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Sodium in PDB 5vm5: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound:
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound, PDB code: 5vm5 was solved by A.R.Buller, P.Van Roye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.123, 108.728, 160.512, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound (pdb code 5vm5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound, PDB code: 5vm5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5vm5

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Sodium binding site 1 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser 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, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.8
occ:1.00
 O A:HOH570 2.5 25.6 1.0
O A:TYR301 2.6 28.9 1.0
O A:HOH585 2.6 30.2 1.0
O A:GLY303 2.7 24.9 1.0
O A:SER263 2.9 26.9 1.0
OG A:SER265 3.0 27.6 1.0
OG A:SER263 3.3 27.2 1.0
O A:GLY227 3.7 21.2 1.0
C A:TYR301 3.8 29.3 1.0
C A:GLY303 3.8 25.4 1.0
CB A:SER265 3.9 27.5 1.0
O A:HOH566 3.9 22.1 1.0
C A:SER263 4.0 27.5 1.0
N A:GLY303 4.1 27.8 1.0
C A:PRO302 4.1 29.1 1.0
CB A:SER263 4.3 27.6 1.0
N A:SER265 4.3 27.7 1.0
C A:GLY227 4.3 20.9 1.0
CA A:GLY303 4.4 26.8 1.0
CA A:PRO302 4.5 30.0 1.0
O A:PRO302 4.5 29.7 1.0
CA A:SER263 4.6 28.0 1.0
N A:PRO302 4.6 29.9 1.0
CA A:GLY227 4.7 20.9 1.0
CA A:SER265 4.7 28.1 1.0
CA A:TYR301 4.7 29.1 1.0
OE2 A:GLU251 4.8 24.2 1.0
N A:VAL304 4.8 24.5 1.0
CB A:TYR301 4.9 28.7 1.0
O A:VAL226 4.9 21.5 1.0
N A:TYR301 4.9 28.8 1.0
CB A:VAL304 4.9 23.3 1.0

Sodium binding site 2 out of 7 in 5vm5

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Sodium binding site 2 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser 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, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:42.3
occ:1.00
 O B:HOH627 2.5 32.0 1.0
O A:HOH636 2.8 29.7 1.0
O B:GLY48 2.8 19.9 1.0
O A:GLY48 3.0 19.6 1.0
O B:PRO50 3.0 19.9 1.0
O A:PRO50 3.6 19.5 1.0
C B:GLY48 4.0 20.1 1.0
C A:GLY48 4.1 19.6 1.0
O B:HOH522 4.1 29.4 1.0
C B:PRO50 4.1 19.9 1.0
O A:HOH527 4.1 31.6 1.0
O A:HOH556 4.3 23.7 1.0
O B:HOH550 4.5 21.2 1.0
CA A:GLY48 4.6 19.6 1.0
CA B:GLY48 4.7 20.2 1.0
C A:PRO50 4.7 19.4 1.0
N B:PRO50 4.8 20.4 1.0
CA B:THR51 4.8 19.5 1.0
C B:ARG49 4.8 20.4 1.0
N B:THR51 4.9 19.7 1.0
N B:ARG49 5.0 20.2 1.0

Sodium binding site 3 out of 7 in 5vm5

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Sodium binding site 3 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser 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, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:21.9
occ:1.00
 O B:HOH601 2.3 26.7 1.0
O B:TYR301 2.5 31.6 1.0
O B:HOH589 2.7 29.0 1.0
O B:GLY303 2.7 27.7 1.0
OG B:SER265 2.7 28.5 1.0
O B:SER263 2.8 27.9 1.0
OG B:SER263 3.3 28.4 1.0
C B:TYR301 3.7 32.2 1.0
C B:GLY303 3.8 28.4 1.0
CB B:SER265 3.8 28.5 1.0
C B:SER263 3.9 28.3 1.0
O B:GLY227 3.9 22.5 1.0
O B:HOH532 4.0 21.1 1.0
N B:GLY303 4.0 31.0 1.0
C B:PRO302 4.1 32.2 1.0
CB B:SER263 4.2 28.5 1.0
N B:SER265 4.2 28.4 1.0
O B:PRO302 4.3 32.6 1.0
CA B:GLY303 4.4 30.1 1.0
C B:GLY227 4.4 22.3 1.0
CA B:SER263 4.4 28.9 1.0
CA B:PRO302 4.5 33.3 1.0
N B:PRO302 4.6 33.2 1.0
CA B:SER265 4.7 28.9 1.0
CA B:TYR301 4.7 32.1 1.0
CB B:TYR301 4.8 31.4 1.0
N B:VAL304 4.8 27.6 1.0
CA B:GLY227 4.8 22.3 1.0
CB B:VAL304 4.9 25.6 1.0
N B:TYR301 4.9 31.6 1.0
N B:ALA264 4.9 28.6 1.0
OE2 B:GLU251 5.0 24.6 1.0
OG B:SER292 5.0 40.9 1.0

Sodium binding site 4 out of 7 in 5vm5

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Sodium binding site 4 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser 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, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:17.6
occ:1.00
 O C:HOH556 2.5 24.0 1.0
O C:TYR301 2.5 28.8 1.0
O C:HOH576 2.7 26.2 1.0
OG C:SER265 2.7 27.1 1.0
O C:GLY303 2.8 24.9 1.0
O C:SER263 2.8 27.1 1.0
OG C:SER263 3.1 27.5 1.0
C C:TYR301 3.7 29.3 1.0
O C:GLY227 3.8 22.1 1.0
C C:SER263 3.8 27.7 1.0
CB C:SER265 3.8 27.1 1.0
C C:GLY303 3.8 25.4 1.0
O C:HOH555 3.9 20.0 1.0
CB C:SER263 4.1 27.8 1.0
C C:PRO302 4.1 28.8 1.0
N C:GLY303 4.2 27.7 1.0
N C:SER265 4.2 27.4 1.0
O C:PRO302 4.3 28.9 1.0
CA C:SER263 4.3 28.4 1.0
C C:GLY227 4.4 21.8 1.0
CA C:PRO302 4.5 29.9 1.0
CA C:GLY303 4.5 26.8 1.0
N C:PRO302 4.6 29.9 1.0
CA C:SER265 4.7 27.7 1.0
CA C:TYR301 4.7 29.3 1.0
OE2 C:GLU251 4.7 24.6 1.0
CA C:GLY227 4.7 21.9 1.0
CB C:TYR301 4.8 28.8 1.0
CB C:VAL304 4.8 23.4 1.0
N C:VAL304 4.8 24.6 1.0
N C:ALA264 4.9 28.0 1.0
N C:TYR301 4.9 29.1 1.0

Sodium binding site 5 out of 7 in 5vm5

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Sodium binding site 5 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:25.1
occ:1.00
 O C:GLY287 2.7 47.5 1.0
OE1 C:GLN283 2.7 35.4 1.0
O C:HOH631 2.8 54.1 1.0
CD C:GLN283 3.6 34.6 1.0
C C:GLY287 3.7 48.0 1.0
CA C:GLY287 4.0 48.6 1.0
NE2 C:GLN283 4.3 33.7 1.0
CG C:GLN283 4.4 34.6 1.0
N C:GLN288 4.9 48.2 1.0
O C:VAL271 5.0 31.9 1.0

Sodium binding site 6 out of 7 in 5vm5

Go back to Sodium Binding Sites List in 5vm5
Sodium binding site 6 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:39.5
occ:1.00
 O D:HOH638 2.3 35.9 1.0
O C:HOH634 2.8 36.9 1.0
O D:GLY48 2.8 23.2 1.0
O D:PRO50 2.9 22.4 1.0
O C:GLY48 3.0 21.5 1.0
O C:PRO50 3.6 21.7 1.0
C D:GLY48 4.0 23.3 1.0
C D:PRO50 4.0 22.4 1.0
C C:GLY48 4.1 21.4 1.0
O C:HOH510 4.1 27.8 1.0
O D:HOH546 4.2 31.3 1.0
O C:HOH569 4.2 27.8 1.0
O D:HOH541 4.4 24.1 1.0
O D:HOH634 4.5 35.1 1.0
CA C:GLY48 4.6 21.4 1.0
CA D:THR51 4.7 21.6 1.0
N D:PRO50 4.7 23.3 1.0
CA D:GLY48 4.7 23.6 1.0
C C:PRO50 4.8 21.5 1.0
N D:THR51 4.8 21.9 1.0
C D:ARG49 4.8 23.4 1.0
CD D:PRO52 4.9 21.6 1.0
N D:ARG49 5.0 23.2 1.0

Sodium binding site 7 out of 7 in 5vm5

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Sodium binding site 7 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:18.2
occ:1.00
 O D:HOH605 2.2 23.6 1.0
O D:TYR301 2.4 30.0 1.0
O D:HOH570 2.6 25.9 1.0
O D:GLY303 2.6 26.2 1.0
OG D:SER265 2.8 27.7 1.0
O D:SER263 2.8 27.1 1.0
C D:TYR301 3.6 31.0 1.0
O D:GLY227 3.7 23.6 1.0
C D:GLY303 3.7 27.1 1.0
O D:HOH544 3.8 22.2 1.0
CB D:SER265 3.9 27.9 1.0
C D:SER263 3.9 27.6 1.0
N D:GLY303 4.0 29.5 1.0
C D:PRO302 4.1 30.6 1.0
CB D:SER263 4.1 27.7 1.0
N D:SER265 4.2 27.8 1.0
C D:GLY227 4.3 23.3 1.0
O D:PRO302 4.4 30.5 1.0
CA D:GLY303 4.4 28.8 1.0
CA D:SER263 4.5 28.1 1.0
CA D:PRO302 4.5 31.6 1.0
O D:LEU299 4.5 26.9 1.0
N D:PRO302 4.5 31.6 1.0
CA D:TYR301 4.6 31.4 1.0
CB D:TYR301 4.6 31.4 1.0
CD2 D:TYR301 4.7 32.0 1.0
CA D:GLY227 4.7 23.2 1.0
CA D:SER265 4.7 28.3 1.0
OE2 D:GLU251 4.7 24.1 1.0
N D:VAL304 4.7 26.4 1.0
N D:TYR301 4.7 30.8 1.0
CB D:VAL304 4.7 24.5 1.0
CA D:VAL304 4.9 25.1 1.0
N D:ALA264 5.0 27.9 1.0
O D:VAL226 5.0 23.4 1.0

Reference:

A.R.Buller, P.Van Roye, J.K.B.Cahn, R.A.Scheele, M.Herger, F.H.Arnold. Directed Evolution Mimics Allosteric Activation By Stepwise Tuning of the Conformational Ensemble. J. Am. Chem. Soc. V. 140 7256 2018.
ISSN: ESSN 1520-5126
PubMed: 29712420
DOI: 10.1021/JACS.8B03490
Page generated: Tue Oct 8 00:52:15 2024

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