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Sodium in PDB 6cuz: Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate

Enzymatic activity of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate

All present enzymatic activity of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate:
4.2.1.20;

Protein crystallography data

The structure of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate, PDB code: 6cuz was solved by R.A.Scheele, A.R.Buller, C.E.Boville, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.222, 109.297, 159.928, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 26.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate (pdb code 6cuz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate, PDB code: 6cuz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6cuz

Go back to Sodium Binding Sites List in 6cuz
Sodium binding site 1 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.7
occ:1.00
 O A:HOH566 2.4 32.7 1.0
O A:TYR301 2.4 42.8 1.0
O A:HOH531 2.6 33.6 1.0
O A:GLY303 2.7 27.9 1.0
OG A:SER265 2.8 30.4 1.0
O A:SER263 3.0 32.0 1.0
C A:TYR301 3.6 44.2 1.0
O A:GLY227 3.7 24.1 1.0
C A:GLY303 3.7 28.1 1.0
CB A:SER265 3.9 30.4 1.0
OG A:SER263 3.9 33.7 1.0
O A:HOH540 3.9 27.1 1.0
N A:GLY303 3.9 30.8 1.0
C A:SER263 4.1 32.9 1.0
C A:PRO302 4.1 32.1 1.0
C A:GLY227 4.2 23.8 1.0
N A:SER265 4.3 31.2 1.0
CA A:GLY303 4.3 29.8 1.0
CA A:PRO302 4.4 33.4 1.0
N A:PRO302 4.4 33.6 1.0
O A:LEU299 4.5 38.7 1.0
CA A:TYR301 4.5 45.0 1.0
CB A:SER263 4.5 33.8 1.0
CA A:GLY227 4.6 24.2 1.0
CB A:TYR301 4.6 45.5 1.0
OE2 A:GLU251 4.6 28.4 1.0
N A:VAL304 4.7 27.0 1.0
O A:PRO302 4.7 32.3 1.0
CA A:SER265 4.7 31.2 1.0
CA A:SER263 4.8 34.2 1.0
N A:TYR301 4.8 43.9 1.0
CB A:VAL304 4.9 25.2 1.0
CD2 A:TYR301 4.9 47.1 1.0
CA A:VAL304 4.9 25.7 1.0
O A:VAL226 5.0 25.3 1.0

Sodium binding site 2 out of 6 in 6cuz

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Sodium binding site 2 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:39.1
occ:1.00
 O B:HOH607 2.7 33.0 1.0
O A:HOH618 2.7 40.8 1.0
O A:GLY48 2.9 25.6 1.0
O B:PRO50 3.1 24.7 1.0
O B:GLY48 3.1 26.2 1.0
O A:PRO50 3.4 24.6 1.0
O A:HOH545 4.0 38.2 1.0
C A:GLY48 4.0 24.7 1.0
O B:HOH540 4.1 32.7 1.0
C B:GLY48 4.2 26.1 1.0
O A:HOH579 4.2 28.7 1.0
C B:PRO50 4.2 24.9 1.0
C A:PRO50 4.5 24.2 1.0
O B:HOH523 4.6 28.6 1.0
CA A:GLY48 4.6 25.0 1.0
CA B:GLY48 4.8 26.5 1.0
N B:PRO50 4.9 25.7 1.0
C A:ARG49 4.9 24.4 1.0
CA B:THR51 4.9 24.2 1.0
C B:ARG49 4.9 25.8 1.0
N A:PRO50 5.0 24.6 1.0

Sodium binding site 3 out of 6 in 6cuz

Go back to Sodium Binding Sites List in 6cuz
Sodium binding site 3 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:26.8
occ:1.00
 O B:HOH584 2.4 34.8 1.0
O B:TYR301 2.5 41.4 1.0
O B:SER263 2.7 38.8 1.0
O B:GLY303 2.7 36.0 1.0
OG B:SER265 2.8 36.4 1.0
O B:GLY227 3.6 29.3 1.0
C B:TYR301 3.7 42.4 1.0
O B:HOH533 3.8 24.9 1.0
C B:GLY303 3.8 36.9 1.0
C B:SER263 3.8 39.0 1.0
CB B:SER265 3.9 35.8 1.0
CB B:SER263 4.0 42.0 1.0
C B:PRO302 4.2 41.9 1.0
N B:GLY303 4.2 40.1 1.0
N B:SER265 4.2 36.4 1.0
C B:GLY227 4.3 29.1 1.0
O B:LEU299 4.3 39.4 1.0
O B:PRO302 4.4 42.5 1.0
CA B:SER263 4.4 40.3 1.0
CA B:GLY303 4.5 39.0 1.0
CA B:GLY227 4.6 29.1 1.0
CA B:TYR301 4.6 42.6 1.0
N B:PRO302 4.6 43.3 1.0
CA B:PRO302 4.6 43.4 1.0
CB B:TYR301 4.6 42.0 1.0
CA B:SER265 4.7 35.8 1.0
CD2 B:TYR301 4.7 42.6 1.0
CB B:VAL304 4.7 34.2 1.0
N B:VAL304 4.7 35.9 1.0
N B:TYR301 4.7 42.3 1.0
OE2 B:GLU251 4.8 32.9 1.0
CA B:VAL304 4.9 34.2 1.0
O B:VAL226 4.9 29.5 1.0
N B:ALA264 4.9 38.2 1.0

Sodium binding site 4 out of 6 in 6cuz

Go back to Sodium Binding Sites List in 6cuz
Sodium binding site 4 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:22.6
occ:1.00
 O C:HOH555 2.4 35.9 1.0
O C:TYR301 2.6 48.4 1.0
O C:GLY303 2.7 26.1 1.0
OG C:SER265 2.8 34.6 1.0
O C:SER263 2.9 39.0 1.0
OG C:SER263 3.0 42.4 1.0
C C:TYR301 3.8 50.0 1.0
C C:GLY303 3.8 26.8 1.0
O C:GLY227 3.8 23.5 1.0
CB C:SER265 3.8 34.0 1.0
O C:HOH566 3.8 27.4 1.0
C C:SER263 3.9 39.5 1.0
CB C:SER263 4.1 43.1 1.0
N C:GLY303 4.1 29.4 1.0
C C:PRO302 4.2 30.7 1.0
N C:SER265 4.2 35.5 1.0
C C:GLY227 4.4 22.9 1.0
O C:PRO302 4.4 31.3 1.0
CA C:GLY303 4.4 28.4 1.0
CA C:SER263 4.5 41.5 1.0
OE2 C:GLU251 4.6 26.8 1.0
CA C:PRO302 4.6 31.5 1.0
N C:PRO302 4.6 30.7 1.0
CA C:SER265 4.7 34.5 1.0
CA C:GLY227 4.7 23.1 1.0
CA C:TYR301 4.7 50.8 1.0
O C:LEU299 4.7 45.0 1.0
N C:VAL304 4.8 26.1 1.0
N C:TYR301 4.8 49.8 1.0
CB C:TYR301 4.8 50.7 1.0
CB C:VAL304 4.8 24.8 1.0
N C:ALA264 4.9 38.7 1.0

Sodium binding site 5 out of 6 in 6cuz

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Sodium binding site 5 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:19.0
occ:1.00
 O D:HOH566 2.4 29.0 1.0
O D:TYR301 2.5 33.0 1.0
O D:HOH513 2.6 33.3 1.0
O D:GLY303 2.6 29.3 1.0
OG D:SER265 2.8 31.1 1.0
O D:SER263 2.8 29.3 1.0
C D:GLY303 3.6 30.2 1.0
O D:GLY227 3.6 24.3 1.0
C D:TYR301 3.7 33.8 1.0
O D:HOH558 3.8 22.9 1.0
CB D:SER265 3.8 31.0 1.0
C D:SER263 3.9 30.1 1.0
N D:GLY303 4.0 32.9 1.0
C D:PRO302 4.0 34.1 1.0
CB D:SER263 4.2 30.0 1.0
C D:GLY227 4.3 23.9 1.0
N D:SER265 4.3 30.6 1.0
O D:PRO302 4.3 34.5 1.0
CA D:GLY303 4.3 32.1 1.0
O D:LEU299 4.5 29.8 1.0
CA D:SER263 4.5 30.7 1.0
CA D:PRO302 4.5 35.4 1.0
CD2 D:TYR301 4.6 33.8 1.0
CA D:TYR301 4.6 34.0 1.0
N D:PRO302 4.6 35.2 1.0
N D:VAL304 4.6 29.5 1.0
CB D:TYR301 4.6 33.7 1.0
CA D:GLY227 4.6 23.6 1.0
CB D:VAL304 4.7 27.9 1.0
CA D:SER265 4.7 31.5 1.0
N D:TYR301 4.7 33.2 1.0
CA D:VAL304 4.8 28.1 1.0
OE2 D:GLU251 4.8 26.1 1.0
CG D:TYR301 5.0 34.5 1.0

Sodium binding site 6 out of 6 in 6cuz

Go back to Sodium Binding Sites List in 6cuz
Sodium binding site 6 out of 6 in the Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Engineered Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3R)- Ethylserine Bound As the Amino-Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:32.4
occ:1.00
 O D:HOH633 2.5 33.0 1.0
O C:HOH620 2.8 35.5 1.0
O D:GLY48 2.9 24.4 1.0
O D:PRO50 2.9 22.4 1.0
O C:GLY48 3.1 21.9 1.0
O C:PRO50 3.7 20.7 1.0
C D:PRO50 4.0 22.7 1.0
C D:GLY48 4.0 24.3 1.0
C C:GLY48 4.1 21.4 1.0
O C:HOH517 4.1 33.4 1.0
O C:HOH575 4.1 27.6 1.0
O D:HOH606 4.1 32.4 1.0
O D:HOH507 4.4 28.2 1.0
O D:HOH550 4.4 33.4 1.0
CA C:GLY48 4.6 21.6 1.0
N D:PRO50 4.7 24.2 1.0
CA D:THR51 4.7 21.5 1.0
C D:ARG49 4.7 24.3 1.0
CA D:GLY48 4.8 24.6 1.0
N D:THR51 4.8 22.0 1.0
CD D:PRO52 4.8 21.2 1.0
C C:PRO50 4.8 20.4 1.0
CD D:PRO50 4.9 25.1 1.0
CA D:PRO50 5.0 23.5 1.0
N D:ARG49 5.0 24.2 1.0

Reference:

C.E.Boville, R.A.Scheele, P.Koch, S.Brinkmann-Chen, A.R.Buller, F.H.Arnold. Engineered Biosynthesis of Beta-Alkyl Tryptophan Analogues. Angew. Chem. Int. Ed. Engl. V. 57 14764 2018.
ISSN: ESSN 1521-3773
PubMed: 30215880
DOI: 10.1002/ANIE.201807998
Page generated: Tue Oct 8 06:47:58 2024

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