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Sodium in PDB 4kkx: Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site

Enzymatic activity of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site

All present enzymatic activity of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site, PDB code: 4kkx was solved by E.Hilario, D.Niks, M.F.Dunn, L.J.Mueller, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.43 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.870, 61.460, 67.390, 90.00, 94.70, 90.00
R / Rfree (%) 15.1 / 19.6

Other elements in 4kkx:

The structure of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site (pdb code 4kkx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site, PDB code: 4kkx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4kkx

Go back to Sodium Binding Sites List in 4kkx
Sodium binding site 1 out of 3 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:23.4
occ:1.00
 O A:HOH691 2.6 23.1 1.0
OD1 A:ASN108 3.0 18.0 1.0
CA A:ASN108 3.0 21.0 1.0
OD1 A:ASN104 3.0 11.2 1.0
OE1 B:GLN288 3.1 12.8 1.0
NE2 B:GLN288 3.4 14.8 1.0
O B:VAL276 3.5 10.6 1.0
CB A:ASN108 3.5 17.0 1.0
O A:ASN108 3.6 29.3 1.0
CD B:GLN288 3.6 13.4 1.0
CG A:ASN108 3.7 20.7 1.0
CG A:ASN104 3.7 10.9 1.0
NH1 B:ARG275 3.7 19.0 1.0
N A:ASN108 3.7 16.7 1.0
C A:ASN108 3.7 25.7 1.0
CD2 A:PHE107 3.8 14.1 1.0
ND2 A:ASN104 3.8 12.8 1.0
CA B:GLY277 3.9 12.1 1.0
O A:ASN104 3.9 12.3 1.0
O B:HOH749 4.1 29.0 1.0
C A:PHE107 4.3 16.2 1.0
CE2 A:PHE107 4.3 12.5 1.0
C B:VAL276 4.5 10.6 1.0
O A:PHE107 4.5 14.2 1.0
CZ B:ARG275 4.5 17.6 1.0
N B:GLY277 4.7 9.4 1.0
NH2 B:ARG275 4.7 18.1 1.0
CG A:PHE107 4.8 12.8 1.0
C A:ASN104 4.9 10.5 1.0
CB A:PHE107 4.9 12.0 1.0
CB A:ASN104 5.0 8.3 1.0
ND2 A:ASN108 5.0 23.6 1.0

Sodium binding site 2 out of 3 in 4kkx

Go back to Sodium Binding Sites List in 4kkx
Sodium binding site 2 out of 3 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:12.2
occ:1.00
 O B:SER308 2.3 9.2 1.0
O B:HOH857 2.3 9.3 1.0
O B:GLY232 2.3 10.2 1.0
O B:HOH505 2.4 8.7 1.0
O B:PHE306 2.5 9.0 1.0
C B:GLY232 3.4 8.8 1.0
C B:SER308 3.5 11.8 1.0
C B:PHE306 3.6 11.3 1.0
CG B:PRO270 3.8 11.4 1.0
CD B:PRO270 3.9 10.8 1.0
O B:GLY268 3.9 8.6 1.0
CA B:GLY232 3.9 7.8 1.0
N B:SER308 4.0 8.3 1.0
CB B:PHE306 4.0 8.8 1.0
CD2 B:PHE306 4.1 11.8 1.0
CA B:PHE306 4.3 9.8 1.0
CA B:SER308 4.4 5.1 1.0
O B:VAL231 4.4 7.8 1.0
CB B:VAL309 4.4 12.1 1.0
N B:VAL309 4.5 10.6 1.0
CG B:PHE306 4.5 9.8 1.0
CA B:VAL309 4.5 9.8 1.0
O B:LEU304 4.5 8.7 1.0
N B:PHE306 4.6 9.5 1.0
N B:GLY233 4.6 7.0 1.0
N B:PRO307 4.6 10.6 1.0
C B:PRO307 4.7 10.9 1.0
OE2 B:GLU256 4.8 10.1 1.0
C B:GLY268 4.8 9.1 1.0
CA B:PRO307 4.8 12.5 1.0
N B:GLY232 4.8 7.7 1.0
CG2 B:VAL309 5.0 11.5 1.0
C B:VAL231 5.0 7.4 1.0
CA B:GLY233 5.0 9.0 1.0

Sodium binding site 3 out of 3 in 4kkx

Go back to Sodium Binding Sites List in 4kkx
Sodium binding site 3 out of 3 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium with 2-Aminophenol Quinonoid in the Beta Site and the F6 Inhibitor in the Alpha Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:17.9
occ:1.00
 O B:CYS230 2.8 6.7 1.0
N B:ALA237 2.9 10.8 1.0
O2P B:AQ3401 2.9 9.7 1.0
CA B:GLY234 3.0 7.8 1.0
C B:GLY234 3.0 9.2 1.0
CB B:ALA237 3.1 7.5 1.0
O3P B:AQ3401 3.1 9.6 1.0
ND2 B:ASN236 3.2 11.3 1.0
N B:SER235 3.4 5.7 1.0
O B:GLY234 3.4 8.3 1.0
N B:ASN236 3.5 8.3 1.0
N B:GLY234 3.5 10.4 1.0
CA B:VAL231 3.6 5.9 1.0
CA B:ALA237 3.6 7.2 1.0
P B:AQ3401 3.6 8.7 1.0
C B:CYS230 3.8 7.6 1.0
CG B:ASN236 3.9 9.8 1.0
C B:ASN236 4.0 9.5 1.0
C B:SER235 4.1 10.6 1.0
CG2 B:VAL231 4.1 11.2 1.0
CA B:ASN236 4.1 10.1 1.0
N B:VAL231 4.2 4.7 1.0
CB B:VAL231 4.2 9.6 1.0
CA B:SER235 4.3 10.5 1.0
N B:GLY232 4.3 7.7 1.0
CG1 B:VAL231 4.3 7.4 1.0
O1P B:AQ3401 4.5 7.2 1.0
CB B:ASN236 4.5 9.3 1.0
C B:VAL231 4.5 7.4 1.0
NE2 B:HIS313 4.6 8.7 1.0
OD1 B:ASN236 4.6 10.5 1.0
N B:ILE238 4.7 10.7 1.0
C B:ALA237 4.7 10.1 1.0
C B:GLY233 4.8 9.0 1.0
O B:SER235 4.9 10.6 1.0
O4P B:AQ3401 5.0 14.4 1.0

Reference:

D.Niks, E.Hilario, A.Dierkers, H.Ngo, D.Borchardt, T.J.Neubauer, L.Fan, L.J.Mueller, M.F.Dunn. Allostery and Substrate Channeling in the Tryptophan Synthase Bienzyme Complex: Evidence For Two Subunit Conformations and Four Quaternary States. Biochemistry V. 52 6396 2013.
ISSN: ISSN 0006-2960
PubMed: 23952479
DOI: 10.1021/BI400795E
Page generated: Mon Oct 7 16:31:36 2024

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