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Sodium in PDB 6am8: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2):
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2), PDB code: 6am8 was solved by A.R.Buller, P.Van Roye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.233, 106.036, 158.709, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2) (pdb code 6am8). 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, PFTRPB2B9 with Trp Bound As E(AEX2), PDB code: 6am8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6am8

Go back to Sodium Binding Sites List in 6am8
Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)


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, PFTRPB2B9 with Trp Bound As E(AEX2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.1
occ:1.00
 O A:HOH533 2.3 31.6 1.0
O A:GLY303 2.5 32.1 1.0
O A:TYR301 2.6 34.0 1.0
O A:SER263 2.6 36.5 1.0
OG A:SER265 2.8 37.0 1.0
O A:GLY227 3.5 29.2 1.0
C A:GLY303 3.6 32.5 1.0
O A:HOH550 3.6 34.4 1.0
C A:TYR301 3.7 34.4 1.0
C A:SER263 3.7 37.4 1.0
CB A:SER265 3.8 36.2 1.0
CB A:SER263 4.0 37.1 1.0
N A:GLY303 4.0 34.0 1.0
N A:SER265 4.1 38.2 1.0
C A:PRO302 4.1 34.9 1.0
CA A:GLY303 4.3 33.6 1.0
CA A:SER263 4.4 37.8 1.0
O A:PRO302 4.5 35.3 1.0
O A:LEU299 4.5 31.8 1.0
C A:GLY227 4.5 28.6 1.0
CA A:PRO302 4.5 35.5 1.0
CB A:TYR301 4.5 33.5 1.0
OE2 A:GLU251 4.5 33.5 1.0
CB A:VAL304 4.6 31.1 1.0
CA A:TYR301 4.6 34.1 1.0
N A:PRO302 4.6 35.1 1.0
N A:VAL304 4.6 31.9 1.0
CA A:SER265 4.6 37.3 1.0
CD2 A:TYR301 4.6 33.7 1.0
N A:TYR301 4.7 33.8 1.0
CA A:VAL304 4.8 31.0 1.0
N A:ALA264 4.8 38.2 1.0
CA A:GLY227 5.0 28.3 1.0
O A:VAL226 5.0 28.7 1.0
CG A:TYR301 5.0 34.0 1.0

Sodium binding site 2 out of 4 in 6am8

Go back to Sodium Binding Sites List in 6am8
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)


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, PFTRPB2B9 with Trp Bound As E(AEX2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:45.0
occ:1.00
 O B:HOH542 2.2 35.9 1.0
O B:GLY303 2.5 34.5 1.0
O B:SER263 2.6 39.2 1.0
O B:TYR301 2.6 36.1 1.0
OG B:SER265 2.9 38.1 1.0
O B:GLY227 3.4 33.8 1.0
O B:HOH551 3.6 38.2 1.0
C B:GLY303 3.6 34.5 1.0
C B:SER263 3.7 40.1 1.0
C B:TYR301 3.8 36.0 1.0
CB B:SER265 3.9 38.4 1.0
CB B:SER263 4.0 39.9 1.0
N B:SER265 4.2 39.8 1.0
N B:GLY303 4.2 35.7 1.0
C B:PRO302 4.2 36.7 1.0
CA B:SER263 4.4 40.3 1.0
O B:LEU299 4.4 34.2 1.0
C B:GLY227 4.4 33.0 1.0
CA B:GLY303 4.4 35.1 1.0
O B:PRO302 4.5 37.0 1.0
CB B:TYR301 4.5 34.7 1.0
CB B:VAL304 4.5 33.5 1.0
CA B:TYR301 4.6 35.5 1.0
N B:VAL304 4.6 33.9 1.0
OE2 B:GLU251 4.6 39.0 1.0
CA B:SER265 4.7 39.7 1.0
N B:PRO302 4.7 36.7 1.0
CD2 B:TYR301 4.7 34.2 1.0
CA B:PRO302 4.7 37.3 1.0
N B:TYR301 4.7 35.6 1.0
CA B:VAL304 4.8 33.0 1.0
N B:ALA264 4.8 41.0 1.0
CA B:GLY227 4.9 32.6 1.0
O B:VAL226 5.0 32.8 1.0
CG2 B:VAL304 5.0 33.2 1.0

Sodium binding site 3 out of 4 in 6am8

Go back to Sodium Binding Sites List in 6am8
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)


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, PFTRPB2B9 with Trp Bound As E(AEX2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:31.5
occ:1.00
 O C:HOH544 2.2 35.5 1.0
O C:HOH543 2.3 32.0 1.0
O C:GLY303 2.4 29.6 1.0
O C:TYR301 2.5 32.2 1.0
O C:SER263 2.6 34.2 1.0
OG C:SER265 2.7 33.9 1.0
C C:GLY303 3.5 30.0 1.0
O C:GLY227 3.6 29.3 1.0
C C:TYR301 3.7 32.4 1.0
C C:SER263 3.7 34.9 1.0
CB C:SER265 3.8 34.1 1.0
O C:HOH545 3.9 31.8 1.0
N C:GLY303 4.0 31.5 1.0
CB C:SER263 4.0 35.4 1.0
C C:PRO302 4.0 32.3 1.0
N C:SER265 4.1 34.8 1.0
CA C:GLY303 4.3 30.9 1.0
CA C:SER263 4.3 35.4 1.0
O C:PRO302 4.3 32.5 1.0
CA C:PRO302 4.5 33.0 1.0
O C:LEU299 4.5 31.6 1.0
N C:VAL304 4.5 29.6 1.0
CB C:TYR301 4.5 31.6 1.0
CB C:VAL304 4.5 28.9 1.0
N C:PRO302 4.5 32.9 1.0
CA C:TYR301 4.5 32.3 1.0
CD2 C:TYR301 4.6 31.7 1.0
C C:GLY227 4.6 28.8 1.0
CA C:SER265 4.6 34.8 1.0
OE2 C:GLU251 4.7 31.5 1.0
N C:TYR301 4.7 32.3 1.0
CA C:VAL304 4.7 28.8 1.0
N C:ALA264 4.8 35.4 1.0
CG C:TYR301 4.9 31.9 1.0

Sodium binding site 4 out of 4 in 6am8

Go back to Sodium Binding Sites List in 6am8
Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 with Trp Bound As E(AEX2)


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, PFTRPB2B9 with Trp Bound As E(AEX2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:43.3
occ:1.00
 O D:HOH511 2.2 33.0 1.0
O D:GLY303 2.5 36.8 1.0
O D:SER263 2.6 39.5 1.0
O D:TYR301 2.7 38.4 1.0
OG D:SER265 3.0 43.0 1.0
O D:GLY227 3.3 32.7 1.0
C D:GLY303 3.6 37.1 1.0
C D:TYR301 3.7 39.1 1.0
O D:HOH525 3.7 30.9 1.0
C D:SER263 3.8 39.9 1.0
CB D:SER263 4.0 39.7 1.0
N D:GLY303 4.1 39.0 1.0
CB D:SER265 4.1 43.2 1.0
C D:GLY227 4.2 32.0 1.0
C D:PRO302 4.3 40.0 1.0
CB D:TYR301 4.3 38.1 1.0
O D:LEU299 4.3 35.0 1.0
N D:SER265 4.3 41.7 1.0
CA D:SER263 4.4 40.5 1.0
CA D:TYR301 4.4 38.8 1.0
CA D:GLY303 4.4 38.6 1.0
OE2 D:GLU251 4.5 37.3 1.0
N D:TYR301 4.5 38.2 1.0
O D:PRO302 4.6 40.4 1.0
CD2 D:TYR301 4.6 38.5 1.0
N D:VAL304 4.7 36.6 1.0
N D:PRO302 4.7 40.2 1.0
CA D:GLY227 4.7 31.2 1.0
CB D:VAL304 4.8 35.1 1.0
CA D:PRO302 4.8 40.8 1.0
CG D:TYR301 4.8 38.8 1.0
CA D:VAL304 4.8 35.3 1.0
N D:ALA264 4.9 40.2 1.0
CA D:SER265 4.9 43.3 1.0
O D:VAL226 4.9 30.2 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 01:51:05 2024

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