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

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

All present enzymatic activity of Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine 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 L- Threonine Non-Covalently Bound in the Active Site, PDB code: 5ixj was solved by A.R.Buller, M.Herger, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.718, 112.367, 160.310, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine Non-Covalently Bound in the Active Site (pdb code 5ixj). 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 L- Threonine Non-Covalently Bound in the Active Site, PDB code: 5ixj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ixj

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Sodium binding site 1 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine 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 L- Threonine Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:37.9
occ:1.00
 OG A:SER265 2.6 27.4 1.0
O A:TYR301 2.6 22.4 1.0
O A:HOH521 2.7 17.0 0.5
O A:SER263 2.8 23.3 1.0
O A:HOH575 3.1 24.7 1.0
OG A:SER263 3.2 26.6 1.0
O A:HOH521 3.2 19.3 0.5
O A:GLY303 3.3 18.9 1.0
N A:GLY303 3.5 20.9 1.0
CB A:SER265 3.6 25.3 1.0
C A:SER263 3.6 24.0 1.0
C A:TYR301 3.7 22.7 1.0
N A:SER265 3.7 23.6 1.0
C A:PRO302 3.8 22.3 1.0
C A:GLY303 3.9 19.1 1.0
CA A:PRO302 3.9 23.3 1.0
CA A:GLY303 4.1 20.2 1.0
CB A:SER263 4.2 25.4 1.0
CD1 A:LEU282 4.2 25.8 1.0
CA A:SER263 4.2 24.8 1.0
CA A:SER265 4.2 24.5 1.0
N A:PRO302 4.3 22.9 1.0
N A:ALA264 4.4 23.3 1.0
O A:PRO302 4.5 23.5 1.0
O A:HOH589 4.6 19.1 1.0
C A:ALA264 4.7 23.8 1.0
O A:GLY227 4.8 19.8 1.0
CA A:ALA264 4.8 23.2 1.0
CG A:LEU282 4.9 25.6 1.0
CA A:TYR301 5.0 22.7 1.0
OE2 A:GLU251 5.0 22.5 1.0

Sodium binding site 2 out of 4 in 5ixj

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Sodium binding site 2 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine 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 L- Threonine Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:28.4
occ:1.00
 O B:HOH576 2.0 17.2 0.5
OG B:SER265 2.6 25.9 1.0
O B:TYR301 2.6 32.4 1.0
O B:HOH600 2.8 28.1 1.0
O B:SER263 2.8 23.4 1.0
O B:HOH576 2.8 16.4 0.5
O B:GLY303 2.9 20.6 1.0
OG B:SER263 3.4 27.6 1.0
CB B:SER265 3.6 24.1 1.0
C B:TYR301 3.8 32.7 1.0
C B:SER263 3.8 23.1 1.0
C B:GLY303 3.8 20.9 1.0
N B:GLY303 3.8 23.2 1.0
C B:PRO302 3.9 25.3 1.0
N B:SER265 3.9 22.2 1.0
CA B:GLY303 4.2 22.5 1.0
CA B:PRO302 4.2 26.1 1.0
O B:HOH608 4.3 20.4 1.0
CB B:SER263 4.3 24.8 1.0
O B:PRO302 4.3 26.6 1.0
O B:GLY227 4.3 20.4 1.0
CA B:SER265 4.3 23.1 1.0
CA B:SER263 4.4 23.8 1.0
N B:PRO302 4.5 26.1 1.0
CD1 B:LEU282 4.5 27.4 1.0
N B:ALA264 4.7 22.2 1.0
O B:LEU299 4.7 31.6 1.0
OE2 B:GLU251 4.8 21.2 1.0
CA B:TYR301 4.9 33.2 1.0
C B:ALA264 4.9 22.1 1.0
N B:VAL304 4.9 19.6 1.0
C B:GLY227 4.9 18.4 1.0
CA B:ALA264 5.0 21.9 1.0

Sodium binding site 3 out of 4 in 5ixj

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Sodium binding site 3 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine 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 L- Threonine Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:39.3
occ:1.00
 O C:HOH624 2.5 15.1 0.5
OG C:SER265 2.7 29.4 1.0
O C:TYR301 2.7 25.0 1.0
O C:SER263 2.8 26.3 1.0
O C:HOH588 3.1 28.1 1.0
O C:HOH624 3.2 21.1 0.5
OG C:SER263 3.2 28.6 1.0
O C:GLY303 3.4 21.3 1.0
C C:SER263 3.6 26.3 1.0
N C:GLY303 3.6 22.8 1.0
CB C:SER265 3.6 26.6 1.0
N C:SER265 3.7 24.8 1.0
C C:TYR301 3.9 24.8 1.0
C C:PRO302 3.9 24.0 1.0
C C:GLY303 4.0 22.0 1.0
CA C:GLY303 4.1 22.8 1.0
CA C:PRO302 4.1 25.0 1.0
CB C:SER263 4.2 28.1 1.0
CA C:SER263 4.2 27.5 1.0
CD1 C:LEU282 4.2 28.2 1.0
CA C:SER265 4.2 25.5 1.0
N C:ALA264 4.4 25.9 1.0
O C:HOH591 4.4 23.7 1.0
N C:PRO302 4.5 24.5 1.0
O C:PRO302 4.6 25.3 1.0
C C:ALA264 4.7 25.4 1.0
O C:GLY227 4.7 24.1 1.0
CA C:ALA264 4.8 25.5 1.0
CG C:LEU282 4.9 27.7 1.0

Sodium binding site 4 out of 4 in 5ixj

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Sodium binding site 4 out of 4 in the Tryptophan Synthase Beta-Subunit From Pyrococcus Furiosus with L- Threonine 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 L- Threonine Non-Covalently Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:32.7
occ:1.00
 O D:HOH551 2.1 19.3 0.5
O D:TYR301 2.5 32.4 1.0
O D:HOH639 2.6 29.8 1.0
OG D:SER265 2.8 30.0 1.0
O D:SER263 2.8 26.6 1.0
O D:HOH551 2.9 19.2 0.5
O D:GLY303 2.9 23.2 1.0
OG D:SER263 3.0 31.2 1.0
C D:TYR301 3.7 33.8 1.0
C D:SER263 3.8 26.1 1.0
CB D:SER265 3.8 28.1 1.0
C D:GLY303 3.9 23.6 1.0
N D:GLY303 3.9 26.2 1.0
C D:PRO302 4.0 28.2 1.0
N D:SER265 4.1 25.6 1.0
CB D:SER263 4.1 28.2 1.0
O D:HOH609 4.2 22.2 1.0
O D:GLY227 4.2 21.6 1.0
CA D:PRO302 4.2 28.2 1.0
CA D:GLY303 4.3 25.2 1.0
CA D:SER263 4.3 27.0 1.0
O D:PRO302 4.4 31.0 1.0
N D:PRO302 4.4 27.8 1.0
CA D:SER265 4.5 26.9 1.0
N D:ALA264 4.7 25.1 1.0
CA D:TYR301 4.7 34.4 1.0
C D:GLY227 4.8 19.2 1.0
CD1 D:LEU282 4.8 29.3 1.0
N D:TYR301 4.9 33.7 1.0
O D:LEU299 4.9 33.5 1.0
OE2 D:GLU251 4.9 23.3 1.0
N D:VAL304 5.0 22.6 1.0
CB D:TYR301 5.0 34.3 1.0

Reference:

M.Herger, P.Van Roye, D.K.Romney, S.Brinkmann-Chen, A.R.Buller, F.H.Arnold. Synthesis of Beta-Branched Tryptophan Analogues Using An Engineered Subunit of Tryptophan Synthase. J.Am.Chem.Soc. V. 138 8388 2016.
ISSN: ESSN 1520-5126
PubMed: 27355405
DOI: 10.1021/JACS.6B04836
Page generated: Mon Oct 7 21:44:43 2024

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