Sodium in PDB 3wnk: Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

All present enzymatic activity of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase:
2.4.1.248;

The structure of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase, PDB code: 3wnk was solved by N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, M.Kobayashi, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.34 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.437, 106.437, 160.625, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 19.2

The structure of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase also contains other interesting chemical elements:

Cadmium	(Cd)	10 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase (pdb code 3wnk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase, PDB code: 3wnk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


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 Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na813 b:37.1 occ:1.00 O A:HOH1386 2.2 59.7 1.0 O A:HOH1316 2.4 42.2 1.0 OD2 A:ASP349 2.5 37.2 1.0 O A:PRO346 2.6 28.9 1.0 O A:HOH1270 2.8 57.5 1.0 OD1 A:ASP349 3.0 35.3 1.0 CG A:ASP349 3.1 34.3 1.0 O A:HOH1541 3.6 54.4 1.0 C A:PRO346 3.6 31.7 1.0 O A:HOH1304 3.7 46.7 1.0 CA A:PRO346 4.1 32.2 1.0 CB A:PRO346 4.4 33.1 1.0 OG A:SER342 4.5 31.9 1.0 CB A:ASP349 4.6 32.4 1.0 NZ A:LYS338 4.7 39.5 1.0 N A:ALA347 4.8 32.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


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 Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na814 b:42.0 occ:1.00 O A:HOH1265 2.3 32.6 1.0 O A:HOH1109 2.4 27.9 1.0 O A:VAL47 2.4 27.5 1.0 O A:ALA133 2.7 27.5 1.0 O A:HOH1099 2.7 27.9 1.0 O A:HOH1096 2.8 33.7 1.0 C A:VAL47 3.5 26.8 1.0 O A:HOH1268 3.8 38.2 1.0 N A:VAL47 3.8 28.1 1.0 C A:ALA133 3.8 27.4 1.0 CA A:VAL47 4.1 26.4 1.0 O A:HOH1139 4.1 33.6 1.0 CB A:THR134 4.1 28.4 1.0 CB A:VAL47 4.1 26.5 1.0 ND2 A:ASN602 4.2 28.3 1.0 OG1 A:THR134 4.2 26.4 1.0 CA A:THR134 4.3 26.9 1.0 N A:THR134 4.5 27.4 1.0 N A:PHE48 4.7 27.1 1.0 O A:HOH1206 4.7 37.6 1.0 OD1 A:ASN602 4.8 29.0 1.0 O A:HOH1463 4.9 40.7 1.0 N A:ALA133 4.9 28.2 1.0 CG A:ASN602 5.0 28.6 1.0 C A:ARG46 5.0 28.8 1.0 CA A:ALA133 5.0 28.0 1.0

N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, S.Suzuki, S.Kitamura, M.Kobayashi, A.Kimura, K.Funane. Structural Elucidation of Cyclization Mechanism of Alpha-1,6-Glucan By Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase To Be Published.