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Sodium in PDB 6am9: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.:
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State., PDB code: 6am9 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 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.502, 109.122, 160.491, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State. (pdb code 6am9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State., PDB code: 6am9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 1 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:42.4
occ:1.00
 O A:HOH519 2.3 56.5 1.0
O A:TYR301 2.5 74.4 1.0
O A:SER263 2.6 60.6 1.0
O A:GLY303 2.7 59.0 1.0
OG A:SER265 2.8 58.4 1.0
OG A:SER263 3.1 65.4 1.0
O A:GLY227 3.6 52.9 1.0
C A:TYR301 3.8 75.5 1.0
C A:SER263 3.8 61.3 1.0
C A:GLY303 3.8 58.7 1.0
CB A:SER265 4.0 59.2 1.0
C A:PRO302 4.0 63.2 1.0
O A:PRO302 4.1 64.8 1.0
O A:HOH502 4.1 50.9 1.0
CB A:SER263 4.1 64.2 1.0
N A:SER265 4.2 59.7 1.0
N A:GLY303 4.2 61.7 1.0
C A:GLY227 4.4 50.8 1.0
CA A:SER263 4.4 62.7 1.0
CA A:GLY303 4.5 60.4 1.0
CA A:PRO302 4.5 64.2 1.0
N A:PRO302 4.6 63.8 1.0
CA A:GLY227 4.7 50.2 1.0
CA A:SER265 4.7 60.0 1.0
CA A:TYR301 4.7 75.3 1.0
N A:VAL304 4.8 57.6 1.0
N A:ALA264 4.8 60.8 1.0
CB A:VAL304 4.9 56.3 1.0
CB A:TYR301 4.9 76.4 1.0
N A:TYR301 4.9 73.1 1.0
OE2 A:GLU251 4.9 57.1 1.0
O A:VAL226 4.9 51.5 1.0

Sodium binding site 2 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 2 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:64.2
occ:1.00
 O A:GLY48 2.9 46.3 1.0
O B:PRO50 3.2 46.6 1.0
O B:GLY48 3.2 45.5 1.0
O A:PRO50 3.3 47.5 1.0
O A:HOH516 3.5 56.8 1.0
C A:GLY48 4.0 45.6 1.0
O B:HOH505 4.2 45.4 1.0
C B:GLY48 4.3 45.7 1.0
C B:PRO50 4.4 46.7 1.0
C A:PRO50 4.4 47.1 1.0
CA A:GLY48 4.5 45.3 1.0
C A:ARG49 4.8 47.6 1.0
N A:PRO50 4.8 48.5 1.0
CD B:PRO52 4.9 45.6 1.0
O A:ARG49 4.9 48.4 1.0
N A:ARG49 5.0 45.5 1.0
N B:PRO50 5.0 47.7 1.0
CA B:GLY48 5.0 45.5 1.0

Sodium binding site 3 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 3 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:34.8
occ:1.00
 O B:HOH513 2.3 48.9 1.0
O B:TYR301 2.5 52.9 1.0
O B:GLY303 2.6 51.3 1.0
OG B:SER265 2.7 52.0 1.0
O B:SER263 2.7 50.2 1.0
O B:GLY227 3.6 46.3 1.0
C B:GLY303 3.7 51.5 1.0
C B:TYR301 3.7 54.5 1.0
O B:HOH509 3.8 43.6 1.0
CB B:SER265 3.8 53.4 1.0
C B:SER263 3.9 51.4 1.0
O B:PRO302 4.0 56.1 1.0
C B:PRO302 4.0 55.3 1.0
CB B:SER263 4.1 50.8 1.0
N B:GLY303 4.2 54.1 1.0
N B:SER265 4.2 53.0 1.0
C B:GLY227 4.3 45.2 1.0
O B:LEU299 4.3 52.8 1.0
CA B:GLY303 4.5 53.5 1.0
CA B:SER263 4.5 52.0 1.0
CB B:TYR301 4.5 54.0 1.0
CA B:TYR301 4.6 54.7 1.0
CA B:PRO302 4.6 56.5 1.0
N B:PRO302 4.7 56.1 1.0
CA B:SER265 4.7 54.0 1.0
N B:TYR301 4.7 54.0 1.0
CA B:GLY227 4.7 44.9 1.0
N B:VAL304 4.7 50.9 1.0
CD2 B:TYR301 4.7 54.9 1.0
CB B:VAL304 4.8 49.1 1.0
OE2 B:GLU251 4.8 47.6 1.0
CA B:VAL304 4.9 49.4 1.0
N B:ALA264 5.0 52.1 1.0

Sodium binding site 4 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 4 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:47.9
occ:1.00
 O C:SER263 2.6 66.2 1.0
O C:GLY303 2.6 65.2 1.0
OG C:SER265 2.8 67.7 1.0
O C:TYR301 2.8 66.4 1.0
O C:GLY227 3.5 57.9 1.0
O C:HOH515 3.5 55.9 1.0
C C:GLY303 3.7 65.6 1.0
C C:SER263 3.8 66.4 1.0
CB C:SER265 3.9 69.7 1.0
C C:TYR301 3.9 66.5 1.0
CB C:SER263 4.1 66.5 1.0
C C:GLY227 4.2 56.4 1.0
N C:SER265 4.2 70.7 1.0
C C:PRO302 4.2 67.7 1.0
O C:PRO302 4.3 70.0 1.0
N C:GLY303 4.3 66.2 1.0
O C:LEU299 4.3 64.6 1.0
CA C:SER263 4.4 65.6 1.0
CA C:GLY303 4.5 65.4 1.0
CA C:GLY227 4.5 55.9 1.0
CB C:VAL304 4.6 67.4 1.0
N C:VAL304 4.6 65.3 1.0
CD2 C:TYR301 4.7 66.9 1.0
CB C:TYR301 4.7 65.9 1.0
OE2 C:GLU251 4.7 60.1 1.0
CA C:SER265 4.7 71.0 1.0
CA C:TYR301 4.7 66.1 1.0
CA C:PRO302 4.8 67.9 1.0
CA C:VAL304 4.8 65.5 1.0
N C:ALA264 4.8 67.8 1.0
N C:PRO302 4.8 67.0 1.0
N C:TYR301 4.9 65.6 1.0
O C:VAL226 5.0 56.2 1.0

Sodium binding site 5 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 5 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:69.9
occ:1.00
 O C:GLY48 2.9 49.3 1.0
O D:GLY48 3.2 47.9 1.0
O C:PRO50 3.2 51.0 1.0
O D:PRO50 3.2 45.6 1.0
C C:GLY48 4.0 48.3 1.0
O D:HOH515 4.1 49.7 1.0
C D:GLY48 4.2 48.1 1.0
C C:PRO50 4.3 50.4 1.0
C D:PRO50 4.4 45.5 1.0
CA C:GLY48 4.6 47.8 1.0
CA D:GLY48 4.8 48.6 1.0
N C:PRO50 4.9 50.4 1.0
C C:ARG49 4.9 49.6 1.0

Sodium binding site 6 out of 6 in 6am9

Go back to Sodium Binding Sites List in 6am9
Sodium binding site 6 out of 6 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, with Ser-Bound in A Predominantly Closed State.


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 in A Predominantly Closed State. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:38.1
occ:1.00
 O D:HOH528 2.3 42.7 1.0
O D:TYR301 2.6 56.0 1.0
O D:GLY303 2.7 55.9 1.0
O D:SER263 2.7 54.3 1.0
OG D:SER265 2.8 58.6 1.0
O D:HOH516 3.6 44.7 1.0
O D:GLY227 3.7 46.3 1.0
C D:GLY303 3.7 56.8 1.0
C D:TYR301 3.8 57.6 1.0
C D:SER263 3.8 55.4 1.0
CB D:SER265 3.9 59.2 1.0
CB D:SER263 4.0 55.5 1.0
C D:PRO302 4.2 63.2 1.0
N D:SER265 4.2 57.7 1.0
C D:GLY227 4.3 45.7 1.0
N D:GLY303 4.3 61.3 1.0
O D:PRO302 4.3 62.9 1.0
O D:LEU299 4.5 55.1 1.0
CA D:SER263 4.5 56.2 1.0
CA D:GLY303 4.5 59.5 1.0
CB D:TYR301 4.6 58.4 1.0
CA D:GLY227 4.6 44.7 1.0
N D:VAL304 4.7 55.1 1.0
CA D:TYR301 4.7 58.6 1.0
CA D:SER265 4.7 59.7 1.0
CD2 D:TYR301 4.8 60.2 1.0
N D:PRO302 4.8 66.2 1.0
CB D:VAL304 4.8 52.0 1.0
N D:TYR301 4.8 58.0 1.0
CA D:PRO302 4.8 65.5 1.0
OE2 D:GLU251 4.8 48.6 1.0
O D:VAL226 4.8 43.9 1.0
CA D:VAL304 4.9 52.8 1.0
N D:ALA264 4.9 55.9 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 01:51:17 2024

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