Sodium in PDB 4yyf: The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155

All present enzymatic activity of The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155:
3.2.1.52;

The structure of The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155, PDB code: 4yyf was solved by K.Tan, C.Hatzos-Skintges, S.Clancy, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.41 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.067, 130.941, 85.986, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21

The binding sites of Sodium atom in the The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155 (pdb code 4yyf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155, PDB code: 4yyf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:20.9 occ:1.00 OG A:SER373 2.2 17.7 1.0 O A:HOH545 2.3 20.6 1.0 O A:HOH597 2.3 32.8 1.0 O A:ALA369 2.3 16.1 1.0 OD1 B:ASP170 2.4 25.8 1.0 C A:ALA369 3.2 21.1 1.0 CG B:ASP170 3.4 26.8 1.0 CB A:SER373 3.4 13.3 1.0 CA A:ALA369 3.5 21.3 1.0 OD2 B:ASP170 3.6 25.3 1.0 CB A:ALA369 3.8 21.2 1.0 N A:SER373 3.9 15.5 1.0 O B:HOH711 3.9 41.5 1.0 O A:ALA338 4.0 17.5 1.0 OD1 A:ASP339 4.1 18.4 1.0 CA A:SER373 4.1 16.5 1.0 N A:VAL370 4.4 18.0 1.0 CB A:ALA372 4.6 20.3 1.0 NH1 A:ARG376 4.7 16.5 1.0 O A:LEU334 4.7 24.8 1.0 CB B:ASP170 4.7 23.2 1.0 O A:GLY337 4.7 15.8 1.0 C A:ALA372 4.8 19.1 1.0 C A:ALA338 4.9 15.9 1.0 N A:ALA369 4.9 15.9 1.0 O A:GLY368 4.9 18.1 1.0 CA A:VAL370 5.0 19.6 1.0 C A:GLY337 5.0 18.0 1.0 CA A:ASP339 5.0 13.7 1.0

Sodium binding site 2 out of 3 in the The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:34.0 occ:1.00 O B:HOH695 2.4 38.1 1.0 OG B:SER282 2.4 24.0 1.0 O B:HOH706 2.4 43.4 1.0 CB B:SER282 3.3 23.7 1.0 N B:SER282 3.8 19.4 1.0 O B:HOH507 4.1 23.6 1.0 CA B:SER282 4.2 19.9 1.0 O B:HOH580 4.6 47.6 1.0 C B:GLY281 4.9 18.3 1.0 C B:SER282 5.0 18.7 1.0

Sodium binding site 3 out of 3 in the The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:21.1 occ:1.00 O B:HOH611 2.3 20.2 1.0 OG B:SER373 2.3 15.5 1.0 O B:ALA369 2.4 13.5 1.0 O B:HOH600 2.5 27.7 1.0 C B:ALA369 3.2 13.5 1.0 CB B:SER373 3.4 11.2 1.0 CA B:ALA369 3.5 15.8 1.0 CB B:ALA369 3.6 16.6 1.0 N B:SER373 3.9 11.1 1.0 OD1 B:ASP339 4.1 17.6 1.0 O B:ALA338 4.1 14.6 1.0 CA B:SER373 4.2 12.4 1.0 N B:VAL370 4.4 13.2 1.0 NH1 B:ARG376 4.5 16.0 1.0 CB B:ALA372 4.5 19.0 1.0 O B:LEU334 4.7 16.2 1.0 C B:ALA372 4.8 20.4 1.0 O B:GLY337 4.9 16.1 1.0 N B:ALA369 4.9 14.3 1.0

K.Tan, C.Hatzos-Skintges, S.Clancy, A.Joachimiak. The Crystal Structure of A Glycosyl Hydrolase of GH3 Family Member From [Mycobacterium Smegmatis Str. MC2 155 To Be Published.