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Sodium in PDB 6cut: Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine

Enzymatic activity of Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine

All present enzymatic activity of Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine:
4.2.1.20;

Protein crystallography data

The structure of Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine, PDB code: 6cut was solved by C.E.Boville, R.A.Scheele, 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 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.225, 107.434, 159.251, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.5

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 6cut

Go back to Sodium Binding Sites List in 6cut
Sodium binding site 1 out of 4 in the Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:45.6
occ:1.00
 O A:HOH535 2.3 39.1 1.0
O A:GLY303 2.5 40.6 1.0
O A:TYR301 2.7 45.5 1.0
O A:SER263 3.0 46.7 1.0
OG A:SER265 3.1 47.6 1.0
O A:GLY227 3.3 33.9 1.0
C A:GLY303 3.6 41.2 1.0
O A:HOH524 3.8 42.8 1.0
C A:TYR301 3.9 46.6 1.0
CB A:SER265 3.9 47.1 1.0
C A:GLY227 4.0 32.7 1.0
N A:GLY303 4.1 43.7 1.0
C A:SER263 4.1 47.2 1.0
CB A:SER263 4.3 47.0 1.0
CA A:GLY303 4.4 42.9 1.0
N A:SER265 4.4 47.0 1.0
C A:PRO302 4.4 45.8 1.0
CA A:GLY227 4.4 32.6 1.0
O A:LEU299 4.4 43.2 1.0
OE2 A:GLU251 4.5 39.5 1.0
N A:VAL304 4.6 40.0 1.0
CB A:VAL304 4.7 39.0 1.0
O A:VAL226 4.7 33.7 1.0
CA A:SER263 4.7 47.7 1.0
CA A:TYR301 4.8 47.2 1.0
CA A:SER265 4.8 47.7 1.0
CB A:TYR301 4.8 46.6 1.0
N A:PRO302 4.8 46.8 1.0
CA A:PRO302 4.8 46.9 1.0
CA A:VAL304 4.8 38.7 1.0
O A:PRO302 4.8 47.1 1.0
N A:TYR301 4.8 47.3 1.0
CD2 A:TYR301 4.9 46.9 1.0

Sodium binding site 2 out of 4 in 6cut

Go back to Sodium Binding Sites List in 6cut
Sodium binding site 2 out of 4 in the Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine


Mono view


Stereo pair view

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

b:34.8
occ:1.00
 O B:HOH557 2.4 39.8 1.0
O B:TYR301 2.5 46.7 1.0
O B:GLY303 2.7 37.6 1.0
OG B:SER265 2.8 39.0 1.0
O B:SER263 2.8 39.3 1.0
OG B:SER263 3.0 42.2 1.0
O B:GLY227 3.6 32.5 1.0
C B:GLY303 3.7 38.3 1.0
C B:TYR301 3.8 47.2 1.0
CB B:SER265 3.8 38.4 1.0
C B:SER263 3.9 40.2 1.0
O B:HOH528 3.9 31.3 1.0
N B:GLY303 4.0 41.6 1.0
C B:PRO302 4.1 43.9 1.0
CB B:SER263 4.1 41.4 1.0
N B:SER265 4.2 38.6 1.0
C B:GLY227 4.3 31.8 1.0
O B:PRO302 4.3 44.3 1.0
O B:LEU299 4.3 42.4 1.0
CA B:GLY303 4.3 40.0 1.0
CA B:SER263 4.5 41.6 1.0
CA B:PRO302 4.6 46.0 1.0
N B:PRO302 4.6 46.6 1.0
CA B:SER265 4.7 38.8 1.0
CA B:GLY227 4.7 31.8 1.0
CA B:TYR301 4.7 47.8 1.0
N B:VAL304 4.7 36.7 1.0
N B:TYR301 4.7 47.7 1.0
CD2 B:TYR301 4.8 47.4 1.0
CB B:TYR301 4.8 47.4 1.0
CB B:VAL304 4.8 35.2 1.0
OE2 B:GLU251 4.9 36.0 1.0
CA B:VAL304 5.0 35.4 1.0
N B:ALA264 5.0 40.3 1.0

Sodium binding site 3 out of 4 in 6cut

Go back to Sodium Binding Sites List in 6cut
Sodium binding site 3 out of 4 in the Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine


Mono view


Stereo pair view

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

b:39.4
occ:1.00
 O C:HOH545 2.4 40.1 1.0
O C:TYR301 2.5 51.0 1.0
O C:GLY303 2.7 43.0 1.0
O C:SER263 2.8 41.1 1.0
OG C:SER265 2.8 45.1 1.0
O C:GLY227 3.6 33.3 1.0
C C:TYR301 3.7 52.0 1.0
C C:GLY303 3.7 43.8 1.0
O C:HOH555 3.8 30.7 1.0
C C:SER263 3.8 42.3 1.0
CB C:SER265 3.9 44.6 1.0
N C:GLY303 4.0 47.4 1.0
CB C:SER263 4.1 43.4 1.0
C C:PRO302 4.1 49.5 1.0
N C:SER265 4.2 43.1 1.0
C C:GLY227 4.3 32.5 1.0
CA C:GLY303 4.4 46.1 1.0
O C:LEU299 4.4 43.0 1.0
CA C:SER263 4.4 43.7 1.0
CA C:PRO302 4.5 51.5 1.0
O C:PRO302 4.5 49.9 1.0
N C:PRO302 4.6 52.1 1.0
CA C:GLY227 4.6 32.0 1.0
OE2 C:GLU251 4.6 37.4 1.0
CA C:TYR301 4.7 52.5 1.0
CD2 C:TYR301 4.7 54.1 1.0
N C:VAL304 4.7 42.2 1.0
CA C:SER265 4.8 44.6 1.0
CB C:TYR301 4.8 52.5 1.0
N C:TYR301 4.8 51.5 1.0
CB C:VAL304 4.9 39.4 1.0
N C:ALA264 4.9 42.6 1.0
O C:VAL226 5.0 32.1 1.0

Sodium binding site 4 out of 4 in 6cut

Go back to Sodium Binding Sites List in 6cut
Sodium binding site 4 out of 4 in the Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Holo Trpb From Pyrococcus Furiosus, PFTRPB7E6 with (2S,3S)- Isopropylserine Bound As the External Aldimine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:35.7
occ:1.00
 O D:HOH558 2.3 38.9 1.0
O D:TYR301 2.6 45.1 1.0
O D:GLY303 2.7 40.2 1.0
OG D:SER265 2.7 44.6 1.0
O D:SER263 2.9 42.8 1.0
O D:GLY227 3.5 35.9 1.0
C D:GLY303 3.7 40.6 1.0
C D:TYR301 3.7 45.6 1.0
CB D:SER265 3.8 44.4 1.0
O D:HOH537 3.9 36.9 1.0
C D:SER263 4.0 44.2 1.0
N D:GLY303 4.0 43.2 1.0
C D:PRO302 4.1 45.1 1.0
CB D:SER263 4.1 44.0 1.0
C D:GLY227 4.2 34.9 1.0
N D:SER265 4.3 44.3 1.0
O D:LEU299 4.3 41.0 1.0
O D:PRO302 4.4 45.9 1.0
CA D:GLY303 4.4 42.2 1.0
CA D:SER263 4.6 45.1 1.0
CA D:GLY227 4.6 34.5 1.0
N D:VAL304 4.6 39.6 1.0
CA D:PRO302 4.6 46.4 1.0
N D:PRO302 4.6 46.1 1.0
OE2 D:GLU251 4.6 39.9 1.0
CA D:TYR301 4.6 45.4 1.0
CB D:VAL304 4.7 37.8 1.0
CD2 D:TYR301 4.7 44.8 1.0
CB D:TYR301 4.7 44.7 1.0
CA D:SER265 4.7 44.9 1.0
N D:TYR301 4.7 45.2 1.0
CA D:VAL304 4.8 37.9 1.0
O D:VAL226 5.0 34.5 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 06:47:27 2024

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