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Sodium in PDB 5t6m: Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound

Enzymatic activity of Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound

All present enzymatic activity of Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound:
4.2.1.20;

Protein crystallography data

The structure of Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound, PDB code: 5t6m was solved by A.R.Buller, P.Van Roye, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.819, 107.705, 160.061, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound (pdb code 5t6m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound, PDB code: 5t6m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5t6m

Go back to Sodium Binding Sites List in 5t6m
Sodium binding site 1 out of 4 in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan 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 Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:37.5
occ:1.00
 O A:HOH548 2.3 49.6 1.0
O A:TYR301 2.5 40.7 1.0
O A:HOH551 2.6 37.8 1.0
O A:GLY303 2.7 33.1 1.0
OG A:SER265 2.7 39.8 1.0
O A:SER263 2.8 37.2 1.0
OG A:SER263 3.5 38.8 1.0
C A:TYR301 3.6 40.9 1.0
O A:GLY227 3.7 29.5 1.0
C A:GLY303 3.8 34.2 1.0
CB A:SER265 3.8 39.4 1.0
C A:SER263 3.8 37.9 1.0
O A:HOH529 4.0 33.4 1.0
N A:GLY303 4.0 37.3 1.0
C A:PRO302 4.0 39.1 1.0
N A:SER265 4.2 38.4 1.0
CB A:SER263 4.3 37.9 1.0
O A:PRO302 4.4 40.3 1.0
CA A:GLY303 4.4 35.8 1.0
C A:GLY227 4.4 28.7 1.0
CA A:PRO302 4.4 40.7 1.0
N A:PRO302 4.5 40.6 1.0
CA A:SER263 4.5 38.4 1.0
CA A:TYR301 4.6 41.9 1.0
CA A:SER265 4.6 39.4 1.0
CB A:TYR301 4.7 40.8 1.0
CD2 A:TYR301 4.8 40.5 1.0
O A:LEU299 4.8 43.4 1.0
CA A:GLY227 4.8 28.3 1.0
N A:TYR301 4.8 43.5 1.0
N A:ALA264 4.8 37.9 1.0
N A:VAL304 4.8 33.0 1.0
OE2 A:GLU251 5.0 35.3 1.0

Sodium binding site 2 out of 4 in 5t6m

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Sodium binding site 2 out of 4 in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan 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 Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:41.0
occ:1.00
 O B:HOH519 2.2 41.1 1.0
O B:HOH549 2.3 42.6 1.0
O B:TYR301 2.6 38.6 1.0
O B:GLY303 2.6 33.0 1.0
OG B:SER265 3.0 40.5 1.0
O B:SER263 3.1 39.1 1.0
O B:GLY227 3.2 32.7 1.0
C B:GLY303 3.7 33.2 1.0
C B:TYR301 3.7 38.9 1.0
OG B:SER263 3.9 42.2 1.0
CB B:SER265 3.9 39.4 1.0
O B:HOH539 3.9 30.3 1.0
N B:GLY303 4.1 35.3 1.0
C B:GLY227 4.2 31.4 1.0
C B:SER263 4.3 39.4 1.0
C B:PRO302 4.3 36.1 1.0
N B:SER265 4.3 39.0 1.0
CA B:GLY303 4.4 34.4 1.0
O B:LEU299 4.5 34.7 1.0
CA B:TYR301 4.6 40.2 1.0
CB B:TYR301 4.6 40.4 1.0
N B:VAL304 4.6 32.5 1.0
N B:PRO302 4.7 38.0 1.0
O B:PRO302 4.7 36.3 1.0
CA B:PRO302 4.7 37.6 1.0
CB B:VAL304 4.7 31.7 1.0
OE2 B:GLU251 4.7 34.8 1.0
N B:TYR301 4.7 40.3 1.0
O B:VAL226 4.7 32.1 1.0
CB B:SER263 4.7 40.7 1.0
CA B:GLY227 4.7 31.6 1.0
CA B:SER265 4.8 39.6 1.0
CA B:VAL304 4.8 31.7 1.0
CD2 B:TYR301 4.8 40.6 1.0

Sodium binding site 3 out of 4 in 5t6m

Go back to Sodium Binding Sites List in 5t6m
Sodium binding site 3 out of 4 in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan 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 Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:37.9
occ:1.00
 O C:HOH524 2.3 41.7 1.0
O C:HOH538 2.3 36.7 1.0
O C:TYR301 2.5 47.0 1.0
O C:GLY303 2.7 36.6 1.0
O C:SER263 3.0 40.7 1.0
OG C:SER265 3.0 41.6 1.0
O C:GLY227 3.4 35.9 1.0
OG C:SER263 3.5 44.6 1.0
C C:TYR301 3.7 47.9 1.0
C C:GLY303 3.8 36.7 1.0
CB C:SER265 3.8 40.2 1.0
O C:HOH519 4.0 33.7 1.0
C C:SER263 4.1 41.6 1.0
N C:GLY303 4.1 39.8 1.0
N C:SER265 4.2 40.8 1.0
C C:PRO302 4.2 41.6 1.0
C C:GLY227 4.3 33.8 1.0
CA C:GLY303 4.5 38.6 1.0
CA C:PRO302 4.5 43.7 1.0
CB C:SER263 4.5 43.8 1.0
N C:PRO302 4.6 43.9 1.0
O C:PRO302 4.6 42.6 1.0
CA C:TYR301 4.6 48.2 1.0
CA C:SER265 4.7 41.2 1.0
CB C:TYR301 4.7 47.7 1.0
O C:LEU299 4.7 41.5 1.0
OE2 C:GLU251 4.7 39.5 1.0
CA C:GLY227 4.7 33.8 1.0
N C:VAL304 4.8 35.1 1.0
CA C:SER263 4.8 42.7 1.0
O C:VAL226 4.8 35.2 1.0
N C:TYR301 4.9 47.7 1.0
CB C:VAL304 4.9 34.2 1.0
CD2 C:TYR301 5.0 49.1 1.0
N C:ALA264 5.0 41.7 1.0

Sodium binding site 4 out of 4 in 5t6m

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Sodium binding site 4 out of 4 in the Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan 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 Structure of the Tryptophan Synthase B-Subunit From Pyroccus Furiosus with B-Methyltryptophan Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:44.6
occ:1.00
 O D:HOH536 2.4 40.3 1.0
O D:TYR301 2.6 42.3 1.0
O D:GLY303 2.7 40.6 1.0
O D:GLY227 3.1 35.8 1.0
OG D:SER265 3.1 50.6 1.0
O D:SER263 3.2 44.7 1.0
OG D:SER263 3.7 47.9 1.0
C D:TYR301 3.7 43.8 1.0
O D:HOH526 3.8 38.4 1.0
C D:GLY303 3.9 41.0 1.0
CB D:SER265 3.9 49.1 1.0
C D:GLY227 3.9 34.4 1.0
N D:SER265 4.3 47.2 1.0
C D:SER263 4.3 44.8 1.0
CA D:GLY227 4.4 34.1 1.0
C D:PRO302 4.5 44.3 1.0
N D:GLY303 4.5 43.2 1.0
CA D:TYR301 4.6 44.5 1.0
CB D:TYR301 4.7 43.9 1.0
CB D:VAL304 4.7 38.8 1.0
N D:PRO302 4.7 44.3 1.0
OE2 D:GLU251 4.7 39.5 1.0
O D:VAL226 4.7 34.8 1.0
CA D:GLY303 4.7 42.3 1.0
CA D:PRO302 4.7 44.8 1.0
N D:TYR301 4.7 45.0 1.0
N D:VAL304 4.8 40.1 1.0
O D:PRO302 4.8 45.1 1.0
CA D:SER265 4.8 48.4 1.0
CB D:SER263 4.8 45.5 1.0
O D:LEU299 4.8 41.8 1.0
CA D:VAL304 4.8 39.0 1.0
O D:HOH527 4.9 41.7 1.0
N D:GLY228 5.0 34.3 1.0
CD2 D:TYR301 5.0 44.6 1.0

Reference:

A.R.Buller, P.Van Roye, J.Murciano-Calles, F.H.Arnold. Tryptophan Synthase Uses An Atypical Mechanism to Achieve Substrate Specificity. Biochemistry V. 55 7043 2016.
ISSN: ISSN 1520-4995
PubMed: 27935677
DOI: 10.1021/ACS.BIOCHEM.6B01127
Page generated: Tue Oct 8 00:03:21 2024

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