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Sodium in PDB 6am7: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9

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

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

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9, PDB code: 6am7 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 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.952, 107.822, 159.772, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9 (pdb code 6am7). 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, PDB code: 6am7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6am7

Go back to Sodium Binding Sites List in 6am7
Sodium binding site 1 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.3
occ:1.00
 O A:HOH502 2.3 26.9 1.0
O A:HOH624 2.3 29.3 1.0
O A:TYR301 2.6 29.0 1.0
O A:GLY303 2.6 24.8 1.0
O A:SER263 2.7 26.3 1.0
OG A:SER265 2.9 27.1 1.0
O A:GLY227 3.5 17.4 1.0
O A:HOH537 3.5 20.9 1.0
C A:GLY303 3.8 24.8 1.0
C A:TYR301 3.8 29.9 1.0
C A:SER263 3.9 26.7 1.0
CB A:SER265 4.0 27.2 1.0
CB A:SER263 4.1 27.4 1.0
N A:GLY303 4.2 27.1 1.0
C A:PRO302 4.2 27.8 1.0
N A:SER265 4.3 27.4 1.0
C A:GLY227 4.3 16.9 1.0
CD2 A:TYR301 4.4 29.7 1.0
O A:PRO302 4.5 27.5 1.0
OE2 A:GLU251 4.5 20.9 1.0
CA A:SER263 4.5 27.1 1.0
CA A:GLY303 4.5 25.9 1.0
O A:LEU299 4.6 27.8 1.0
CA A:PRO302 4.6 29.4 1.0
CB A:TYR301 4.6 30.4 1.0
N A:PRO302 4.7 30.1 1.0
CA A:TYR301 4.7 30.8 1.0
CB A:VAL304 4.7 23.0 1.0
N A:VAL304 4.7 24.0 1.0
CA A:GLY227 4.8 16.7 1.0
CA A:SER265 4.8 27.8 1.0
O A:VAL226 4.8 16.8 1.0
N A:TYR301 4.9 30.8 1.0
CG A:TYR301 4.9 30.6 1.0
N A:ALA264 5.0 27.1 1.0
CA A:VAL304 5.0 23.3 1.0

Sodium binding site 2 out of 7 in 6am7

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Sodium binding site 2 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.9
occ:1.00
 O B:HOH704 2.6 27.1 1.0
O B:GLY48 2.8 15.6 1.0
O A:HOH695 2.9 26.2 1.0
O B:PRO50 3.1 16.2 1.0
O A:GLY48 3.1 16.3 1.0
O A:PRO50 3.5 16.0 1.0
C B:GLY48 3.9 15.4 1.0
C A:GLY48 4.1 16.4 1.0
O A:HOH626 4.2 26.9 1.0
O B:HOH505 4.2 25.1 1.0
C B:PRO50 4.2 16.1 1.0
O A:HOH508 4.2 25.1 1.0
O B:HOH622 4.3 22.8 1.0
C A:PRO50 4.6 15.9 1.0
CA B:GLY48 4.6 15.3 1.0
CA A:GLY48 4.7 16.7 1.0
C B:ARG49 4.8 16.3 1.0
N B:PRO50 4.8 16.5 1.0
N B:ARG49 4.9 15.5 1.0
CA B:THR51 5.0 15.8 1.0
N B:THR51 5.0 15.9 1.0

Sodium binding site 3 out of 7 in 6am7

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Sodium binding site 3 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:18.8
occ:1.00
 O B:HOH557 2.4 23.7 1.0
O B:HOH554 2.4 29.3 1.0
O B:TYR301 2.5 32.4 1.0
O B:GLY303 2.6 23.6 1.0
OG B:SER265 2.8 21.6 1.0
O B:SER263 2.9 21.1 1.0
OG B:SER263 3.1 20.9 0.5
O B:GLY227 3.5 15.7 1.0
C B:TYR301 3.7 33.6 1.0
C B:GLY303 3.8 24.6 1.0
O B:HOH578 3.8 19.1 1.0
CB B:SER265 3.9 21.7 1.0
C B:SER263 4.0 21.7 1.0
C B:PRO302 4.1 32.9 1.0
N B:GLY303 4.1 30.3 1.0
CB B:SER263 4.1 21.5 0.5
CB B:SER263 4.1 21.5 0.5
C B:GLY227 4.2 15.2 1.0
O B:PRO302 4.3 33.2 1.0
N B:SER265 4.3 22.4 1.0
CA B:GLY303 4.4 28.0 1.0
CA B:PRO302 4.5 35.3 1.0
CA B:SER263 4.5 21.9 0.5
CA B:SER263 4.5 21.9 0.5
N B:PRO302 4.6 35.2 1.0
CA B:GLY227 4.7 15.1 1.0
CA B:TYR301 4.7 33.8 1.0
O B:LEU299 4.7 28.9 1.0
OE2 B:GLU251 4.7 18.9 1.0
CA B:SER265 4.7 22.6 1.0
CB B:TYR301 4.8 32.2 1.0
N B:TYR301 4.8 33.1 1.0
N B:VAL304 4.8 22.8 1.0
CB B:VAL304 4.9 19.7 1.0

Sodium binding site 4 out of 7 in 6am7

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Sodium binding site 4 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:19.3
occ:1.00
 O C:HOH578 2.4 27.8 1.0
O C:TYR301 2.5 38.6 1.0
O C:HOH530 2.7 26.4 1.0
O C:GLY303 2.7 21.7 1.0
O C:SER263 2.8 24.5 1.0
OG C:SER265 2.9 22.2 1.0
OG C:SER263 3.1 25.4 1.0
O C:GLY227 3.6 16.1 1.0
C C:TYR301 3.7 39.3 1.0
C C:GLY303 3.8 22.2 1.0
O C:HOH610 3.8 19.4 1.0
C C:SER263 3.9 25.1 1.0
CB C:SER265 3.9 22.0 1.0
CB C:SER263 4.1 26.2 1.0
C C:PRO302 4.1 27.1 1.0
N C:GLY303 4.2 25.4 1.0
C C:GLY227 4.2 15.7 1.0
N C:SER265 4.3 23.5 1.0
O C:PRO302 4.4 27.9 1.0
CA C:GLY303 4.5 24.2 1.0
CA C:SER263 4.5 25.9 1.0
CA C:PRO302 4.5 28.2 1.0
N C:PRO302 4.6 27.9 1.0
CA C:GLY227 4.6 15.8 1.0
CA C:SER265 4.7 22.9 1.0
OE2 C:GLU251 4.7 20.2 1.0
CA C:TYR301 4.7 39.6 1.0
N C:VAL304 4.8 21.1 1.0
CB C:TYR301 4.8 40.3 1.0
N C:TYR301 4.9 38.0 1.0
N C:ALA264 4.9 25.4 1.0

Sodium binding site 5 out of 7 in 6am7

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:22.9
occ:1.00
 O C:HOH518 2.4 20.9 1.0
O C:GLY4 3.3 23.4 1.0
CE3 C:TRP2 3.4 22.1 1.0
CD2 C:TRP2 3.5 23.5 1.0
O C:GLU5 3.6 22.1 1.0
CZ3 C:TRP2 3.8 22.9 1.0
CE2 C:TRP2 3.9 25.6 1.0
CA C:GLU5 3.9 23.1 1.0
C C:GLU5 4.0 21.3 1.0
CG C:TRP2 4.0 24.0 1.0
CH2 C:TRP2 4.2 25.0 1.0
CZ2 C:TRP2 4.2 26.4 1.0
C C:GLY4 4.3 23.0 1.0
O C:HOH509 4.3 21.8 1.0
NE1 C:TRP2 4.5 27.3 1.0
CB C:TRP2 4.5 22.9 1.0
CD1 C:TRP2 4.6 26.3 1.0
N C:GLU5 4.6 22.8 1.0
N C:PHE6 4.9 19.5 1.0

Sodium binding site 6 out of 7 in 6am7

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Sodium binding site 6 out of 7 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB2B9


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:35.3
occ:1.00
 O D:HOH659 2.4 31.6 1.0
O D:GLY48 2.8 17.0 1.0
O D:PRO50 2.9 17.3 1.0
O C:HOH703 3.0 34.1 1.0
O C:GLY48 3.1 15.3 1.0
O C:PRO50 3.8 15.3 1.0
C D:PRO50 4.0 17.2 1.0
C D:GLY48 4.0 17.0 1.0
O C:HOH506 4.1 23.6 1.0
O C:HOH666 4.1 24.7 1.0
C C:GLY48 4.1 15.2 1.0
O D:HOH506 4.2 23.2 1.0
CA C:GLY48 4.6 15.5 1.0
O D:HOH577 4.6 23.5 1.0
CA D:THR51 4.6 16.5 1.0
N D:THR51 4.7 16.7 1.0
N D:PRO50 4.8 18.0 1.0
CA D:GLY48 4.8 17.2 1.0
C D:ARG49 4.8 17.7 1.0
CD D:PRO52 4.8 16.8 1.0
N D:ARG49 5.0 17.0 1.0
C C:PRO50 5.0 15.0 1.0
CA D:PRO50 5.0 17.6 1.0

Sodium binding site 7 out of 7 in 6am7

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:20.9
occ:1.00
 O D:HOH542 2.3 36.0 1.0
O D:GLY303 2.7 23.8 1.0
O D:TYR301 2.7 26.5 1.0
O D:SER263 2.7 26.7 1.0
OG D:SER265 3.0 27.6 1.0
OG D:SER263 3.1 26.9 0.5
O D:GLY227 3.2 20.3 1.0
O D:HOH594 3.4 21.9 1.0
C D:GLY303 3.8 24.0 1.0
C D:TYR301 3.9 26.9 1.0
C D:SER263 3.9 27.6 1.0
CB D:SER265 4.0 27.7 1.0
C D:GLY227 4.1 19.8 1.0
CB D:SER263 4.1 27.0 0.5
CB D:SER263 4.2 27.2 0.5
N D:SER265 4.3 28.3 1.0
N D:GLY303 4.4 26.0 1.0
CD2 D:TYR301 4.4 26.8 1.0
C D:PRO302 4.4 27.4 1.0
OE2 D:GLU251 4.5 25.7 1.0
CA D:GLY227 4.5 19.5 1.0
CA D:SER263 4.5 27.9 0.5
O D:LEU299 4.5 24.3 1.0
CA D:SER263 4.5 28.1 0.5
O D:VAL226 4.6 19.8 1.0
CB D:TYR301 4.6 26.8 1.0
CA D:GLY303 4.7 25.1 1.0
O D:PRO302 4.7 28.0 1.0
CA D:TYR301 4.7 27.1 1.0
CB D:VAL304 4.7 22.4 1.0
N D:PRO302 4.8 28.0 1.0
N D:VAL304 4.8 23.0 1.0
CA D:SER265 4.8 28.7 1.0
CA D:PRO302 4.8 28.4 1.0
N D:TYR301 4.9 26.8 1.0
CA D:VAL304 4.9 22.0 1.0
N D:ALA264 4.9 28.6 1.0
CG D:TYR301 5.0 27.3 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 01:51:04 2024

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