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Sodium in PDB 5dw3: Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site

Enzymatic activity of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site

All present enzymatic activity of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site:
4.2.1.20;

Protein crystallography data

The structure of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site, PDB code: 5dw3 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 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.738, 108.931, 160.106, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site (pdb code 5dw3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site, PDB code: 5dw3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5dw3

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Sodium binding site 1 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:39.4
occ:1.00
 OG A:SER265 2.3 39.9 1.0
O A:TYR301 2.4 40.8 1.0
O A:HOH555 2.5 39.5 1.0
O A:HOH503 2.5 45.5 1.0
O A:GLY303 2.7 35.5 1.0
O A:SER263 2.7 38.0 1.0
OG A:SER263 3.4 45.6 1.0
CB A:SER265 3.5 36.2 1.0
C A:TYR301 3.6 43.2 1.0
C A:GLY303 3.7 36.3 1.0
C A:SER263 3.8 34.5 1.0
C A:PRO302 3.8 39.7 1.0
N A:SER265 3.9 36.3 1.0
N A:GLY303 3.9 38.8 1.0
O A:GLY227 4.0 34.3 1.0
O A:HOH552 4.1 31.1 1.0
O A:PRO302 4.2 41.8 1.0
CA A:PRO302 4.2 41.6 1.0
CA A:SER265 4.3 36.7 1.0
CA A:GLY303 4.3 36.9 1.0
CB A:SER263 4.4 37.4 1.0
N A:PRO302 4.4 41.3 1.0
CA A:SER263 4.5 36.8 1.0
CA A:TYR301 4.5 40.5 1.0
O A:LEU299 4.6 39.8 1.0
OE2 A:GLU251 4.7 35.8 1.0
N A:TYR301 4.7 42.7 1.0
N A:VAL304 4.8 34.1 1.0
N A:ALA264 4.8 35.7 1.0
C A:GLY227 4.8 29.3 1.0
CB A:VAL304 4.8 33.1 1.0
CB A:TYR301 4.9 40.2 1.0
CD1 A:LEU282 4.9 44.4 1.0
C A:ALA264 4.9 36.8 1.0

Sodium binding site 2 out of 4 in 5dw3

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Sodium binding site 2 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:35.4
occ:1.00
 O B:HOH543 2.2 40.4 1.0
O B:TYR301 2.5 30.4 1.0
O B:HOH508 2.5 35.8 1.0
O B:GLY303 2.6 29.9 1.0
OG B:SER265 2.7 35.2 1.0
O B:SER263 2.9 31.3 1.0
OG B:SER263 3.6 38.0 1.0
C B:GLY303 3.7 30.5 1.0
CB B:SER265 3.7 31.4 1.0
C B:TYR301 3.7 32.5 1.0
O B:GLY227 3.7 31.2 1.0
O B:HOH548 4.0 28.3 1.0
C B:SER263 4.0 31.1 1.0
N B:SER265 4.1 29.6 1.0
N B:GLY303 4.1 30.7 1.0
C B:PRO302 4.1 33.0 1.0
CA B:GLY303 4.4 32.3 1.0
O B:PRO302 4.4 33.7 1.0
CA B:PRO302 4.4 32.2 1.0
O B:LEU299 4.5 33.3 1.0
N B:PRO302 4.5 31.9 1.0
CA B:SER265 4.5 30.6 1.0
CB B:SER263 4.6 32.7 1.0
C B:GLY227 4.6 28.0 1.0
OE2 B:GLU251 4.6 29.5 1.0
CA B:TYR301 4.6 34.1 1.0
N B:TYR301 4.6 34.5 1.0
CB B:TYR301 4.7 32.8 1.0
N B:VAL304 4.7 27.6 1.0
CA B:SER263 4.7 32.0 1.0
CD2 B:TYR301 4.8 33.5 1.0
CB B:VAL304 4.8 28.2 1.0
CA B:VAL304 4.9 28.0 1.0
N B:ALA264 4.9 30.8 1.0

Sodium binding site 3 out of 4 in 5dw3

Go back to Sodium Binding Sites List in 5dw3
Sodium binding site 3 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:37.5
occ:1.00
 O C:HOH527 2.4 44.7 1.0
O C:TYR301 2.5 39.8 1.0
OG C:SER265 2.7 43.2 1.0
O C:SER263 2.7 37.1 1.0
O C:GLY303 2.8 31.0 1.0
O C:HOH502 2.8 40.7 1.0
OG C:SER263 3.4 44.4 1.0
C C:TYR301 3.6 41.0 1.0
CB C:SER265 3.7 38.2 1.0
C C:SER263 3.7 39.0 1.0
C C:GLY303 3.8 31.1 1.0
N C:GLY303 3.9 36.5 1.0
N C:SER265 3.9 36.8 1.0
C C:PRO302 4.0 42.5 1.0
O C:GLY227 4.1 30.7 1.0
O C:HOH523 4.1 29.9 1.0
O C:PRO302 4.2 44.8 1.0
CA C:PRO302 4.3 43.2 1.0
CA C:GLY303 4.3 34.2 1.0
N C:PRO302 4.4 42.6 1.0
CA C:SER265 4.4 39.0 1.0
CB C:SER263 4.4 36.5 1.0
CA C:SER263 4.5 38.6 1.0
O C:LEU299 4.5 38.2 1.0
CA C:TYR301 4.6 41.2 1.0
N C:ALA264 4.7 40.2 1.0
OE2 C:GLU251 4.7 40.1 1.0
CB C:TYR301 4.8 42.7 1.0
C C:GLY227 4.8 28.7 1.0
N C:VAL304 4.8 30.3 1.0
N C:TYR301 4.9 44.3 1.0
C C:ALA264 4.9 39.6 1.0
CD1 C:LEU282 4.9 52.4 1.0
CA C:ALA264 4.9 40.0 1.0

Sodium binding site 4 out of 4 in 5dw3

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Sodium binding site 4 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with Product L-Tryptophan Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:41.2
occ:1.00
 O D:HOH511 2.4 54.4 1.0
OG D:SER265 2.4 50.2 1.0
O D:TYR301 2.5 49.1 1.0
O D:HOH538 2.6 44.9 1.0
O D:GLY303 2.7 39.5 1.0
O D:SER263 2.8 39.9 1.0
OG D:SER263 3.5 53.3 1.0
CB D:SER265 3.5 41.9 1.0
C D:TYR301 3.7 51.0 1.0
C D:GLY303 3.7 39.8 1.0
C D:SER263 3.9 40.1 1.0
N D:GLY303 4.0 45.4 1.0
N D:SER265 4.0 40.2 1.0
O D:GLY227 4.0 36.8 1.0
C D:PRO302 4.0 48.2 1.0
O D:PRO302 4.3 51.3 1.0
O D:HOH526 4.3 33.6 1.0
CA D:GLY303 4.3 42.8 1.0
CA D:SER265 4.3 40.5 1.0
CA D:PRO302 4.5 53.5 1.0
CB D:SER263 4.5 44.8 1.0
N D:PRO302 4.5 52.0 1.0
CA D:SER263 4.6 41.8 1.0
O D:LEU299 4.6 44.6 1.0
CA D:TYR301 4.7 54.6 1.0
N D:VAL304 4.7 39.2 1.0
C D:GLY227 4.8 33.2 1.0
N D:TYR301 4.8 54.8 1.0
OE2 D:GLU251 4.8 35.7 1.0
N D:ALA264 4.9 39.6 1.0
CB D:VAL304 4.9 36.7 1.0
CB D:TYR301 4.9 57.2 1.0

Reference:

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
Page generated: Mon Oct 7 20:41:17 2024

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