Atomistry » Sodium » PDB 5ddq-5dy9 » 5dw3
Atomistry »
  Sodium »
    PDB 5ddq-5dy9 »
      5dw3 »

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

Go back to Sodium Binding Sites List in 5dw3
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

Go back to Sodium Binding Sites List in 5dw3
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

Go back to Sodium Binding Sites List in 5dw3
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy