Sodium in PDB 3msd: Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus.

All present enzymatic activity of Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus.:
3.2.1.8;

The structure of Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus., PDB code: 3msd was solved by V.Solomon, G.Zolotnitsky, R.Alhadeff, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.48 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.265, 80.993, 79.277, 90.00, 91.95, 90.00
R / Rfree (%)	19.7 / 20.9

The binding sites of Sodium atom in the Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus. (pdb code 3msd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus., PDB code: 3msd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:22.9 occ:1.00 O A:ASP15 2.2 22.3 1.0 O A:ARG282 2.2 21.6 1.0 O A:HOH1134 2.5 29.3 1.0 O A:ILE285 2.5 18.8 1.0 OE1 A:GLN286 2.5 32.8 1.0 CD A:GLN286 3.1 31.1 1.0 NE2 A:GLN286 3.3 32.0 1.0 C A:ARG282 3.3 22.2 1.0 C A:ASP15 3.4 21.9 1.0 C A:ILE285 3.6 19.2 1.0 O A:HOH946 3.9 46.7 1.0 CA A:GLN286 3.9 19.6 1.0 CA A:ARG282 3.9 22.2 1.0 N A:GLN286 4.2 19.7 1.0 CA A:ASP15 4.2 23.1 1.0 CB A:ARG282 4.2 24.5 1.0 N A:PHE16 4.3 21.4 1.0 CG A:GLN286 4.4 26.7 1.0 CB A:PHE16 4.4 19.7 1.0 CA A:PHE16 4.4 20.0 1.0 N A:ASP283 4.5 23.0 1.0 O A:HOH833 4.6 36.0 1.0 N A:ILE285 4.6 20.5 1.0 CB A:GLN286 4.6 22.4 1.0 CA A:ILE285 4.7 19.7 1.0 CD2 A:PHE16 4.7 19.9 1.0 CA A:ASP283 4.8 24.3 1.0 C A:ASP283 4.8 23.9 1.0 C A:GLN286 4.9 19.0 1.0 O A:HOH780 4.9 40.1 1.0 N A:VAL284 5.0 22.9 0.4 N A:VAL284 5.0 23.2 0.6

Sodium binding site 2 out of 2 in the Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:29.1 occ:1.00 O B:ASP15 2.2 23.6 1.0 O B:ARG282 2.2 32.0 1.0 O B:ILE285 2.4 25.0 1.0 O B:HOH1074 2.5 33.6 1.0 OE1 B:GLN286 2.9 33.4 0.5 NE2 B:GLN286 3.0 31.6 0.5 CD B:GLN286 3.2 30.8 0.5 C B:ARG282 3.3 33.5 1.0 C B:ASP15 3.4 24.2 1.0 C B:ILE285 3.5 25.6 1.0 CA B:ARG282 3.9 33.0 1.0 CA B:GLN286 3.9 24.6 0.5 CA B:GLN286 4.0 24.0 0.5 CA B:ASP15 4.2 25.8 1.0 N B:GLN286 4.2 25.0 0.5 N B:GLN286 4.2 24.6 0.5 NE2 B:GLN286 4.2 30.7 0.5 CB B:ARG282 4.2 33.7 1.0 N B:PHE16 4.3 22.7 1.0 CG B:GLN286 4.4 29.2 0.5 O B:HOH973 4.4 43.7 1.0 N B:ASP283 4.4 33.6 1.0 CB B:PHE16 4.4 21.8 1.0 CA B:PHE16 4.5 22.1 1.0 CG B:GLN286 4.6 27.8 0.5 N B:ILE285 4.6 29.4 1.0 CA B:ILE285 4.6 26.6 1.0 CB B:GLN286 4.7 26.8 0.5 CD B:GLN286 4.7 29.1 0.5 CD2 B:PHE16 4.8 21.7 1.0 CA B:ASP283 4.8 35.1 1.0 CB B:GLN286 4.8 25.8 0.5 C B:ASP283 4.9 35.1 1.0 C B:GLN286 4.9 23.1 0.5 C B:GLN286 4.9 22.6 0.5 O B:ASN14 4.9 29.4 1.0

V.Solomon, G.Zolotnitsky, R.Alhadeff, Y.Shoham, G.Shoham. Enzyme-Substrate Interactions of IXT6, the Intracellular Xylanase of G. Stearothermophilus. To Be Published.