Atomistry » Sodium » PDB 6ahh-6awy » 6ami
Atomistry »
  Sodium »
    PDB 6ahh-6awy »
      6ami »

Sodium in PDB 6ami: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound:
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound, PDB code: 6ami was solved by A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.682, 109.921, 160.267, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound (pdb code 6ami). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound, PDB code: 6ami:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 1 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp 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 Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:46.0
occ:1.00
 O A:HOH543 2.3 35.9 1.0
O A:GLY303 2.5 48.5 1.0
O A:TYR301 2.6 48.2 1.0
OG A:SER265 2.6 47.3 1.0
O A:SER263 2.7 49.7 1.0
O A:GLY227 3.6 48.0 1.0
C A:GLY303 3.6 49.5 1.0
C A:TYR301 3.7 48.8 1.0
CB A:SER265 3.7 47.6 1.0
C A:SER263 3.8 49.8 1.0
O A:HOH525 3.9 40.3 1.0
N A:GLY303 4.1 51.6 1.0
C A:PRO302 4.1 52.7 1.0
CB A:SER263 4.1 51.6 1.0
N A:SER265 4.2 48.9 1.0
O A:PRO302 4.4 53.3 1.0
CA A:GLY303 4.4 51.2 1.0
C A:GLY227 4.4 46.6 1.0
CA A:SER263 4.5 50.1 1.0
CB A:VAL304 4.5 47.6 1.0
N A:VAL304 4.6 49.0 1.0
CA A:PRO302 4.6 53.2 1.0
CA A:SER265 4.6 48.2 1.0
N A:PRO302 4.6 52.4 1.0
CA A:TYR301 4.6 48.8 1.0
CB A:TYR301 4.6 49.2 1.0
O A:LEU299 4.7 46.3 1.0
CD2 A:TYR301 4.7 51.4 1.0
CA A:VAL304 4.7 47.6 1.0
N A:TYR301 4.8 47.9 1.0
OE2 A:GLU251 4.8 51.6 1.0
CA A:GLY227 4.8 45.1 1.0
N A:ALA264 4.9 50.0 1.0

Sodium binding site 2 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 2 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp 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 Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:36.8
occ:1.00
 O B:HOH529 2.2 34.9 1.0
O B:GLY303 2.5 35.4 1.0
O B:TYR301 2.5 35.9 1.0
O B:SER263 2.6 36.2 1.0
OG B:SER265 2.9 35.0 1.0
O B:GLY227 3.4 32.2 1.0
C B:GLY303 3.6 36.0 1.0
C B:TYR301 3.7 36.4 1.0
C B:SER263 3.7 36.5 1.0
O B:HOH540 3.8 33.8 1.0
CB B:SER265 3.9 35.3 1.0
CB B:SER263 4.0 37.4 1.0
N B:GLY303 4.1 37.1 1.0
C B:PRO302 4.1 37.6 1.0
N B:SER265 4.2 36.2 1.0
C B:GLY227 4.3 31.6 1.0
CA B:SER263 4.4 37.1 1.0
CA B:GLY303 4.4 37.0 1.0
O B:PRO302 4.4 38.1 1.0
O B:LEU299 4.5 34.3 1.0
CD2 B:TYR301 4.5 35.7 1.0
OE2 B:GLU251 4.6 35.7 1.0
CA B:PRO302 4.6 38.0 1.0
N B:PRO302 4.6 37.4 1.0
CA B:TYR301 4.6 36.0 1.0
N B:VAL304 4.6 36.1 1.0
CB B:TYR301 4.6 35.4 1.0
CA B:SER265 4.7 36.0 1.0
CB B:VAL304 4.7 35.5 1.0
N B:TYR301 4.7 35.6 1.0
N B:ALA264 4.8 36.9 1.0
CA B:GLY227 4.8 31.3 1.0
CA B:VAL304 4.8 35.5 1.0

Sodium binding site 3 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 3 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp 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 Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:34.0
occ:1.00
 O C:HOH531 2.3 29.6 1.0
O C:GLY303 2.5 36.5 1.0
O C:TYR301 2.5 37.0 1.0
O C:SER263 2.5 39.6 1.0
OG C:SER265 2.7 44.0 1.0
O C:GLY227 3.6 37.9 1.0
C C:GLY303 3.6 37.3 1.0
C C:TYR301 3.7 37.7 1.0
C C:SER263 3.7 39.5 1.0
CB C:SER265 3.8 45.0 1.0
O C:HOH530 3.9 35.2 1.0
CB C:SER263 4.0 38.9 1.0
C C:PRO302 4.1 39.4 1.0
N C:SER265 4.1 42.5 1.0
N C:GLY303 4.1 38.8 1.0
O C:PRO302 4.3 39.9 1.0
CA C:SER263 4.3 39.4 1.0
CA C:GLY303 4.4 38.6 1.0
O C:LEU299 4.5 34.7 1.0
CA C:TYR301 4.5 37.2 1.0
CB C:TYR301 4.5 36.4 1.0
C C:GLY227 4.5 37.1 1.0
CA C:PRO302 4.6 39.9 1.0
N C:PRO302 4.6 39.1 1.0
CA C:SER265 4.6 44.7 1.0
N C:TYR301 4.6 36.6 1.0
N C:VAL304 4.6 37.5 1.0
OE2 C:GLU251 4.7 39.9 1.0
CD2 C:TYR301 4.7 37.0 1.0
CB C:VAL304 4.7 36.7 1.0
N C:ALA264 4.8 39.7 1.0
CA C:VAL304 4.9 36.7 1.0

Sodium binding site 4 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 4 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp 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 Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:34.9
occ:1.00
 OE1 C:GLN283 2.7 50.1 1.0
O C:GLY287 2.7 55.2 1.0
CD C:GLN283 3.5 48.5 1.0
C C:GLY287 3.7 56.5 1.0
CA C:GLY287 3.9 57.6 1.0
NE2 C:GLN283 4.2 47.4 1.0
CG C:GLN283 4.4 48.0 1.0
O C:VAL271 4.8 48.4 1.0
N C:GLN288 4.9 57.5 1.0

Sodium binding site 5 out of 5 in 6ami

Go back to Sodium Binding Sites List in 6ami
Sodium binding site 5 out of 5 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:48.8
occ:1.00
 O D:GLY303 2.5 49.4 1.0
O D:SER263 2.6 51.1 1.0
O D:TYR301 2.7 51.3 1.0
OG D:SER265 2.9 50.1 1.0
O D:GLY227 3.3 44.7 1.0
C D:GLY303 3.6 49.9 1.0
C D:SER263 3.8 51.1 1.0
C D:TYR301 3.8 52.0 1.0
CB D:SER265 3.9 50.1 1.0
N D:SER265 4.1 50.8 1.0
CB D:SER263 4.1 53.3 1.0
N D:GLY303 4.2 52.4 1.0
C D:GLY227 4.3 43.8 1.0
C D:PRO302 4.3 53.5 1.0
CA D:GLY303 4.4 51.7 1.0
OE2 D:GLU251 4.4 48.2 1.0
O D:LEU299 4.5 46.8 1.0
CA D:SER263 4.5 51.6 1.0
CB D:TYR301 4.5 50.5 1.0
O D:PRO302 4.6 53.9 1.0
CD2 D:TYR301 4.6 51.0 1.0
CA D:TYR301 4.6 51.5 1.0
CA D:SER265 4.6 50.4 1.0
N D:VAL304 4.6 49.4 1.0
CB D:VAL304 4.7 47.6 1.0
N D:TYR301 4.7 50.6 1.0
N D:ALA264 4.8 51.2 1.0
N D:PRO302 4.8 53.5 1.0
CA D:GLY227 4.8 42.6 1.0
CA D:VAL304 4.9 48.0 1.0
O D:VAL226 4.9 42.9 1.0
CA D:PRO302 4.9 54.5 1.0
CG D:TYR301 4.9 51.5 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 01:51:21 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy