Atomistry » Sodium » PDB 6cto-6d4o » 6cut
Atomistry »
  Sodium »
    PDB 6cto-6d4o »
      6cut »

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

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