Sodium in PDB 3bmx: Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis

The structure of Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis, PDB code: 3bmx was solved by S.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.84 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.385, 73.085, 83.567, 79.79, 69.61, 88.25
R / Rfree (%)	12.7 / 16.6

The binding sites of Sodium atom in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis (pdb code 3bmx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis, PDB code: 3bmx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na646 b:16.2 occ:1.00 OD2 A:ASP318 2.7 9.0 1.0 OG A:SER233 2.9 10.9 1.0 N A:HIS270 2.9 9.4 1.0 CD2 A:HIS226 3.5 8.0 1.0 CB A:SER233 3.6 10.4 1.0 CA A:ALA269 3.6 10.2 1.0 NE2 A:HIS226 3.7 8.8 1.0 CG A:ASP318 3.7 7.9 1.0 C A:ALA269 3.7 8.8 1.0 OXT A:ACT643 3.7 15.1 1.0 CG A:HIS270 3.8 8.5 1.0 CB A:HIS270 3.8 9.8 1.0 CA A:HIS270 3.8 9.6 1.0 CD2 A:HIS270 3.9 9.2 1.0 CB A:ASP318 3.9 8.4 1.0 CE A:MET322 4.0 6.5 0.5 CB A:ALA269 4.3 9.9 1.0 CH3 A:ACT643 4.3 6.6 1.0 O A:THR268 4.4 9.4 1.0 C A:HIS270 4.4 8.9 1.0 C A:ACT643 4.5 9.7 1.0 O A:HIS270 4.6 11.1 1.0 ND1 A:HIS270 4.6 8.7 1.0 NE2 A:HIS270 4.7 9.1 1.0 SD A:MET322 4.7 8.3 0.5 N A:ALA269 4.7 9.0 1.0 CD2 A:HIS222 4.8 8.8 1.0 CG2 A:VAL271 4.8 9.4 1.0 SD A:MET322 4.8 11.2 0.5 CG A:HIS226 4.8 8.4 1.0 OD1 A:ASP318 4.9 9.0 1.0 O A:ALA269 4.9 9.3 1.0 CG A:HIS222 5.0 8.1 1.0 CB A:HIS222 5.0 8.3 1.0 C A:THR268 5.0 8.6 1.0 CE1 A:HIS226 5.0 8.8 1.0

Sodium binding site 2 out of 4 in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na647 b:34.4 occ:1.00 OD1 A:ASP318 2.6 9.0 1.0 O A:HOH942 2.8 38.5 1.0 O A:HOH696 2.9 13.4 1.0 CH3 A:ACT643 2.9 6.6 1.0 O A:HOH1388 3.0 47.8 1.0 CE A:MET322 3.2 7.8 0.5 O A:HOH986 3.7 35.8 1.0 CG A:ASP318 3.7 7.9 1.0 O A:HOH1272 3.9 49.2 1.0 OD2 A:ASP318 4.0 9.0 1.0 C A:ACT643 4.1 9.7 1.0 O A:ACT643 4.2 10.3 1.0 SD A:MET322 4.3 8.3 0.5 N A:ALA319 4.6 9.5 1.0 SD A:MET322 4.6 11.2 0.5 NE2 A:HIS234 4.6 12.9 1.0 SD A:MET267 4.6 10.5 1.0 OD1 A:ASP123 4.6 14.5 1.0 OD2 A:ASP123 4.7 13.5 1.0 CB A:ALA319 4.7 10.3 1.0 NE2 A:HIS222 4.8 8.9 1.0 CG A:ASP123 5.0 12.0 1.0

Sodium binding site 3 out of 4 in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na647 b:17.6 occ:1.00 OD2 B:ASP318 2.8 10.2 1.0 N B:HIS270 2.9 9.5 1.0 OG B:SER233 2.9 10.7 1.0 CD2 B:HIS226 3.6 10.2 1.0 CB B:SER233 3.6 10.6 1.0 CA B:ALA269 3.6 9.6 1.0 CH3 B:ACT643 3.7 11.3 1.0 CG B:HIS270 3.7 10.8 1.0 CB B:HIS270 3.7 10.0 1.0 C B:ALA269 3.7 9.9 1.0 CG B:ASP318 3.7 10.2 1.0 NE2 B:HIS226 3.8 10.5 1.0 CD2 B:HIS270 3.8 10.1 1.0 CA B:HIS270 3.8 9.2 1.0 CE B:MET322 3.9 7.7 0.5 CB B:ASP318 3.9 9.7 1.0 O B:THR268 4.3 10.7 1.0 O B:ACT643 4.3 11.6 1.0 CB B:ALA269 4.3 10.4 1.0 C B:HIS270 4.4 10.4 1.0 ND1 B:HIS270 4.5 10.5 1.0 C B:ACT643 4.5 10.9 1.0 O B:HIS270 4.6 10.9 1.0 NE2 B:HIS270 4.6 9.9 1.0 SD B:MET322 4.7 10.9 0.5 N B:ALA269 4.7 10.2 1.0 SD B:MET322 4.8 12.3 0.5 CD2 B:HIS222 4.8 9.0 1.0 CG2 B:VAL271 4.8 12.1 1.0 OD1 B:ASP318 4.9 10.1 1.0 CG B:HIS226 4.9 10.0 1.0 O B:ALA269 4.9 10.8 1.0 C B:THR268 4.9 9.6 1.0 CE1 B:HIS270 5.0 9.9 1.0

Sodium binding site 4 out of 4 in the Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na648 b:39.4 occ:1.00 O B:HOH1124 2.6 33.4 1.0 OD1 B:ASP318 2.6 10.1 1.0 O B:ACT643 2.8 11.6 1.0 O B:HOH780 2.9 13.7 1.0 C B:ACT646 2.9 33.0 1.0 CE B:MET322 3.1 8.2 0.5 OXT B:ACT646 3.1 33.3 1.0 O B:ACT646 3.2 31.6 1.0 CH3 B:ACT646 3.2 34.4 1.0 CG B:ASP318 3.6 10.2 1.0 C B:ACT643 3.8 10.9 1.0 OD2 B:ASP318 3.9 10.2 1.0 O B:HOH1057 3.9 32.4 1.0 OXT B:ACT643 4.0 11.9 1.0 SD B:MET322 4.3 12.3 0.5 SD B:MET322 4.5 10.9 0.5 NE2 B:HIS234 4.5 14.7 1.0 SD B:MET267 4.6 12.0 1.0 N B:ALA319 4.7 10.6 1.0 NE2 B:HIS222 4.7 9.1 1.0 OD1 B:ASP123 4.7 13.5 1.0 OD2 B:ASP123 4.7 14.2 1.0 CB B:ALA319 4.8 11.7 1.0

S.Litzinger, S.Fischer, P.Polzer, K.Diederichs, W.Welte, C.Mayer. Structural and Kinetic Analysis of Bacillus Subtilis N-Acetylglucosaminidase Reveals A Unique Asp-His Dyad Mechanism J.Biol.Chem. V. 285 35675 2010.
ISSN: ISSN 0021-9258
PubMed: 20826810
DOI: 10.1074/JBC.M110.131037