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Sodium in PDB 7rnp: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound:
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound, PDB code: 7rnp was solved by P.M.Higgins, A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.162, 81.198, 321.014, 90, 90, 90
R / Rfree (%) 22.7 / 26.7

Other elements in 7rnp:

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound (pdb code 7rnp). 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 Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound, PDB code: 7rnp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-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, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:47.4
occ:1.00
 O A:SER263 2.6 51.8 1.0
O A:GLY303 2.6 50.2 1.0
O A:TYR301 2.7 55.6 1.0
OG A:SER265 3.0 53.4 1.0
O A:GLY227 3.2 46.5 1.0
C A:GLY303 3.7 51.1 1.0
C A:SER263 3.8 51.4 1.0
C A:TYR301 3.8 56.2 1.0
CB A:SER263 4.0 51.7 1.0
CB A:SER265 4.0 53.2 1.0
OE2 A:GLU251 4.1 62.1 1.0
C A:GLY227 4.2 46.0 1.0
N A:GLY303 4.3 53.9 1.0
N A:SER265 4.3 52.8 1.0
O A:LEU299 4.3 61.0 1.0
CA A:SER263 4.4 51.5 1.0
C A:PRO302 4.4 55.1 1.0
CB A:TYR301 4.6 55.7 1.0
CA A:GLY227 4.6 44.5 1.0
CA A:GLY303 4.6 53.2 1.0
CA A:TYR301 4.6 56.2 1.0
O A:PRO302 4.6 56.4 1.0
N A:VAL304 4.6 50.3 1.0
CB A:VAL304 4.6 49.1 1.0
N A:TYR301 4.7 55.0 1.0
O A:VAL226 4.7 47.4 1.0
CA A:VAL304 4.8 49.2 1.0
CA A:SER265 4.8 53.5 1.0
N A:PRO302 4.8 55.8 1.0
CD2 A:TYR301 4.8 57.1 1.0
N A:ALA264 4.9 51.7 1.0
CA A:PRO302 4.9 56.2 1.0
CD A:GLU251 5.0 59.0 1.0

Sodium binding site 2 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-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, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:64.1
occ:1.00
 O B:TYR301 2.5 75.4 1.0
O B:GLY303 2.6 70.5 1.0
O B:SER263 2.6 94.9 1.0
O B:GLY227 2.9 69.9 1.0
OG B:SER265 3.1 80.9 1.0
C B:TYR301 3.6 76.7 1.0
C B:GLY303 3.8 69.2 1.0
C B:SER263 3.8 93.5 1.0
OE2 B:GLU251 3.9 100.3 1.0
C B:GLY227 4.0 66.1 1.0
CB B:SER265 4.1 81.6 1.0
CB B:TYR301 4.2 73.1 1.0
CB B:SER263 4.2 93.3 1.0
N B:GLY303 4.2 73.3 1.0
CA B:TYR301 4.3 75.3 1.0
O B:LEU299 4.3 71.7 1.0
C B:PRO302 4.3 75.9 1.0
N B:SER265 4.4 83.2 1.0
CA B:GLY227 4.4 64.4 1.0
N B:TYR301 4.4 75.8 1.0
CA B:SER263 4.5 93.0 1.0
O B:PRO302 4.6 76.2 1.0
CA B:GLY303 4.6 72.1 1.0
N B:PRO302 4.6 77.3 1.0
CD2 B:TYR301 4.6 71.8 1.0
N B:VAL304 4.7 67.5 1.0
O B:VAL226 4.7 64.1 1.0
CD B:GLU251 4.8 99.0 1.0
CG B:TYR301 4.8 73.2 1.0
CA B:PRO302 4.8 78.5 1.0
CB B:VAL304 4.9 65.9 1.0
CA B:VAL304 4.9 65.7 1.0
CA B:SER265 4.9 82.9 1.0
N B:ALA264 4.9 83.0 1.0

Sodium binding site 3 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-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, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:71.2
occ:1.00
 O C:TYR301 2.6 77.0 1.0
O C:SER263 2.6 76.3 1.0
O C:GLY303 2.6 72.6 1.0
O C:GLY227 3.0 63.1 1.0
OG C:SER265 3.2 77.5 1.0
OE2 C:GLU251 3.4 74.5 1.0
C C:TYR301 3.7 79.5 1.0
C C:SER263 3.8 78.7 1.0
C C:GLY303 3.9 72.6 1.0
C C:GLY227 4.0 60.7 1.0
CB C:SER265 4.0 77.6 1.0
N C:SER265 4.2 78.2 1.0
O C:LEU299 4.2 72.7 1.0
CB C:TYR301 4.2 76.4 1.0
CB C:SER263 4.3 81.1 1.0
CD C:GLU251 4.4 73.0 1.0
CA C:TYR301 4.4 78.8 1.0
CA C:GLY227 4.4 61.2 1.0
O C:VAL226 4.6 63.1 1.0
C C:PRO302 4.6 80.6 1.0
CB C:VAL304 4.6 68.5 1.0
CA C:SER263 4.6 80.6 1.0
N C:GLY303 4.6 78.0 1.0
CD2 C:TYR301 4.6 75.5 1.0
N C:TYR301 4.6 78.1 1.0
N C:VAL304 4.7 71.1 1.0
O C:PRO302 4.7 81.1 1.0
CA C:VAL304 4.8 68.3 1.0
CA C:SER265 4.8 78.3 1.0
N C:PRO302 4.8 81.8 1.0
CG2 C:VAL304 4.8 66.5 1.0
CA C:GLY303 4.8 76.0 1.0
CG C:TYR301 4.9 77.8 1.0
CG C:GLU251 4.9 69.1 1.0
N C:ALA264 4.9 78.7 1.0

Sodium binding site 4 out of 4 in 7rnp

Go back to Sodium Binding Sites List in 7rnp
Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9_H275E with 4-Cl-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, PFTRPB2B9_H275E with 4-Cl-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:80.4
occ:1.00
 O D:SER263 2.6 86.2 1.0
O D:GLY303 2.8 79.4 1.0
O D:TYR301 2.9 85.3 1.0
O D:GLY227 3.0 70.3 1.0
OG D:SER265 3.7 89.3 1.0
C D:SER263 3.9 86.8 1.0
OE2 D:GLU251 4.0 85.7 1.0
C D:GLY303 4.0 79.4 1.0
C D:TYR301 4.0 86.2 1.0
C D:GLY227 4.1 69.3 1.0
O D:LEU299 4.1 82.7 1.0
CB D:TYR301 4.3 84.0 1.0
N D:SER265 4.3 91.1 1.0
CB D:SER265 4.3 89.6 1.0
CA D:GLY227 4.5 69.6 1.0
O D:VAL226 4.5 74.8 1.0
CA D:TYR301 4.5 85.3 1.0
CB D:SER263 4.5 87.8 1.0
N D:TYR301 4.6 85.5 1.0
CD D:GLU251 4.6 84.9 1.0
N D:GLY303 4.7 82.8 1.0
CB D:VAL304 4.7 76.1 1.0
CA D:SER263 4.7 87.8 1.0
C D:PRO302 4.8 85.7 1.0
CD2 D:TYR301 4.8 83.9 1.0
N D:ALA264 4.8 88.2 1.0
N D:VAL304 4.8 77.6 1.0
CA D:GLY303 4.9 81.7 1.0
CG D:GLU251 4.9 81.3 1.0
CA D:VAL304 4.9 74.4 1.0
O D:PRO302 4.9 87.2 1.0
CA D:ALA264 4.9 90.6 1.0
CA D:SER265 5.0 90.3 1.0
CG D:TYR301 5.0 85.0 1.0

Reference:

P.M.Higgins, A.R.Buller. Direct Assessment of Promiscuity During Protein Engineering By Substrate Multiplexed Screening To Be Published.
Page generated: Fri Apr 7 16:09:52 2023

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