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Sodium in PDB 7rof: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-Trp Non-Covalently Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-Trp Non-Covalently Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-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 L-Trp Non-Covalently Bound, PDB code: 7rof 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) 46.70 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.402, 82.658, 322.255, 90, 90, 90
R / Rfree (%) 22.7 / 27.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-Trp Non-Covalently Bound (pdb code 7rof). 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 L-Trp Non-Covalently Bound, PDB code: 7rof:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rof

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Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-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 L-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:51.2
occ:1.00
 O A:GLY303 2.6 52.2 1.0
O A:SER263 2.8 51.0 1.0
O A:TYR301 2.9 56.3 1.0
O A:GLY227 3.0 50.3 1.0
OG A:SER265 3.4 59.4 1.0
OE2 A:GLU251 3.7 60.1 1.0
C A:GLY303 3.8 53.0 1.0
C A:SER263 4.0 51.2 1.0
C A:TYR301 4.0 58.0 1.0
C A:GLY227 4.0 50.4 1.0
CB A:SER263 4.1 50.7 1.0
CB A:SER265 4.3 58.5 1.0
O A:LEU299 4.3 52.6 1.0
CA A:GLY227 4.4 50.1 1.0
O A:VAL226 4.4 53.3 1.0
N A:GLY303 4.5 56.4 1.0
N A:SER265 4.5 55.5 1.0
CB A:VAL304 4.5 48.9 1.0
CB A:TYR301 4.6 62.3 1.0
CA A:SER263 4.6 51.5 1.0
CD2 A:TYR301 4.6 68.2 1.0
CD A:GLU251 4.6 59.6 1.0
C A:PRO302 4.6 58.1 1.0
N A:VAL304 4.7 52.2 1.0
CA A:TYR301 4.7 60.0 1.0
CA A:GLY303 4.8 55.8 1.0
CA A:VAL304 4.8 50.2 1.0
CG A:GLU251 4.9 56.2 1.0
N A:TYR301 4.9 57.9 1.0
O A:PRO302 5.0 58.5 1.0
N A:PRO302 5.0 59.0 1.0

Sodium binding site 2 out of 4 in 7rof

Go back to Sodium Binding Sites List in 7rof
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-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 L-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:85.6
occ:1.00
 O B:SER263 2.6 103.5 1.0
O B:TYR301 2.7 88.0 1.0
O B:GLY303 2.9 102.0 1.0
OG B:SER265 3.2 102.7 1.0
O B:GLY227 3.2 79.9 1.0
C B:SER263 3.8 105.1 1.0
C B:TYR301 3.9 88.3 1.0
C B:GLY303 4.0 101.2 1.0
CB B:SER263 4.1 107.3 1.0
CB B:SER265 4.2 101.7 1.0
O B:LEU299 4.2 86.8 1.0
C B:GLY227 4.2 77.2 1.0
N B:SER265 4.3 103.4 1.0
CA B:SER263 4.4 106.4 1.0
C B:PRO302 4.5 107.9 1.0
O B:PRO302 4.5 108.5 1.0
CB B:TYR301 4.6 91.0 1.0
CA B:TYR301 4.6 89.9 1.0
N B:GLY303 4.6 105.1 1.0
CA B:GLY227 4.6 76.8 1.0
O B:VAL226 4.7 79.3 1.0
N B:TYR301 4.7 89.9 1.0
CB B:VAL304 4.7 97.9 1.0
N B:VAL304 4.7 99.2 1.0
OE2 B:GLU251 4.8 96.8 1.0
N B:ALA264 4.8 105.9 1.0
CA B:VAL304 4.8 97.0 1.0
N B:PRO302 4.9 110.5 1.0
CA B:SER265 4.9 102.6 1.0
CA B:GLY303 4.9 103.0 1.0
CA B:PRO302 5.0 110.6 1.0
CD2 B:TYR301 5.0 94.8 1.0

Sodium binding site 3 out of 4 in 7rof

Go back to Sodium Binding Sites List in 7rof
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-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 L-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:85.2
occ:1.00
 O C:GLY303 2.7 81.1 1.0
O C:SER263 2.7 99.4 1.0
O C:TYR301 2.8 104.9 1.0
O C:GLY227 2.9 80.8 1.0
OG C:SER265 3.2 101.5 1.0
OE2 C:GLU251 3.8 82.7 1.0
C C:GLY303 3.9 82.3 1.0
C C:GLY227 3.9 79.3 1.0
C C:SER263 3.9 101.1 1.0
C C:TYR301 4.0 106.2 1.0
CA C:GLY227 4.2 78.2 1.0
CB C:SER263 4.2 101.5 1.0
CB C:SER265 4.2 101.8 1.0
O C:LEU299 4.3 97.6 1.0
N C:SER265 4.4 102.1 1.0
CB C:VAL304 4.6 77.6 1.0
CA C:SER263 4.6 102.4 1.0
O C:VAL226 4.6 78.1 1.0
N C:VAL304 4.7 80.9 1.0
CD C:GLU251 4.7 81.6 1.0
CA C:VAL304 4.7 78.1 1.0
C C:PRO302 4.7 87.2 1.0
CB C:TYR301 4.7 105.6 1.0
CD2 C:TYR301 4.7 106.0 1.0
N C:GLY303 4.7 86.2 1.0
CA C:TYR301 4.8 106.1 1.0
O C:PRO302 4.8 87.6 1.0
N C:TYR301 4.9 105.1 1.0
CG2 C:VAL304 4.9 75.6 1.0
CA C:GLY303 4.9 85.2 1.0
N C:ALA264 5.0 102.0 1.0
CA C:SER265 5.0 102.7 1.0
CG C:GLU251 5.0 78.8 1.0

Sodium binding site 4 out of 4 in 7rof

Go back to Sodium Binding Sites List in 7rof
Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9-H275E with L-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 L-Trp Non-Covalently Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:87.6
occ:1.00
 O D:GLY303 2.6 79.7 1.0
O D:SER263 2.7 107.3 1.0
O D:TYR301 2.8 87.9 1.0
OG D:SER265 3.1 102.0 1.0
O D:GLY227 3.1 78.2 1.0
C D:GLY303 3.8 79.6 1.0
C D:SER263 3.9 108.8 1.0
C D:TYR301 3.9 91.0 1.0
CB D:SER263 4.0 108.9 1.0
CB D:SER265 4.1 102.1 1.0
C D:GLY227 4.1 75.1 1.0
O D:PRO302 4.2 89.5 1.0
C D:PRO302 4.3 89.9 1.0
N D:SER265 4.3 106.9 1.0
O D:LEU299 4.4 84.6 1.0
N D:GLY303 4.4 87.3 1.0
CA D:SER263 4.5 109.0 1.0
CA D:GLY227 4.5 74.6 1.0
N D:VAL304 4.6 76.4 1.0
OE2 D:GLU251 4.6 87.8 1.0
O D:VAL226 4.6 75.8 1.0
CB D:VAL304 4.7 71.7 1.0
CA D:GLY303 4.7 83.6 1.0
CA D:TYR301 4.7 91.8 1.0
CA D:VAL304 4.7 72.6 1.0
CB D:TYR301 4.8 89.3 1.0
N D:TYR301 4.8 91.6 1.0
CA D:SER265 4.8 104.5 1.0
N D:PRO302 4.9 93.1 1.0
CA D:PRO302 4.9 93.3 1.0
CD2 D:TYR301 5.0 86.0 1.0
N D:ALA264 5.0 110.8 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: Wed Oct 9 08:39:21 2024

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