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Sodium in PDB 7a20: Azobenzene-Based Inhibitors For Tryptophan Synthase

Enzymatic activity of Azobenzene-Based Inhibitors For Tryptophan Synthase

All present enzymatic activity of Azobenzene-Based Inhibitors For Tryptophan Synthase:
4.2.1.20;

Protein crystallography data

The structure of Azobenzene-Based Inhibitors For Tryptophan Synthase, PDB code: 7a20 was solved by C.Rajendran, R.Sterner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.368, 95.968, 184.719, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Azobenzene-Based Inhibitors For Tryptophan Synthase (pdb code 7a20). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Azobenzene-Based Inhibitors For Tryptophan Synthase, PDB code: 7a20:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7a20

Go back to Sodium Binding Sites List in 7a20
Sodium binding site 1 out of 2 in the Azobenzene-Based Inhibitors For Tryptophan Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Azobenzene-Based Inhibitors For Tryptophan Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:65.4
occ:1.00
O B:SER308 2.5 59.4 1.0
O B:PHE306 2.7 64.6 1.0
O B:GLY232 3.1 54.4 1.0
O B:GLY268 3.4 65.8 1.0
C B:PHE306 3.7 63.2 1.0
C B:GLY232 3.7 58.0 1.0
C B:SER308 3.8 58.9 1.0
CB B:PHE306 3.9 60.5 1.0
CA B:GLY232 3.9 59.4 1.0
CD B:PRO270 3.9 60.0 1.0
CG B:PRO270 4.1 59.6 1.0
O B:VAL231 4.1 57.3 1.0
O B:LEU304 4.2 65.0 1.0
CA B:PHE306 4.2 58.5 1.0
N B:SER308 4.3 57.1 1.0
N B:PHE306 4.3 57.6 1.0
CD2 B:PHE306 4.3 58.9 1.0
C B:GLY268 4.5 63.8 1.0
CG B:PHE306 4.6 61.4 1.0
CA B:SER308 4.6 56.4 1.0
N B:VAL309 4.7 51.0 1.0
N B:PRO307 4.7 62.8 1.0
OE1 B:GLU256 4.8 68.6 1.0
C B:PRO307 4.8 61.0 1.0
CB B:VAL309 4.8 52.2 1.0
CA B:VAL309 4.8 53.6 1.0
N B:GLY232 4.9 58.5 1.0
N B:GLY233 4.9 59.9 1.0
C B:VAL231 4.9 59.0 1.0

Sodium binding site 2 out of 2 in 7a20

Go back to Sodium Binding Sites List in 7a20
Sodium binding site 2 out of 2 in the Azobenzene-Based Inhibitors For Tryptophan Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Azobenzene-Based Inhibitors For Tryptophan Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:66.3
occ:1.00
O D:GLY232 2.6 56.4 1.0
O D:SER308 2.7 61.5 1.0
O D:PHE306 2.9 67.3 1.0
O D:GLY268 3.4 65.4 1.0
C D:GLY232 3.5 57.0 1.0
O D:VAL231 3.5 52.3 1.0
CA D:GLY232 3.6 55.6 1.0
CD D:PRO270 3.9 57.5 1.0
CG D:PRO270 3.9 61.9 1.0
C D:SER308 3.9 61.1 1.0
C D:PHE306 4.0 62.4 1.0
O D:LEU304 4.0 57.4 1.0
CB D:PHE306 4.1 59.3 1.0
C D:VAL231 4.4 60.1 1.0
OE1 D:GLU256 4.4 60.6 1.0
CA D:PHE306 4.5 64.3 1.0
C D:GLY268 4.5 61.8 1.0
N D:GLY232 4.5 59.1 1.0
N D:PHE306 4.5 66.3 1.0
CD2 D:PHE306 4.5 66.6 1.0
CB D:VAL309 4.6 54.1 1.0
N D:SER308 4.6 62.2 1.0
N D:GLY233 4.7 61.4 1.0
N D:VAL309 4.8 57.6 1.0
CA D:VAL309 4.8 58.8 1.0
CA D:SER308 4.8 62.8 1.0
CG D:PHE306 4.8 63.3 1.0
CD D:PRO257 4.9 56.0 1.0

Reference:

N.A.Simeth, T.Kinateder, C.Rajendran, J.Nazet, R.Merkl, R.Sterner, B.Konig, A.C.Kneuttinger. Towards Photochromic Azobenzene-Based Inhibitors For Tryptophan Synthase. Chemistry 2020.
ISSN: ISSN 0947-6539
PubMed: 33078454
DOI: 10.1002/CHEM.202004061
Page generated: Tue Dec 15 17:19:13 2020

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