 D:GLU251 4.4 48.2 1.0
O D:LEU299 4.5 46.8 1.0
CA D:SER263 4.5 51.6 1.0
CB D:TYR301 4.5 50.5 1.0
O D:PRO302 4.6 53.9 1.0
CD2 D:TYR301 4.6 51.0 1.0
CA D:TYR301 4.6 51.5 1.0
CA D:SER265 4.6 50.4 1.0
N D:VAL304 4.6 49.4 1.0
CB D:VAL304 4.7 47.6 1.0
N D:TYR301 4.7 50.6 1.0
N D:ALA264 4.8 51.2 1.0
N D:PRO302 4.8 53.5 1.0
CA D:GLY227 4.8 42.6 1.0
CA D:VAL304 4.9 48.0 1.0
O D:VAL226 4.9 42.9 1.0
CA D:PRO302 4.9 54.5 1.0
CG D:TYR301 4.9 51.5 1.0

Reference:

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
Page generated: Tue Oct 8 01:51:21 2024

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